Academic Appointments

Administrative Appointments

  • Director, NIH Center of Excellence in Genomic Science at Stanford: The Genomic Basis of Vertebrate Diversity (2007 - 2012)
  • Co-Director, Genetics and Developmental Biology Training Grant (2008 - 2023)
  • Associate Chairman, Department of Developmental Biology (2012 - 2023)

Honors & Awards

  • Scholar in Biomedical Research, Lucille P. Markey Foundation (1989 to 1996)
  • Investigator, Howard Hughes Medical Institute (1997 to present)
  • Fellow, American Academy of Arts and Sciences (2005)
  • Conklin Medal for outstanding research in Developmental Biology, Society for Developmental Biology (2009)
  • Member, National Academy of Sciences (2011)
  • GSA Medal for outstanding research in Genetics, Genetic Society of America (2017)

Professional Education

  • B.S., Yale, Biology (1981)
  • Ph.D., MIT, Biology (1986)
  • Postdoc, National Cancer Institute - Frederick, Mouse genetics (1987)


  • David Kingsley. "United States Patent 7,122,328 Gene involved in mineral deposition and uses thereof", Oct 17, 2006

Current Research and Scholarly Interests

Wild species show spectacular differences in morphology, physiology, behavior, disease susceptibility, and lifespan. Although many organisms have now been sequenced, we still know relatively little about the specific DNA sequence changes that underlie key species-specific traits. My laboratory uses a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates, with a focus on 5 fundamental questions:

1. Are new evolutionary traits controlled by countless genetic differences of small effect, or by a few genetic changes with large effects?

2. What genes have changed to produce interesting evolutionary differences in nature?

3. What kinds of mutations have occurred in these genes (e.g., dominant or recessive, coding or regulatory, preexisting or de novo)?

4. How predictable is evolution? If you know how evolution has occurred in one population, can you predict the genes and mutations that underlie the same trait in different populations?

5. How has evolution produced the unique characteristics of humans?

We study these questions using a variety of methods in stickleback fish, mice, and humans.

Stickleback fish have recently diversified in thousands of new postglacial environments, offering an unusually powerful system for mapping the molecular basis of vertebrate evolution. My lab pioneered the development of many new genetic and genomic resources for sticklebacks, including crosses between divergent populations, genetic mapping of traits, comparative genome sequencing, and testing the molecular basis of evolutionary differences using transgenic and CRISPR methods. Our studies have revealed the molecular mechanisms that control repeated evolution of armor plate patterning, pelvic reduction, and spine and skin color changes in nature. We find that big evolutionary changes are controlled by regulatory changes in key developmental control genes. Although inactivating mutations in such genes are deleterious or lethal, evolution can preserve viability and increase fitness of wild populations by tweaking the expression of key control genes in particular tissues. Interestingly, the same genes are used repeatedly when similar phenotypes evolve in different populations, revealing a surprising commonality to the molecular mechanisms controlling evolutionary change in diverse organisms.

Mice are also a powerful system for studying traits and diseases in mammals, and for testing the phenotypic effects of particular sequence changes that have occurred in other species. Our genetic studies in mice have identified fundamental signaling pathways that control formation and patterning of cartilage, bone, and joints, and have revealed the regulatory sequences that control expression of many key genes during development and tissue injury. We also use genome editing in mice to model sequence changes that underlie common traits in other species, including some of the most prevalent pigmentation, height, and arthritis traits found in humans.

The genes and mechanisms that we have identified in fish and mice turn out to control major differences in human morphology, hair color, arthritis susceptibility, and incidence of major psychiatric diseases in billions of people around the world. To further study the genomic changes that underlie key evolutionary traits and diseases in humans, we are developing innovative new genetic approaches to compare gene expression and developmental differences between human and chimpanzee cells in vitro, and to map the specific genomic regions controlling these differences using targeted modification and recombination between primate chromosomes. Although we are still far from knowing the detailed molecular basis of most human traits, we are optimistic that many aspects of this problem can now be studied computationally and experimentally, providing new insights into both human origins and human medicine.

2023-24 Courses

Stanford Advisees

All Publications

  • Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Molecular biology and evolution Chen, H. I., Turakhia, Y., Bejerano, G., Kingsley, D. M. 2023; 40 (9)


    Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.

    View details for DOI 10.1093/molbev/msad188

    View details for PubMedID 37739926

  • Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nature ecology & evolution Wucherpfennig, J. I., Howes, T. R., Au, J. N., Au, E. H., Roberts Kingman, G. A., Brady, S. D., Herbert, A. L., Reimchen, T. E., Bell, M. A., Lowe, C. B., Dalziel, A. C., Kingsley, D. M. 2022


    Understanding the mechanisms leading to new traits or additional features in organisms is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different fish genera to alter the length and number of the prominent dorsal spines used to classify stickleback species. In Gasterosteus aculeatus (typically 'three-spine sticklebacks'), a variant HOXDB allele is genetically linked to shortening an existing spine and adding an additional spine. In Apeltes quadracus (typically 'four-spine sticklebacks'), a variant HOXDB allele is associated with lengthening a spine and adding an additional spine in natural populations. The variant alleles alter the same non-coding enhancer region in the HOXDB locus but do so by diverse mechanisms, including single-nucleotide polymorphisms, deletions and transposable element insertions. The independent regulatory changes are linked to anterior expansion or contraction of HOXDB expression. We propose that associated changes in spine lengths and numbers are partial identity transformations in a repeating skeletal series that forms major defensive structures in fish. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

    View details for DOI 10.1038/s41559-022-01855-3

    View details for PubMedID 36050398

  • Genetic studies of human-chimpanzee divergence using stem cell fusions. Proceedings of the National Academy of Sciences of the United States of America Song, J. H., Grant, R. L., Behrens, V. C., Kucka, M., Roberts Kingman, G. A., Soltys, V., Chan, Y. F., Kingsley, D. M. 1800; 118 (51)


    Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee autotetraploids and allotetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or autotetraploid iPSCs. Analysis of gene expression patterns in interspecific allotetraploid iPSCs shows that human-chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allotetraploid cells. We successfully generated derivative cells with nested deletions or interspecific recombination on the X chromosome. These studies confirm an important role for the X chromosome in trans regulation of expression differences between species and illustrate the potential of this system for more detailed cis and trans mapping of the molecular basis of human and chimpanzee evolution.

    View details for DOI 10.1073/pnas.2117557118

    View details for PubMedID 34921118

  • DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science (New York, N.Y.) Xie, K. T., Wang, G., Thompson, A. C., Wucherpfennig, J. I., Reimchen, T. E., MacColl, A. D., Schluter, D., Bell, M. A., Vasquez, K. M., Kingsley, D. M. 2019; 363 (6422): 81–84


    Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.

    View details for PubMedID 30606845

  • Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia. American journal of human genetics Song, J. H., Lowe, C. B., Kingsley, D. M. 2018


    Bipolar disorder (BD) and schizophrenia (SCZ) are highly heritable diseases that affect more than 3% of individuals worldwide. Genome-wide association studies have strongly and repeatedly linked risk for both of these neuropsychiatric diseases to a 100 kb interval in the third intron of the human calcium channel gene CACNA1C. However, the causative mutation is not yet known. We have identified a human-specific tandem repeat in this region that is composed of 30bp units, often repeated hundreds of times. This large tandem repeat is unstable using standard polymerase chain reaction and bacterial cloning techniques, which may have resulted in its incorrect size in the human reference genome. The large 30-mer repeat region is polymorphic in both size and sequence in human populations. Particular sequence variants of the 30-mer are associated with risk status at several flanking single-nucleotide polymorphisms in the third intron of CACNA1C that have previously been linked to BD and SCZ. The tandem repeat arrays function as enhancers that increase reporter gene expression in a human neural progenitor cell line. Different human arrays vary in the magnitude of enhancer activity, and the 30-mer arrays associated with increased psychiatric disease risk status have decreased enhancer activity. Changes in the structure and sequence of these arrays likely contribute to changes in CACNA1C function during human evolution and may modulate neuropsychiatric disease risk in modern human populations.

    View details for PubMedID 30100087

  • Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nature genetics Capellini, T. D., Chen, H. n., Cao, J. n., Doxey, A. C., Kiapour, A. M., Schoor, M. n., Kingsley, D. M. 2017; 49 (8): 1202–10


    Variants in GDF5 are associated with human arthritis and decreased height, but the causal mutations are still unknown. We surveyed the Gdf5 locus for regulatory regions in transgenic mice and fine-mapped separate enhancers controlling expression in joints versus growing ends of long bones. A large downstream regulatory region contains a novel growth enhancer (GROW1), which is required for normal Gdf5 expression at ends of developing bones and for normal bone lengths in vivo. Human GROW1 contains a common base-pair change that decreases enhancer activity and colocalizes with peaks of positive selection in humans. The derived allele is rare in Africa but common in Eurasia and is found in Neandertals and Denisovans. Our results suggest that an ancient regulatory variant in GROW1 has been repeatedly selected in northern environments and that past selection on growth phenotypes explains the high frequency of a GDF5 haplotype that also increases arthritis susceptibility in many human populations.

    View details for PubMedID 28671685

  • A molecular basis for classic blond hair color in Europeans. Nature genetics Guenther, C. A., Tasic, B., Luo, L., Bedell, M. A., Kingsley, D. M. 2014; 46 (7): 748-752


    Hair color differences are among the most obvious examples of phenotypic variation in humans. Although genome-wide association studies (GWAS) have implicated multiple loci in human pigment variation, the causative base-pair changes are still largely unknown. Here we dissect a regulatory region of the KITLG gene (encoding KIT ligand) that is significantly associated with common blond hair color in northern Europeans. Functional tests demonstrate that the region contains a regulatory enhancer that drives expression in developing hair follicles. This enhancer contains a common SNP (rs12821256) that alters a binding site for the lymphoid enhancer-binding factor 1 (LEF1) transcription factor, reducing LEF1 responsiveness and enhancer activity in cultured human keratinocytes. Mice carrying ancestral or derived variants of the human KITLG enhancer exhibit significant differences in hair pigmentation, confirming that altered regulation of an essential growth factor contributes to the classic blond hair phenotype found in northern Europeans.

    View details for DOI 10.1038/ng.2991

    View details for PubMedID 24880339

  • The genomic basis of adaptive evolution in threespine sticklebacks. Nature Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R., Knecht, A. K., Brady, S. D., Zhang, H., Pollen, A. A., Howes, T., Amemiya, C., Baldwin, J., Bloom, T., Jaffe, D. B., Nicol, R., Wilkinson, J., Lander, E. S., Di Palma, F., Lindblad-Toh, K., Kingsley, D. M. 2012; 484 (7392): 55-61


    Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

    View details for DOI 10.1038/nature10944

    View details for PubMedID 22481358

    View details for PubMedCentralID PMC3322419

  • Human-specific loss of regulatory DNA and the evolution of human-specific traits NATURE McLean, C. Y., Reno, P. L., Pollen, A. A., Bassan, A. I., Capellini, T. D., Guenther, C., Indjeian, V. B., Lim, X., Menke, D. B., Schaar, B. T., Wenger, A. M., Bejerano, G., Kingsley, D. M. 2011; 471 (7337): 216-219


    Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.

    View details for DOI 10.1038/nature09774

    View details for Web of Science ID 000288170200037

    View details for PubMedID 21390129

    View details for PubMedCentralID PMC3071156

  • Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. Nature ecology & evolution Venu, V., Harjunmaa, E., Dreau, A., Brady, S., Absher, D., Kingsley, D. M., Jones, F. C. 2024


    Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

    View details for DOI 10.1038/s41559-024-02434-4

    View details for PubMedID 38839849

  • Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. Nature genetics Hung, T. C., Kingsley, D. M., Boettiger, A. N. 2024


    Although promoters and their enhancers are frequently contained within a topologically associating domain (TAD), some developmentally important genes have their promoter and enhancers within different TADs. Hypotheses about molecular mechanisms enabling cross-TAD interactions remain to be assessed. To test these hypotheses, we used optical reconstruction of chromatin architecture to characterize the conformations of the Pitx1 locus on single chromosomes in developing mouse limbs. Our data support a model in which neighboring boundaries are stacked as a result of loop extrusion, bringing boundary-proximal cis-elements into contact. This stacking interaction also contributes to the appearance of architectural stripes in the population average maps. Through molecular dynamics simulations, we found that increasing boundary strengths facilitates the formation of the stacked boundary conformation, counter-intuitively facilitating border bypass. This work provides a revised view of the TAD borders' function, both facilitating and preventing cis-regulatory interactions, and introduces a framework to distinguish border-crossing from border-respecting enhancer-promoter pairs.

    View details for DOI 10.1038/s41588-023-01641-2

    View details for PubMedID 38238628

    View details for PubMedCentralID 5371509

  • The genetic basis of novel trait gain in walking fish. bioRxiv : the preprint server for biology Herbert, A. L., Allard, C. A., McCoy, M. J., Wucherpfennig, J. I., Krueger, S. P., Chen, H. I., Gourlay, A. N., Jackson, K. D., Abbo, L. A., Bennett, S. H., Sears, J. D., Rhyne, A. L., Bellono, N. W., Kingsley, D. M. 2023


    A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.

    View details for DOI 10.1101/2023.10.14.562356

    View details for PubMedID 37873105

    View details for PubMedCentralID PMC10592820

  • Sea robins CURRENT BIOLOGY Allard, C. H., Herbert, A. L., Kingsley, D. M., Bellono, N. W. 2023; 33 (13): R704-R706
  • Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution; international journal of organic evolution Marques, D. A., Jones, F. C., Palma, F. D., Kingsley, D. M., Reimchen, T. E. 2022


    In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1111/evo.14490

    View details for PubMedID 35398888

  • Characterization of mouse Bmp5 regulatory injury element in zebrafish wound models. Bone Heller, I. S., Guenther, C. A., Meireles, A. M., Talbot, W. S., Kingsley, D. M. 2021: 116263


    Many key signaling molecules used to build tissues during embryonic development are re-activated at injury sites to stimulate tissue regeneration and repair. Bone morphogenetic proteins provide a classic example, but the mechanisms that lead to reactivation of BMPs following injury are still unknown. Previous studies have mapped a large "injury response element" (IRE) in the mouse Bmp5 gene that drives gene expression following bone fractures and other types of injury. Here we show that the large mouse IRE region is also activated in both zebrafish tail resection and mechanosensory hair cell injury models. Using the ability to test multiple constructs and image temporal and spatial dynamics following injury responses, we have narrowed the original size of the mouse IRE region by over 100 fold and identified a small 142 bp minimal enhancer that is rapidly induced in both mesenchymal and epithelial tissues after injury. These studies identify a small sequence that responds to evolutionarily conserved local signals in wounded tissues and suggest candidate pathways that contribute to BMP reactivation after injury.

    View details for DOI 10.1016/j.bone.2021.116263

    View details for PubMedID 34826632

  • Longer or shorter spines: Reciprocal trait evolution in stickleback via triallelic regulatory changes in Stanniocalcin2a. Proceedings of the National Academy of Sciences of the United States of America Roberts Kingman, G. A., Lee, D., Jones, F. C., Desmet, D., Bell, M. A., Kingsley, D. M. 2021; 118 (31)


    Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different freshwater environments. Here we identify a regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (major spine enhancer). Maser maps in a closely linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. The distinct freshwater alleles either increase or decrease expression of the bone growth inhibitor gene Stanniocalcin2a in developing spines, providing a simple genetic mechanism for either increasing or decreasing spine lengths in natural populations. Genomic surveys suggest many recurrently differentiated loci in sticklebacks are similarly specialized into three or more distinct alleles, providing multiple ancient standing variants in particular genes that may contribute to a range of phenotypes in different environments.

    View details for DOI 10.1073/pnas.2100694118

    View details for PubMedID 34321354

  • Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. Science advances Roberts Kingman, G. A., Vyas, D. N., Jones, F. C., Brady, S. D., Chen, H. I., Reid, K., Milhaven, M., Bertino, T. S., Aguirre, W. E., Heins, D. C., von Hippel, F. A., Park, P. J., Kirch, M., Absher, D. M., Myers, R. M., Di Palma, F., Bell, M. A., Kingsley, D. M., Veeramah, K. R. 2021; 7 (25)


    Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.

    View details for DOI 10.1126/sciadv.abg5285

    View details for PubMedID 34144992

  • Fitness maps to a large-effect locus in introduced stickleback populations. Proceedings of the National Academy of Sciences of the United States of America Schluter, D. n., Marchinko, K. B., Arnegard, M. E., Zhang, H. n., Brady, S. D., Jones, F. C., Bell, M. A., Kingsley, D. M. 2021; 118 (3)


    Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.

    View details for DOI 10.1073/pnas.1914889118

    View details for PubMedID 33414274

  • Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome biology Peichel, C. L., McCann, S. R., Ross, J. A., Naftaly, A. F., Urton, J. R., Cech, J. N., Grimwood, J. n., Schmutz, J. n., Myers, R. M., Kingsley, D. M., White, M. A. 2020; 21 (1): 177


    Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome.We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy).Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.

    View details for DOI 10.1186/s13059-020-02097-x

    View details for PubMedID 32684159

  • Predictive covariation among trophic, isotopic, and genomic traits is consistent with intrapopulation diversifying selection EVOLUTIONARY ECOLOGY RESEARCH Reimchen, T. E., Frey, S., Brady, S. D., Kingsley, D. M. 2019; 20 (2): 231–45
  • DNA fragility in the parallel evolution of pelvic reduction in stickleback fish SCIENCE Xie, K. T., Wang, G., Thompson, A. C., Wucherpfennig, J. I., Reimchen, T. E., MacColl, A. C., Schluter, D., Bell, M. A., Vasquez, K. M., Kingsley, D. M. 2019; 363 (6422): 81-+
  • Efficient CRISPR-Cas9 editing of major evolutionary loci in sticklebacks EVOLUTIONARY ECOLOGY RESEARCH Wucherpfennig, J., Miller, C. T., Kingsley, D. M. 2019; 20 (1)
  • Efficient CRISPR-Cas9 editing of major evolutionary loci in sticklebacks. Evolutionary ecology research Wucherpfennig, J. I., Miller, C. T., Kingsley, D. M. 2019; 20 (1): 107-132


    Stickleback fish are widely used to study the genetic and ecological basis of phenotypic evolution. Although several major loci have now been identified that contribute to evolutionary differences between wild populations, further study of the phenotypes associated with particular genes and mutations has been limited by the difficulty of generating targeted mutations at precise locations in the stickleback genome.We compared different methods of expressing single-guide RNAs (sgRNAs) and Cas9 activity in fertilized stickleback eggs. We used an easily scored pigmentation gene (SLC24A5) to screen for molecular lesions, phenotypic effects, and possible germline transmission of newly induced alleles. We then used the optimized CRISPR methods to target two major evolutionary loci in sticklebacks, KITLG and EDA. We hypothesized that coding region mutations in the KITLG gene would alter body pigmentation and possibly sex determination, and that mutations in the EDA gene would disrupt the formation of most armor plates, fin rays, spines, teeth, and gill rakers.Targeted deletions were successfully induced at each target locus by co-injecting one-cell stage stickleback embryos with either Cas9 mRNA or Cas9 protein, together with sgRNAs designed to protein-coding exons. Founder animals were typically mosaic for multiple mutations, which they transmitted through the germline at overall rates of 21 to 100%. We found that the copy of KITLG on the X chromosome (KITLGX) has diverged from the KITLG on the Y chromosome (KITLGY). Predicted loss-of-function mutations in the KITLGX gene dramatically altered pigmentation in both external skin and internal organ, but the same was not true for KITLGY mutations. Predicted loss-of-function mutations in either the KITLGX or KITLGY genes did not lead to sex reversal or prevent fertility. Homozygous loss-of-function mutations in the EDA gene led to complete loss of armor plates, severe reduction or loss of most soft rays in the dorsal, anal, and caudal fins, and severe reductions in tooth and gill raker number. In contrast, long dorsal and pelvic spines remained intact in EDA mutant animals, suggesting that common co-segregation of plate loss and spine reduction in wild populations is unlikely to be due to pleiotropic effects of EDA mutations.CRISPR-Cas9 approaches can be used to induce germline mutations in key evolutionary loci in sticklebacks. Targeted coding region mutations confirm an important role for KITLG and EDA in skin pigmentation and armor plate reduction, respectively. They also provide new information about the functions of these genes in other body structures.

    View details for PubMedID 34899072

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  • A novel enhancer near the Pitx1 gene influences development and evolution of pelvic appendages in vertebrates. eLife Thompson, A. C., Capellini, T. D., Guenther, C. A., Chan, Y. F., Infante, C. R., Menke, D. B., Kingsley, D. M. 2018; 7


    Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of Pitx1. The sequence of this upstream PelA enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse Pitx1 gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, PelB, that maps downstream rather than upstream of Pitx1. PelB drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. PelB sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of PelB, suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature.

    View details for PubMedID 30499775

  • A novel enhancer near the Pitx1 gene influences development and evolution o pelvic appendages in vertebrates ELIFE Thompson, A. C., Capellini, T. D., Guenther, C. A., Chan, Y., Infante, C. R., Menke, D. B., Kingsley, D. M. 2018; 7
  • Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia AMERICAN JOURNAL OF HUMAN GENETICS Song, J. T., Lowe, C. B., Kingsley, D. M. 2018; 103 (3): 421-430
  • Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nature ecology & evolution Marques, D. A., Jones, F. C., Di Palma, F. n., Kingsley, D. M., Reimchen, T. E. 2018; 2 (7): 1128–38


    A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages specialized to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-year selection experiment, we let giant sticklebacks from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. A total of 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the change between 12,000-year-old ecotypes. Genomic change was as fast as phenotypic change in defence and trophic morphology, and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived radiation members, allowing adaptive radiations to unfold very rapidly.

    View details for PubMedID 29942074

  • Detecting differential copy number variation between groups of samples. Genome research Lowe, C. B., Sanchez-Luege, N. n., Howes, T. R., Brady, S. D., Daugherty, R. R., Jones, F. C., Bell, M. A., Kingsley, D. M. 2018; 28 (2): 256–65


    We present a method to detect copy number variants (CNVs) that are differentially present between two groups of sequenced samples. We use a finite-state transducer where the emitted read depth is conditioned on the mappability and GC-content of all reads that occur at a given base position. In this model, the read depth within a region is a mixture of binomials, which in simulations matches the read depth more closely than the often-used negative binomial distribution. The method analyzes all samples simultaneously, preserving uncertainty as to the breakpoints and magnitude of CNVs present in an individual when it identifies CNVs differentially present between the two groups. We apply this method to identify CNVs that are recurrently associated with postglacial adaptation of marine threespine stickleback (Gasterosteus aculeatus) to freshwater. We identify 6664 regions of the stickleback genome, totaling 1.7 Mbp, which show consistent copy number differences between marine and freshwater populations. These deletions and duplications affect both protein-coding genes andcis-regulatory elements, including a noncoding intronic telencephalon enhancer ofDCHS1The functions of the genes near or included within the 6664 CNVs are enriched for immunity and muscle development, as well as head and limb morphology. Although freshwater stickleback have repeatedly evolved from marine populations, we show that freshwater stickleback also act as reservoirs for ancient ancestral sequences that are highly conserved among distantly related teleosts, but largely missing from marine stickleback due to recent selective sweeps in marine populations.

    View details for PubMedID 29229672

    View details for PubMedCentralID PMC5793789

  • Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS biology Lickwar, C. R., Camp, J. G., Weiser, M., Cocchiaro, J. L., Kingsley, D. M., Furey, T. S., Sheikh, S. Z., Rawls, J. F. 2017; 15 (8): e2002054


    The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology.

    View details for DOI 10.1371/journal.pbio.2002054

    View details for PubMedID 28850571

    View details for PubMedCentralID PMC5574553

  • Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments PLOS BIOLOGY Marques, D. A., Taylor, J. S., Jones, F. C., Di Palma, F., Kingsley, D. M., Reimchen, T. E. 2017; 15 (4)


    Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

    View details for DOI 10.1371/journal.pbio.2001627

    View details for Web of Science ID 000400423600016

    View details for PubMedID 28399148

  • Dorsal spine evolution in threespine sticklebacks via a splicing change in MSX2A. BMC biology Howes, T. R., Summers, B. R., Kingsley, D. M. 2017; 15 (1): 115


    Dorsal spine reduction in threespine sticklebacks (Gasterosteus aculeatus) is a classic example of recurrent skeletal evolution in nature. Sticklebacks in marine environments typically have long spines that form part of their skeletal armor. Many derived freshwater populations have evolved shorter spines. Changes in spine length are controlled in part by a quantitative trait locus (QTL) previously mapped to chromosome 4, but the causative gene and mutations underlying the repeated evolution of this interesting skeletal trait have not been identified.Refined mapping of the spine length QTL shows that it lies near the MSX2A transcription factor gene. MSX2A is expressed in developing spines. In F1 marine × freshwater fish, the marine allele is preferentially expressed. Differences in expression can be attributed to splicing regulation. Due to the use of an alternative 5'splice site within the first exon, the freshwater allele produces greater amounts of a shortened, non-functional transcript and makes less of the full-length transcript. Sequence changes in the MSX2A region are shared by many freshwater fish, suggesting that repeated evolution occurs by reuse of a spine-reduction variant. To demonstrate the effect of full-length MSX2A on spine length, we produced transgenic freshwater fish expressing a copy of marine MSX2A. The spines of the transgenic fish were significantly longer on average than those of their non-transgenic siblings, partially reversing the reduced spine lengths that have evolved in freshwater populations.MSX2A is a major gene underlying dorsal spine reduction in freshwater sticklebacks. The gene is linked to a separate gene controlling bony plate loss, helping explain the concerted effects of chromosome 4 on multiple armor-reduction traits. The nature of the molecular changes provides an interesting example of morphological evolution occurring not through a simple amino acid change, nor through a change only in gene expression levels, but through a change in the ratio of splice products encoding both normal and truncated proteins.

    View details for PubMedID 29212540

    View details for PubMedCentralID PMC5719529

  • Genetic Coupling of Female Mate Choice with Polygenic Ecological Divergence Facilitates Stickleback Speciation. Current biology : CB Bay, R. A., Arnegard, M. E., Conte, G. L., Best, J. n., Bedford, N. L., McCann, S. R., Dubin, M. E., Chan, Y. F., Jones, F. C., Kingsley, D. M., Schluter, D. n., Peichel, C. L. 2017; 27 (21): 3344–49.e4


    Ecological speciation with gene flow is widespread in nature [1], but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, "genetic coupling") can facilitate speciation [2-4]. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic model of ecological speciation: sympatric benthic and limnetic threespine stickleback (Gasterosteus aculeatus). By measuring mate choice in F2 hybrid females, we allowed for recombination between loci underlying assortative mating and those under divergent ecological selection. In semi-natural mating arenas in which females had access to both benthic and limnetic males, we found that F2 females mated with males similar to themselves in body size and shape. In addition, we found two quantitative trait loci (QTLs) associated with female mate choice that also predicted female morphology along the benthic-limnetic trait axis. Furthermore, a polygenic genetic model that explains adaptation to contrasting benthic and limnetic feeding niches [5] also predicted F2 female mate choice. Together, these results provide empirical evidence that genetic coupling of assortative mating with traits under divergent ecological selection helps maintain species in the face of gene flow, despite a polygenic basis for adaptation to divergent environments.

    View details for PubMedID 29056455

    View details for PubMedCentralID PMC5687276

  • Beautiful Piles of Bones: An Interview with 2017 Genetics Society of America Medal Recipient David M. Kingsley. Genetics Kingsley, D. M. 2017; 207 (4): 1221–22


    The Genetics Society of America Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, exemplifying the ingenuity of GSA membership. The 2017 recipient is David M. Kingsley, whose work in mouse, sticklebacks, and humans has shifted paradigms about how vertebrates evolve. Kingsley first fell in love with genetics in graduate school, where he worked on receptor mediated endocytosis with Monty Krieger. In his postdoctoral training he was able to unite genetics with his first scientific love: vertebrate morphology. He joined the group of Neal Copeland and Nancy Jenkins, where he led efforts to map the classical mouse skeletal mutationshort earConvinced that experimental genetics had a unique power to reveal the inner workings of evolution, Kingsley then established the stickleback fish as an extraordinarily productive model of quantitative trait evolution in wild species. He and his colleagues revealed many important insights, including the discoveries that major morphological differences can map to key loci with large effects, that regulatory changes in essential developmental control genes have produced advantageous new traits, and that nature has selected the same genes over and over again to drive the stickleback's skeletal evolution. Recently, Kingsley's group has been using these lessons to reveal more about how our own species evolved.This is an abridged version of the interview. The full interview is available on theGenes to Genomesblog, at

    View details for PubMedID 29203698

    View details for PubMedCentralID PMC5714440

  • An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell Martin, A. R., Lin, M. n., Granka, J. M., Myrick, J. W., Liu, X. n., Sockell, A. n., Atkinson, E. G., Werely, C. J., Möller, M. n., Sandhu, M. S., Kingsley, D. M., Hoal, E. G., Liu, X. n., Daly, M. J., Feldman, M. W., Gignoux, C. R., Bustamante, C. D., Henn, B. M. 2017; 171 (6): 1340–53.e14


    Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

    View details for PubMedID 29195075

  • Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton PLOS GENETICS Chen, H., Capellini, T. D., Schoor, M., Mortlock, D. P., Reddi, A. H., Kingsley, D. M. 2016; 12 (11)


    Synovial joints are crucial for support and locomotion in vertebrates, and are the frequent site of serious skeletal defects and degenerative diseases in humans. Growth and differentiation factor 5 (Gdf5) is one of the earliest markers of joint formation, is required for normal joint development in both mice and humans, and has been genetically linked to risk of common osteoarthritis in Eurasian populations. Here, we systematically survey the mouse Gdf5 gene for regulatory elements controlling expression in synovial joints. We identify separate regions of the locus that control expression in axial tissues, in proximal versus distal joints in the limbs, and in remarkably specific sub-sets of composite joints like the elbow. Predicted transcription factor binding sites within Gdf5 regulatory enhancers are required for expression in particular joints. The multiple enhancers that control Gdf5 expression in different joints are distributed over a hundred kilobases of DNA, including regions both upstream and downstream of Gdf5 coding exons. Functional rescue tests in mice confirm that the large flanking regions are required to restore normal joint formation and patterning. Orthologs of these enhancers are located throughout the large genomic region previously associated with common osteoarthritis risk in humans. The large array of modular enhancers for Gdf5 provide a new foundation for studying the spatial specificity of joint patterning in vertebrates, as well as new candidates for regulatory regions that may also influence osteoarthritis risk in human populations.

    View details for DOI 10.1371/journal.pgen.1006454

    View details for Web of Science ID 000392129600046

    View details for PubMedID 27902701

    View details for PubMedCentralID PMC5130176

  • Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins. Cell Indjeian, V. B., Kingman, G. A., Jones, F. C., Guenther, C. A., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M. 2016; 164 (1-2): 45-56


    Changes in bone size and shape are defining features of many vertebrates. Here we use genetic crosses and comparative genomics to identify specific regulatory DNA alterations controlling skeletal evolution. Armor bone-size differences in sticklebacks map to a major effect locus overlapping BMP family member GDF6. Freshwater fish express more GDF6 due in part to a transposon insertion, and transgenic overexpression of GDF6 phenocopies evolutionary changes in armor-plate size. The human GDF6 locus also has undergone distinctive regulatory evolution, including complete loss of an enhancer that is otherwise highly conserved between chimps and other mammals. Functional tests show that the ancestral enhancer drives expression in hindlimbs but not forelimbs, in locations that have been specifically modified during the human transition to bipedalism. Both gain and loss of regulatory elements can localize BMP changes to specific anatomical locations, providing a flexible regulatory basis for evolving species-specific changes in skeletal form.

    View details for DOI 10.1016/j.cell.2015.12.007

    View details for PubMedID 26774823

    View details for PubMedCentralID PMC4759241

  • Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback GENETICS Conte, G. L., Arnegard, M. E., Best, J., Chan, Y. F., Jones, F. C., Kingsley, D. M., Schluter, D., Peichel, C. L. 2015; 201 (3): 1189-U730


    How predictable is the genetic basis of phenotypic adaptation? Answering this question begins by estimating the repeatability of adaptation at the genetic level. Here, we provide a comprehensive estimate of the repeatability of the genetic basis of adaptive phenotypic evolution in a natural system. We used quantitative trait locus (QTL) mapping to discover genomic regions controlling a large number of morphological traits that have diverged in parallel between pairs of threespine stickleback (Gasterosteus aculeatus species complex) in Paxton and Priest lakes, British Columbia. We found that nearly half of QTL affected the same traits in the same direction in both species pairs. Another 40% influenced a parallel phenotypic trait in one lake but not the other. The remaining 10% of QTL had phenotypic effects in opposite directions in the two species pairs. Similarity in the proportional contributions of all QTL to parallel trait differences was about 0.4. Surprisingly, QTL reuse was unrelated to phenotypic effect size. Our results indicate that repeated use of the same genomic regions is a pervasive feature of parallel phenotypic adaptation, at least in sticklebacks. Identifying the causes of this pattern would aid prediction of the genetic basis of phenotypic evolution.

    View details for DOI 10.1534/genetics.115.182550

    View details for Web of Science ID 000365517200028

    View details for PubMedID 26384359

    View details for PubMedCentralID PMC4649644

  • A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury. Bone Guenther, C. A., Wang, Z., Li, E., Tran, M. C., Logan, C. Y., Nusse, R., Pantalena-Filho, L., Yang, G. P., Kingsley, D. M. 2015; 77: 31-41


    Bone morphogenetic proteins (BMPs) are key signaling molecules required for normal development of bones and other tissues. Previous studies have shown that null mutations in the mouse Bmp5 gene alter the size, shape and number of multiple bone and cartilage structures during development. Bmp5 mutations also delay healing of rib fractures in adult mutants, suggesting that the same signals used to pattern embryonic bone and cartilage are also reused during skeletal regeneration and repair. Despite intense interest in BMPs as agents for stimulating bone formation in clinical applications, little is known about the regulatory elements that control developmental or injury-induced BMP expression. To compare the DNA sequences that activate gene expression during embryonic bone formation and following acute injuries in adult animals, we assayed regions surrounding the Bmp5 gene for their ability to stimulate lacZ reporter gene expression in transgenic mice. Multiple genomic fragments, distributed across the Bmp5 locus, collectively coordinate expression in discrete anatomic domains during normal development, including in embryonic ribs. In contrast, a distinct regulatory region activated expression following rib fracture in adult animals. The same injury control region triggered gene expression in mesenchymal cells following tibia fracture, in migrating keratinocytes following dorsal skin wounding, and in regenerating epithelial cells following lung injury. The Bmp5 gene thus contains an "injury response" control region that is distinct from embryonic enhancers, and that is activated by multiple types of injury in adult animals.

    View details for DOI 10.1016/j.bone.2015.04.010

    View details for PubMedID 25886903

    View details for PubMedCentralID PMC4447581

  • A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA ELIFE O'Brown, N. M., Summers, B. R., Jones, F. C., Brady, S. D., Kingsley, D. M. 2015; 4


    Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

    View details for DOI 10.7554/eLife.05290

    View details for Web of Science ID 000348682400001

  • Mesenchymal cells. Defining a mesenchymal progenitor niche at single-cell resolution. Science Kumar, M. E., Bogard, P. E., Espinoza, F. H., Menke, D. B., Kingsley, D. M., Krasnow, M. A. 2014; 346 (6211)


    Most vertebrate organs are composed of epithelium surrounded by support and stromal tissues formed from mesenchyme cells, which are not generally thought to form organized progenitor pools. Here, we use clonal cell labeling with multicolor reporters to characterize individual mesenchymal progenitors in the developing mouse lung. We observe a diversity of mesenchymal progenitor populations with different locations, movements, and lineage boundaries. Airway smooth muscle (ASM) progenitors map exclusively to mesenchyme ahead of budding airways. Progenitors recruited from these tip pools differentiate into ASM around airway stalks; flanking stalk mesenchyme can be induced to form an ASM niche by a lateral bud or by an airway tip plus focal Wnt signal. Thus, mesenchymal progenitors can be organized into localized and carefully controlled domains that rival epithelial progenitor niches in regulatory sophistication.

    View details for DOI 10.1126/science.1258810

    View details for PubMedID 25395543

    View details for PubMedCentralID PMC4269943

  • The phosphate exporter xpr1b is required for differentiation of tissue-resident macrophages. Cell reports Meireles, A. M., Shiau, C. E., Guenther, C. A., Sidik, H., Kingsley, D. M., Talbot, W. S. 2014; 8 (6): 1659-1667


    Phosphate concentration is tightly regulated at the cellular and organismal levels. The first metazoan phosphate exporter, XPR1, was recently identified, but its in vivo function remains unknown. In a genetic screen, we identified a mutation in a zebrafish ortholog of human XPR1, xpr1b. xpr1b mutants lack microglia, the specialized macrophages that reside in the brain, and also displayed an osteopetrotic phenotype characteristic of defects in osteoclast function. Transgenic expression studies indicated that xpr1b acts autonomously in developing macrophages. xpr1b mutants display no gross developmental defects that may arise from phosphate imbalance. We constructed a targeted mutation of xpr1a, a duplicate of xpr1b in the zebrafish genome, to determine whether Xpr1a and Xpr1b have redundant functions. Single mutants for xpr1a were viable, and double mutants for xpr1b;xpr1a were similar to xpr1b single mutants. Our genetic analysis reveals a specific role for the phosphate exporter Xpr1 in the differentiation of tissue macrophages.

    View details for DOI 10.1016/j.celrep.2014.08.018

    View details for PubMedID 25220463

  • Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proceedings of the National Academy of Sciences of the United States of America Cleves, P. A., Ellis, N. A., Jimenez, M. T., Nunez, S. M., Schluter, D., Kingsley, D. M., Miller, C. T. 2014; 111 (38): 13912-13917


    Developmental genetic studies of evolved differences in morphology have led to the hypothesis that cis-regulatory changes often underlie morphological evolution. However, because most of these studies focus on evolved loss of traits, the genetic architecture and possible association with cis-regulatory changes of gain traits are less understood. Here we show that a derived benthic freshwater stickleback population has evolved an approximate twofold gain in ventral pharyngeal tooth number compared with their ancestral marine counterparts. Comparing laboratory-reared developmental time courses of a low-toothed marine population and this high-toothed benthic population reveals that increases in tooth number and tooth plate area and decreases in tooth spacing arise at late juvenile stages. Genome-wide linkage mapping identifies largely separate sets of quantitative trait loci affecting different aspects of dental patterning. One large-effect quantitative trait locus controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, and no coding changes are found between the high- and low-toothed populations. However, quantitative allele-specific expression assays of Bmp6 in developing teeth in F1 hybrids show that cis-regulatory changes have elevated the relative expression level of the freshwater benthic Bmp6 allele at late, but not early, stages of stickleback development. Collectively, our data support a model where a late-acting cis-regulatory up-regulation of Bmp6 expression underlies a significant increase in tooth number in derived benthic sticklebacks.

    View details for DOI 10.1073/pnas.1407567111

    View details for PubMedID 25205810

    View details for PubMedCentralID PMC4183278

  • Genetics of ecological divergence during speciation. Nature Arnegard, M. E., Mcgee, M. D., Matthews, B., Marchinko, K. B., Conte, G. L., Kabir, S., Bedford, N., Bergek, S., Chan, Y. F., Jones, F. C., Kingsley, D. M., Peichel, C. L., Schluter, D. 2014; 511 (7509): 307-311


    Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.

    View details for DOI 10.1038/nature13301

    View details for PubMedID 24909991

  • Efficient Imputation of Missing Markers in Low-Coverage Genotyping-by-Sequencing Data from Multiparental Crosses GENETICS Miller, C. T., Glazer, A. M., Summers, B. R., Blackman, B. K., Norman, A. R., Shapiro, M. D., Cole, B. L., Peichel, C. L., Schluter, D., Kingsley, D. M. 2014; 197 (1): 405-?


    Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.

    View details for DOI 10.1534/genetics.113.158014

    View details for Web of Science ID 000335858900031

    View details for PubMedCentralID PMC4012497

  • A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife O'Brown, N. M., Summers, B. R., Jones, F. C., Brady, S. D., Kingsley, D. M. 2014; 4


    Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

    View details for DOI 10.7554/eLife.05290

    View details for PubMedID 25629660

  • Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping MOLECULAR ECOLOGY Deagle, B. E., Jones, F. C., Absher, D. M., Kingsley, D. M., Reimchen, T. E. 2013; 22 (7): 1917-1932


    Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent adaptive divergences.

    View details for DOI 10.1111/mec.12215

    View details for Web of Science ID 000316575800012

    View details for PubMedID 23452150

    View details for PubMedCentralID PMC3604130

  • Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements DEVELOPMENTAL BIOLOGY Infante, C. R., Park, S., Mihala, A. G., Kingsley, D. M., Menke, D. B. 2013; 374 (1): 234-244


    Extensive functional analyses have demonstrated that the pituitary homeodomain transcription factor Pitx1 plays a critical role in specifying hindlimb morphology in vertebrates. However, much less is known regarding the target genes and cis-regulatory elements through which Pitx1 acts. Earlier studies suggested that the hindlimb transcription factors Tbx4, HoxC10, and HoxC11 might be transcriptional targets of Pitx1, but definitive evidence for direct regulatory interactions has been lacking. Using ChIP-Seq on embryonic mouse hindlimbs, we have pinpointed the genome-wide location of Pitx1 binding sites during mouse hindlimb development and identified potential gene targets for Pitx1. We determined that Pitx1 binding is significantly enriched near genes involved in limb morphogenesis, including Tbx4, HoxC10, and HoxC11. Notably, Pitx1 is bound to the previously identified HLEA and HLEB hindlimb enhancers of the Tbx4 gene and to a newly identified Tbx2 hindlimb enhancer. Moreover, Pitx1 binding is significantly enriched on hindlimb relative to forelimb-specific cis-regulatory features that are differentially marked by H3K27ac. However, our analysis revealed that Pitx1 also strongly associates with many functionally verified limb enhancers that exhibit similar levels of activity in the embryonic mesenchyme of forelimbs and hindlimbs. We speculate that Pitx1 influences hindlimb morphology both through the activation of hindlimb-specific enhancers as well as through the hindlimb-specific modulation of enhancers that are active in both sets of limbs.

    View details for DOI 10.1016/j.ydbio.2012.11.017

    View details for Web of Science ID 000314145300021

    View details for PubMedID 23201014

    View details for PubMedCentralID PMC3640454

  • A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PloS one Reno, P. L., McLean, C. Y., Hines, J. E., Capellini, T. D., Bejerano, G., Kingsley, D. M. 2013; 8 (12)


    Previous studies show that humans have a large genomic deletion downstream of the Androgen Receptor gene that eliminates an ancestral mammalian regulatory enhancer that drives expression in developing penile spines and sensory vibrissae. Here we use a combination of large-scale sequence analysis and PCR amplification to demonstrate that the penile spine/vibrissa enhancer is missing in all humans surveyed and in the Neandertal and Denisovan genomes, but is present in DNA samples of chimpanzees and bonobos, as well as in multiple other great apes and primates that maintain some form of penile integumentary appendage and facial vibrissae. These results further strengthen the association between the presence of the penile spine/vibrissa enhancer and the presence of penile spines and macro- or micro- vibrissae in non-human primates as well as show that loss of the enhancer is both a distinctive and characteristic feature of the human lineage.

    View details for DOI 10.1371/journal.pone.0084258

    View details for PubMedID 24367647

    View details for PubMedCentralID PMC3868586

  • A "Forward Genomics'' Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species CELL REPORTS Hiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., Bejerano, G. 2012; 2 (4): 817-823


    Genotype-phenotype mapping is hampered by countless genomic changes between species. We introduce a computational "forward genomics" strategy that-given only an independently lost phenotype and whole genomes-matches genomic and phenotypic loss patterns to associate specific genomic regions with this phenotype. We conducted genome-wide screens for two metabolic phenotypes. First, our approach correctly matches the inactivated Gulo gene exactly with the species that lost the ability to synthesize vitamin C. Second, we attribute naturally low biliary phospholipid levels in guinea pigs and horses to the inactivated phospholipid transporter Abcb4. Human ABCB4 mutations also result in low phospholipid levels but lead to severe liver disease, suggesting compensatory mechanisms in guinea pig and horse. Our simulation studies, counts of independent changes in existing phenotype surveys, and the forthcoming availability of many new genomes all suggest that forward genomics can be applied to many phenotypes, including those relevant for human evolution and disease.

    View details for DOI 10.1016/j.celrep.2012.08.032

    View details for Web of Science ID 000314455600014

    View details for PubMedID 23022484

    View details for PubMedCentralID PMC3572205

  • Genetic Architecture of Variation in the Lateral Line Sensory System of Threespine Sticklebacks G3-GENES GENOMES GENETICS Wark, A. R., Mills, M. G., Dang, L., Chan, Y. F., Jones, F. C., Brady, S. D., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., Peichel, C. L. 2012; 2 (9): 1047-1056


    Vertebrate sensory systems have evolved remarkable diversity, but little is known about the underlying genetic mechanisms. The lateral line sensory system of aquatic vertebrates is a promising model for genetic investigations of sensory evolution because there is extensive variation within and between species, and this variation is easily quantified. In the present study, we compare the lateral line sensory system of threespine sticklebacks (Gasterosteus aculeatus) from an ancestral marine and a derived benthic lake population. We show that lab-raised individuals from these populations display differences in sensory neuromast number, neuromast patterning, and groove morphology. Using genetic linkage mapping, we identify regions of the genome that influence different aspects of lateral line morphology. Distinct loci independently affect neuromast number on different body regions, suggesting that a modular genetic structure underlies the evolution of peripheral receptor number in this sensory system. Pleiotropy and/or tight linkage are also important, as we identify a region on linkage group 21 that affects multiple aspects of lateral line morphology. Finally, we detect epistasis between a locus on linkage group 4 and a locus on linkage group 21; interactions between these loci contribute to variation in neuromast pattern. Our results reveal a complex genetic architecture underlying the evolution of the stickleback lateral line sensory system. This study further uncovers a genetic relationship between sensory morphology and non-neural traits (bony lateral plates), creating an opportunity to investigate morphological constraints on sensory evolution in a vertebrate model system.

    View details for DOI 10.1534/g3.112.003079

    View details for Web of Science ID 000312456100008

    View details for PubMedID 22973542

    View details for PubMedCentralID PMC3429919

  • GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK EVOLUTION Rogers, S. M., Tamkee, P., Summers, B., Balabahadra, S., Marks, M., Kingsley, D. M., Schluter, D. 2012; 66 (8): 2439-2450


    Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.

    View details for DOI 10.1111/j.1558-5646.2012.01622.x

    View details for Web of Science ID 000306804100008

    View details for PubMedID 22834743

  • Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Deagle, B. E., Jones, F. C., Chan, Y. F., Absher, D. M., Kingsley, D. M., Reimchen, T. E. 2012; 279 (1732): 1277-1286


    Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream-lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F(ST) between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream-lake outlier regions match those previously identified in marine-freshwater and benthic-limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream-lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

    View details for DOI 10.1098/rspb.2011.1552

    View details for Web of Science ID 000300822400004

    View details for PubMedID 21976692

    View details for PubMedCentralID PMC3282360

  • The genomic basis of adaptive evolution in threespine sticklebacks NATURE Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M. C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M. C., Myers, R. M., Miller, C. T., Summers, B. R., Knecht, A. K., Brady, S. D., Zhang, H., Pollen, A. A., Howes, T., Amemiya, C., Lander, E. S., Di Palma, F., Lindblad-Toh, K., Kingsley, D. M. 2012; 484 (7392): 55-61


    Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

    View details for DOI 10.1038/nature10944

    View details for Web of Science ID 000302343400033

    View details for PubMedCentralID PMC3322419

  • A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks CURRENT BIOLOGY Jones, F. C., Chan, Y. F., Schmutz, J., Grimwood, J., Brady, S. D., Southwick, A. M., Absher, D. M., Myers, R. M., Reimchen, T. E., Deagle, B. E., Schluter, D., Kingsley, D. M. 2012; 22 (1): 83-90


    Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine-freshwater species pairs and a small number of benthic-limnetic species pairs found within single lakes [1]. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine-freshwater or benthic-limnetic species pairs. Surveying 34 global populations with 1,159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detected large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine-freshwater and benthic-limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic-limnetic species pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species pairs.

    View details for DOI 10.1016/j.cub.2011.11.045

    View details for Web of Science ID 000299144200027

    View details for PubMedID 22197244

    View details for PubMedCentralID PMC3319444

  • Three Periods of Regulatory Innovation During Vertebrate Evolution SCIENCE Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. 2011; 333 (6045): 1019-1024


    The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.

    View details for DOI 10.1126/science.1202702

    View details for Web of Science ID 000294000400056

    View details for PubMedID 21852499

    View details for PubMedCentralID PMC3511857

  • The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks HEREDITY Greenwood, A. K., Jones, F. C., Chan, Y. F., Brady, S. D., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., KINGSLEY, D. M., Peichel, C. L. 2011; 107 (2): 155-166


    Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.

    View details for DOI 10.1038/hdy.2011.1

    View details for Web of Science ID 000292911500007

    View details for PubMedID 21304547

  • The Progressive Ankylosis Protein Regulates Cementum Apposition and Extracellular Matrix Composition CELLS TISSUES ORGANS Foster, B. L., Nagatomo, K. J., Bamashmous, S. O., Tompkins, K. A., Fong, H., Dunn, D., Chu, E. Y., Guenther, C., KINGSLEY, D. M., Rutherford, R. B., Somerman, M. J. 2011; 194 (5): 382-405


    Tooth root cementum is sensitive to modulation of inorganic pyrophosphate (PP(i)), an inhibitor of hydroxyapatite precipitation. Factors increasing PP(i) include progressive ankylosis protein (ANK) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) while tissue nonspecific alkaline phosphatase hydrolyzes PP(i). Studies here aimed to define the role of ANK in root and cementum by analyzing tooth development in Ank knock-out (KO) mice versus wild type.Periodontal development in KO versus control mice was analyzed by histology, histomorphometry, immunohistochemistry, in situ hybridization, electron microscopy, and nanoindentation. Cementoblast cultures were used in vitro to provide mechanistic underpinnings for PP(i) modulation of cell function.Over the course of root development, Ank KO cervical cementum became 8- to 12-fold thicker than control cervical cementum. Periodontal ligament width was maintained and other dentoalveolar tissues, including apical cementum, were unaltered. Cervical cementum uncharacteristically included numerous cells, from rapid cementogenesis. Ank KO increased osteopontin and dentin matrix protein 1 gene and protein expression, and markedly increased NPP1 protein expression in cementoblasts but not in other cell types. Conditional ablation of Ank in joints and periodontia confirmed a local role for ANK in cementogenesis. In vitro studies employing cementoblasts indicated that Ank and Enpp1 mRNA levels increased in step with mineral nodule formation, supporting a role for these factors in regulation of cementum matrix mineralization.ANK, by modulating local PP(i), controls cervical cementum apposition and extracellular matrix. Loss of ANK created a local environment conducive to rapid cementogenesis; therefore, approaches modulating PP(i) in periodontal tissues have potential to promote cementum regeneration.

    View details for DOI 10.1159/000323457

    View details for Web of Science ID 000296044900004

    View details for PubMedID 21389671

  • Human-specific loss of an androgen receptor enhancer is associated with the loss of vibrissae and penile spines 80th Annual Meeting of the American-Association-of-Physical-Anthropologists Reno, P. L., McLean, C. Y., Pollen, A. A., Bejerano, G., Kingsley, D. M. WILEY-BLACKWELL. 2011: 252–252
  • Synovial joint morphogenesis requires the chondrogenic action of Sox5 and Sox6 in growth plate and articular cartilage DEVELOPMENTAL BIOLOGY Dy, P., Smits, P., Silvester, A., Penzo-Mendez, A., Dumitriu, B., Han, Y., de la Motte, C. A., Kingsley, D. M., Lefebvre, V. 2010; 341 (2): 346-359


    The mechanisms underlying synovial joint development remain poorly understood. Here we use complete and cell-specific gene inactivation to identify the roles of the redundant chondrogenic transcription factors Sox5 and Sox6 in this process. We show that joint development aborts early in complete mutants (Sox5(-/-)6(-/-)). Gdf5 and Wnt9a expression is punctual in articular progenitor cells, but Sox9 downregulation and cell condensation in joint interzones are late. Joint cell differentiation is unsuccessful, regardless of lineage, and cavitation fails. Sox5 and Sox6 restricted expression to chondrocytes in wild-type embryos and continued Erg expression and weak Ihh expression in Sox5(-/-)6(-/-) growth plates suggest that growth plate failure contribute to this Sox5(-/-)6(-/-) joint morphogenesis block. Sox5/6 inactivation in specified joint cells and chondrocytes (Sox5(fl/fl)6(fl/fl)Col2Cre) also results in a joint morphogenesis block, whereas Sox5/6 inactivation in specified joint cells only (Sox5(fl/fl)6(fl/fl)Gdf5Cre) results in milder joint defects and normal growth plates. Sox5(fl/fl)6(fl/fl)Gdf5Cre articular chondrocytes remain undifferentiated, as shown by continued Gdf5 expression and pancartilaginous gene downregulation. Along with Prg4 downregulation, these defects likely account for joint tissue overgrowth and incomplete cavitation in adult mice. Together, these data suggest that synovial joint morphogenesis relies on essential roles for Sox5/6 in promoting both growth plate and articular chondrocyte differentiation.

    View details for DOI 10.1016/j.ydbio.2010.02.024

    View details for Web of Science ID 000277404300002

    View details for PubMedID 20206616

    View details for PubMedCentralID PMC2862098

  • Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer SCIENCE Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal, G., Shapiro, M. D., Brady, S. D., Southwick, A. M., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Petrov, D., Jonsson, B., Schluter, D., Bell, M. A., Kingsley, D. M. 2010; 327 (5963): 302-305


    The molecular mechanisms underlying major phenotypic changes that have evolved repeatedly in nature are generally unknown. Pelvic loss in different natural populations of threespine stickleback fish has occurred through regulatory mutations deleting a tissue-specific enhancer of the Pituitary homeobox transcription factor 1 (Pitx1) gene. The high prevalence of deletion mutations at Pitx1 may be influenced by inherent structural features of the locus. Although Pitx1 null mutations are lethal in laboratory animals, Pitx1 regulatory mutations show molecular signatures of positive selection in pelvic-reduced populations. These studies illustrate how major expression and morphological changes can arise from single mutational leaps in natural populations, producing new adaptive alleles via recurrent regulatory alterations in a key developmental control gene.

    View details for DOI 10.1126/science.1182213

    View details for Web of Science ID 000273629700034

    View details for PubMedID 20007865

    View details for PubMedCentralID PMC3109066

  • Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species JOURNAL OF HEREDITY Haussler, D., O'Brien, S. J., Ryder, O. A., Barker, F. K., Clamp, M., Crawford, A. J., Hanner, R., Hanotte, O., Johnson, W. E., McGuire, J. A., Miller, W., Murphy, R. W., Murphy, W. J., Sheldon, F. H., Sinervo, B., Venkatesh, B., Wiley, E. O., Allendorf, F. W., Amato, G., Baker, C. S., Bauer, A., Beja-Pereira, A., Bermingham, E., Bernardi, G., Bonvicino, C. R., Brenner, S., Burke, T., Cracraft, J., Diekhans, M., Edwards, S., Ericson, P. G., Estes, J., Fjelsda, J., Flesness, N., Gamble, T., Gaubert, P., Graphodatsky, A. S., Graves, J. A., Green, E. D., Green, R. E., Hackett, S., Hebert, P., Helgen, K. M., Joseph, L., Kessing, B., Kingsley, D. M., Lewin, H. A., Luikart, G., Martelli, P., Moreira, M. A., Nguyen, N., Orti, G., Pike, B. L., Rawson, D. M., Schuster, S. C., Seuanez, H. N., Shaffer, H. B., Springer, M. S., Stuart, J. M., Sumner, J., Teeling, E., Vrijenhoek, R. C., Ward, R. D., Warren, W. C., Wayne, R., Williams, T. M., Wolfe, N. D., Zhang, Y., Graph-Odatsky, A., Johnson, W. E., Felsenfeld, A., Turner, S. 2009; 100 (6): 659-674


    The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

    View details for DOI 10.1093/jhered/esp086

    View details for Web of Science ID 000271817600001

    View details for PubMedID 19892720

    View details for PubMedCentralID PMC2877544

  • A role for a neo-sex chromosome in stickleback speciation NATURE Kitano, J., Ross, J. A., Mori, S., Kume, M., Jones, F. C., Chan, Y. F., Absher, D. M., Grimwood, J., Schmutz, J., Myers, R. M., Kingsley, D. M., Peichel, C. L. 2009; 461 (7267): 1079-1083


    Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex-chromosome turnover and speciation. Although closely related species often have different sex-chromosome systems, it is unknown whether sex-chromosome turnover contributes to the evolution of reproductive isolation between species. Here we show that a newly evolved sex chromosome contains genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome contains loci for male courtship display traits that contribute to behavioural isolation, whereas the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large X-effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data indicate that sex-chromosome turnover might have a greater role in speciation than was previously appreciated.

    View details for DOI 10.1038/nature08441

    View details for Web of Science ID 000270987600035

    View details for PubMedID 19783981

    View details for PubMedCentralID PMC2776091

  • The Genetic Architecture of Skeletal Convergence and Sex Determination in Ninespine Sticklebacks CURRENT BIOLOGY Shapiro, M. D., Summers, B. R., Balabhadra, S., Aldenhoven, J. T., Miller, A. L., Cunningham, C. B., Bell, M. A., Kingsley, D. M. 2009; 19 (13): 1140-1145


    The history of life offers plentiful examples of convergent evolution, the independent derivation of similar phenotypes in distinct lineages. The emergence of convergent phenotypes among closely related lineages (frequently termed "parallel" evolution) is often assumed to result from changes in similar genes or developmental pathways, but the genetic origins of convergence remains poorly understood. Ninespine (Pungitius pungitius) and threespine (Gasterosteus aculeatus) stickleback fish provide many examples of convergent evolution of adaptive phenotypes, both within and between genera. The genetic architecture of several important traits is now known for threespine sticklebacks; thus, ninespine sticklebacks provide a unique opportunity to critically test whether similar or different chromosome regions control similar phenotypes in these lineages. We have generated the first genome-wide linkage map for ninespine sticklebacks and used quantitative trait locus mapping to identify chromosome regions controlling several skeletal traits and sex determination. In ninespine sticklebacks, these traits mapped to chromosome regions not previously known to control the corresponding traits in threespine sticklebacks. Therefore, convergent morphological evolution in these related, but independent, vertebrate lineages might have different genetic origins. Comparative genetics in sticklebacks provides an exciting opportunity to study the mechanisms controlling similar phenotypic changes in different animal groups.

    View details for DOI 10.1016/j.cub.2009.05.029

    View details for Web of Science ID 000268059200026

    View details for PubMedID 19500990

    View details for PubMedCentralID PMC2735127

  • Muscle Contraction Is Necessary to Maintain Joint Progenitor Cell Fate DEVELOPMENTAL CELL Kahn, J., Shwartz, Y., Blitz, E., Krief, S., Sharir, A., Breitel, D. A., Rattenbach, R., Relaix, F., Maire, P., Rountree, R. B., Kingsley, D. M., Zelzer, E. 2009; 16 (5): 734-743


    During embryogenesis, organ development is dependent upon maintaining appropriate progenitor cell commitment. Synovial joints develop from a pool of progenitor cells that differentiate into various cell types constituting the mature joint. The involvement of the musculature in joint formation has long been recognized. However, the mechanism by which the musculature regulates joint formation has remained elusive. In this study, we demonstrate, utilizing various murine models devoid of limb musculature or its contraction, that the contracting musculature is fundamental in maintaining joint progenitors committed to their fate, a requirement for correct joint cavitation and morphogenesis. Furthermore, contraction-dependent activation of beta-catenin, a key modulator of joint formation, provides a molecular mechanism for this regulation. In conclusion, our findings provide the missing link between progenitor cell fate determination and embryonic movement, two processes shown to be essential for correct organogenesis.

    View details for DOI 10.1016/j.devcel.2009.04.013

    View details for Web of Science ID 000266347100015

    View details for PubMedID 19460349

  • From Atoms to Traits SCIENTIFIC AMERICAN Kingsley, D. M. 2009; 300 (1): 52-59

    View details for Web of Science ID 000261816200029

    View details for PubMedID 19186749

  • Shaping Skeletal Growth by Modular Regulatory Elements in the Bmp5 Gene PLOS GENETICS Guenther, C., Pantalena-Filho, L., Kingsley, D. M. 2008; 4 (12)


    Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

    View details for DOI 10.1371/journal.pgen.1000308

    View details for Web of Science ID 000263667900023

    View details for PubMedID 19096511

    View details for PubMedCentralID PMC2592695

  • Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs DEVELOPMENT Menke, D. B., Guenther, C., Kingsley, D. M. 2008; 135 (15): 2543-2553


    The Tbx4 transcription factor is crucial for normal hindlimb and vascular development, yet little is known about how its highly conserved expression patterns are generated. We have used comparative genomics and functional scanning in transgenic mice to identify a dispersed group of enhancers controlling Tbx4 expression in different tissues. Two independent enhancers control hindlimb expression, one located upstream and one downstream of the Tbx4 coding exons. These two enhancers, hindlimb enhancer A and hindlimb enhancer B (HLEA and HLEB), differ in their primary sequence, in their precise patterns of activity within the hindlimb, and in their degree of sequence conservation across animals. HLEB is highly conserved from fish to mammals. Although Tbx4 expression and hindlimb development occur at different axial levels in fish and mammals, HLEB cloned from either fish or mouse is capable of driving expression at the appropriate position of hindlimb development in mouse embryos. HLEA is highly conserved only in mammals. Deletion of HLEA from the endogenous mouse locus reduces expression of Tbx4 in the hindlimb during embryogenesis, bypasses the embryonic lethality of Tbx4-null mutations, and produces viable, fertile mice with characteristic changes in the size of bones in the hindlimb but not the forelimb. We speculate that dual hindlimb enhancers provide a flexible genomic mechanism for altering the strength and location of Tbx4 expression during normal development, making it possible to separately modify the size of forelimb and hindlimb bones during vertebrate evolution.

    View details for DOI 10.1242/dev.017384

    View details for Web of Science ID 000257557200006

    View details for PubMedID 18579682

  • Dominant negative Bmp5 mutation reveals key role of BMPs in skeletal response to mechanical stimulation BMC DEVELOPMENTAL BIOLOGY Ho, A. M., Marker, P. C., Peng, H., Quintero, A. J., Kingsley, D. M., Huard, J. 2008; 8


    Over a hundred years ago, Wolff originally observed that bone growth and remodeling are exquisitely sensitive to mechanical forces acting on the skeleton. Clinical studies have noted that the size and the strength of bone increase with weight bearing and muscular activity and decrease with bed rest and disuse. Although the processes of mechanotransduction and functional response of bone to mechanical strain have been extensively studied, the molecular signaling mechanisms that mediate the response of bone cells to mechanical stimulation remain unclear.Here, we identify a novel germline mutation at the mouse Bone morphogenetic protein 5 (Bmp5) locus. Genetic analysis shows that the mutation occurs at a site encoding the proteolytic processing sequence of the BMP5 protein and blocks proper processing of BMP5. Anatomic studies reveal that this mutation affects the formation of multiple skeletal features including several muscle-induced skeletal sites in vivo. Biomechanical studies of osteoblasts from these anatomic sites show that the mutation inhibits the proper response of bone cells to mechanical stimulation.The results from these genetic, biochemical, and biomechanical studies suggest that BMPs are required not only for skeletal patterning during embryonic development, but also for bone response and remodeling to mechanical stimulation at specific anatomic sites in the skeleton.

    View details for DOI 10.1186/1471-213X-8-35

    View details for Web of Science ID 000255931900001

    View details for PubMedID 18380899

    View details for PubMedCentralID PMC2335095

  • A distinct cohort of progenitor cells participates in synovial Joint and articular cartilage formation during mouse limb skeletogenesis DEVELOPMENTAL BIOLOGY Koyama, E., Shibukawa, Y., Nagayama, M., Sugito, H., Young, B., Yuasa, T., Okabe, T., Ochiai, T., Kamiya, N., Rountree, R. B., Kingsley, D. M., Iwamoto, M., Enomoto-Iwamoto, M., Pacifici, M. 2008; 316 (1): 62-73


    The origin, roles and fate of progenitor cells forming synovial joints during limb skeletogenesis remain largely unclear. Here we produced prenatal and postnatal genetic cell fate-maps by mating ROSA-LacZ-reporter mice with mice expressing Cre-recombinase at prospective joint sites under the control of Gdf5 regulatory sequences (Gdf5-Cre). Reporter-expressing cells initially constituted the interzone, a compact mesenchymal structure representing the first overt sign of joint formation, and displayed a gradient-like distribution along the ventral-to-dorsal axis. The cells expressed genes such as Wnt9a, Erg and collagen IIA, remained predominant in the joint-forming sites over time, gave rise to articular cartilage, synovial lining and other joint tissues, but contributed little if any to underlying growth plate cartilage and shaft. To study their developmental properties more directly, we isolated the joint-forming cells from prospective autopod joint sites using a novel microsurgical procedure and tested them in vitro. The cells displayed a propensity to undergo chondrogenesis that was enhanced by treatment with exogenous rGdf5 but blocked by Wnt9a over-expression. To test roles for such Wnt-mediated anti-chondrogenic capacity in vivo, we created conditional mutants deficient in Wnt/beta-catenin signaling using Col2-Cre or Gdf5-Cre. Synovial joints did form in both mutants; however, the joints displayed a defective flat cell layer normally abutting the synovial cavity and expressed markedly reduced levels of lubricin. In sum, our data indicate that cells present at prospective joint sites and expressing Gdf5 constitute a distinct cohort of progenitor cells responsible for limb joint formation. The cells appear to be patterned along specific limb symmetry axes and rely on local signaling tools to make distinct contributions to joint formation.

    View details for DOI 10.1016/j.ydbio.2008.01.012

    View details for Web of Science ID 000254845200006

    View details for PubMedID 18295755

    View details for PubMedCentralID PMC2373417

  • The genetics of adaptive shape shift in stickleback: Pleiotropy and effect size EVOLUTION Albert, A. Y., Sawaya, S., Vines, T. H., Knecht, A. K., Miller, C. T., Summers, B. R., Balabhadra, S., Kingsley, D. M., Schluter, D. 2008; 62 (1): 76-85


    The distribution of effect sizes of genes underlying adaptation is unknown (Orr 2005). Are suites of traits that diverged under natural selection controlled by a few pleiotropic genes of large effect (major genes model), by many independently acting genes of small effect (infinitesimal model), or by a combination, with frequency inversely related to effect size (geometric model)? To address this we carried out a quantitative trait loci (QTL) study of a suite of 54 position traits describing body shapes of two threespine stickleback species: an ancestral Pacific marine form and a highly derived benthic species inhabiting a geologically young lake. About half of the 26 detected QTL affected just one coordinate and had small net effects, but several genomic regions affected multiple aspects of shape and had large net effects. The distribution of effect sizes followed the gamma distribution, as predicted by the geometric model of adaptation when detection limits are taken into account. The sex-determining chromosome region had the largest effect of any QTL. Ancestral sexual dimorphism was similar to the direction of divergence, and was largely eliminated during freshwater adaptation, suggesting that sex differences may provide variation upon which selection can act. Several shape QTL are linked to Eda, a major gene responsible for reduction of lateral body armor in freshwater. Our results are consistent with predictions of the geometric model of adaptation. Shape evolution in stickleback results from a few genes with large and possibly widespread effects and multiple genes of smaller effect.

    View details for DOI 10.1111/j.1558-5646.2007.00259.x

    View details for Web of Science ID 000252108700007

    View details for PubMedID 18005154

  • cis-regulatory changes in kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans CELL Miller, C. T., Beleza, S., Pollen, A. A., Schluter, D., Kittles, R. A., Shriver, M. D., Kingsley, D. M. 2007; 131 (6): 1179-1189


    Dramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans.

    View details for DOI 10.1016/j.cell.2007.10.055

    View details for Web of Science ID 000252217100024

    View details for PubMedID 18083106

    View details for PubMedCentralID PMC2900316

  • Over-expression of BMP4 and BMP5 in a child with axial skeletal malformations and heterotopic ossification: A new syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Feldman, G. J., Billings, P. C., Patel, R. V., Caron, R. J., Guenther, C., Kingsley, D. M., Kaplan, F. S., Shore, E. M. 2007; 143A (7): 699-706


    Bone morphogenetic proteins (BMPs) are a highly conserved class of signaling molecules that induce ectopic cartilage and bone formation in vivo. Dysregulated expression of bone morphogenetic protein 4 (BMP4) is found in the cells of patients who have fibrodysplasia ossificans progressiva (FOP), a genetic disorder of axial and appendicular skeletal malformation and progressive heterotopic ossification. Loss of function mutations in the bone morphogenetic protein 5 (bmp5) gene leading to under-expression of BMP5 cause the murine short ear syndrome, characterized by small malformed ears and a broad range of axial skeletal malformations. We found features reminiscent of both the short ear mouse and FOP in a child with malformed external ears, multiple malformations of the axial skeleton, and progressive heterotopic ossification in the neck and back. We examined BMP mRNA expression in transformed lymphocytes by semi-quantitative RT-PCR and protein expression by ELISA assays and immunohistochemistry. Elevated levels of BMP4 and BMP5 mRNA and protein were detected in the patient's cells while levels of BMP2 mRNA were unchanged. Our data suggest that dysregulated expression of BMP4 and BMP5 genes is associated with an array of human axial skeletal abnormalities similar to the short ear mouse and FOP.

    View details for DOI 10.1002/ajmg.a.31649

    View details for Web of Science ID 000245450200009

  • Constraints on utilization of the EDA-signaling pathway in threespine stickleback evolution EVOLUTION & DEVELOPMENT Knecht, A. K., Hosemann, K. E., Kingsley, D. M. 2007; 9 (2): 141-154


    Many traits evolve in parallel in widely separated populations. The evolutionary radiation of threespine sticklebacks provides a powerful model for testing the molecular basis of parallel evolution in vertebrates. Although marine sticklebacks are completely covered with bony armor plates, most freshwater populations have dramatic reductions in plates. Recent genetic studies have shown that major changes in armor patterning are likely due to regulatory alterations in the gene encoding the secreted signaling molecule ectodysplasin (EDA). In mammals, mutations in many different components of the EDA-signaling pathway produce similar changes in hair, teeth, sweat glands, and dermal bones. To test whether other genes in the EDA pathway also control natural variation in armor plates, we identified and mapped stickleback EDA Receptor (EDAR), the EDAR-Associated Death Domain adaptor, Tumor Necrosis Factor Receptor (TNFR) SuperFamily member 19, its adaptor TNFR-Associated Factor 6, and the downstream regulator nuclear factor kappa B Essential Modulator (NEMO). In contrast to the diversity of genes underlying ectodermal dysplasia disease phenotypes in humans, none of these EDA pathway components map to chromosomes previously shown to modify armor plates in natural populations, though EDAR showed a small but significant effect on plate number. We further investigated whether these genes exhibit differences in copy number, target size, or genomic organization that might make them less suitable targets for evolutionary change. In comparison with EDA, all these genes have smaller surrounding noncoding (putative regulatory) regions, with fewer evolutionarily conserved regions. We suggest that the presence of highly modular cis-acting control sequences may be a key factor influencing the likelihood that particular genes will serve as the basis of major phenotypic changes in nature.

    View details for Web of Science ID 000244942700004

    View details for PubMedID 17371397

  • Synovial joint formation during mouse limb skeletogenesis - Roles of Indian hedgehog signaling 2nd Conference on Skeletal Biology and Medicine Koyama, E., Ochiai, T., Rountree, R. B., Kingsley, D. M., Enomoto-Iwamoto, M., Iwamoto, M., Pacifici, M. BLACKWELL PUBLISHING. 2007: 100–112


    Indian hedgehog (Ihh) has been previously found to regulate synovial joint formation. To analyze mechanisms, we carried out morphological, molecular, and cell fate map analyses of interzone and joint development in wild-type and Ihh(-/-) mouse embryo long bones. We found that Ihh(-/-) cartilaginous digit anlagen remained fused and lacked interzones or mature joints, whereas wrist skeletal elements were not fused but their joints were morphologically abnormal. E14.5 and E17.5 wild-type digit and ankle prospective joints expressed hedgehog target genes including Gli1 and Gli2 and interzone-associated genes including Gdf5, Erg, and tenascin-C, but expression of all these genes was barely detectable in mutant joints. For cell fate map analysis of joint progenitor cells, we mated Gdf5-Cre(+/-)/Rosa R26R(+/-) double transgenic mice with heterozygous Ihh(+/-) mice and monitored reporter beta-galactosidase activity and gene expression in triple-transgenic progeny. In control Gdf5-Cre(+/-)/R26R(+/-)/Ihh(+/-) limbs, reporter-positive cells were present in developing interzones, articulating layers, and synovial lining tissue and absent from underlying growth plates. In mutant Gdf5-Cre(+/-)/R26R(+/-)/Ihh(-/-) specimens, reporter-positive cells were present also. However, the cells were mostly located around the prospective and uninterrupted digit joint sites and, interestingly, still expressed Erg, tenascin-C, and Gdf5. Topographical analysis revealed that interzone and associated cells were not uniformly distributed, but were much more numerous ventrally. A similar topographical bias was seen for cavitation process and capsule primordia formation. In sum, Ihh is a critical and possibly direct regulator of joint development. In its absence, distribution and function of Gdf5-expressing interzone-associated cells are abnormal, but their patterning at prospective joint sites still occurs. The joint-forming functions of the cells appear to normally involve a previously unsuspected asymmetric distribution along the ventral-to-dorsal plane of the developing joint.

    View details for DOI 10.1196/annals.1402.063

    View details for Web of Science ID 000251898900007

    View details for PubMedID 18083924

    View details for PubMedCentralID PMC2673545

  • Biochemical and genetic analysis of ANK in arthritis and bone disease AMERICAN JOURNAL OF HUMAN GENETICS Gurley, K. A., Reimer, R. J., Kingsley, D. M. 2006; 79 (6): 1017-1029


    Mutations in the progressive ankylosis gene (Ank/ANKH) cause surprisingly different skeletal phenotypes in mice and humans. In mice, recessive loss-of-function mutations cause arthritis, ectopic crystal formation, and joint fusion throughout the body. In humans, some dominant mutations cause chondrocalcinosis, an adult-onset disease characterized by the deposition of ectopic joint crystals. Other dominant mutations cause craniometaphyseal dysplasia, a childhood disease characterized by sclerosis of the skull and abnormal modeling of the long bones, with little or no joint pathology. Ank encodes a multiple-pass transmembrane protein that regulates pyrophosphate levels inside and outside tissue culture cells in vitro, but its mechanism of action is not yet clear, and conflicting models have been proposed to explain the effects of the human mutations. Here, we test wild-type and mutant forms of ANK for radiolabeled pyrophosphate-transport activity in frog oocytes. We also reconstruct two human mutations in a bacterial artificial chromosome and test them in transgenic mice for rescue of the Ank null phenotype and for induction of new skeletal phenotypes. Wild-type ANK stimulates saturable transport of pyrophosphate ions across the plasma membrane, with half maximal rates attained at physiological levels of pyrophosphate. Chondrocalcinosis mutations retain apparently wild-type transport activity and can rescue the joint-fusion phenotype of Ank null mice. Craniometaphyseal dysplasia mutations do not transport pyrophosphate and cannot rescue the defects of Ank null mice. Furthermore, microcomputed tomography revealed previously unappreciated phenotypes in Ank null mice that are reminiscent of craniometaphyseal dysplasia. The combination of biochemical and genetic analyses presented here provides insight into how mutations in ANKH cause human skeletal disease.

    View details for Web of Science ID 000242131600003

    View details for PubMedID 17186460

  • Parallel genetic origins of pelvic reduction in vertebrates PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Shapiro, M. D., Bell, M. A., Kingsley, D. M. 2006; 103 (37): 13753-13758


    Despite longstanding interest in parallel evolution, little is known about the genes that control similar traits in different lineages of vertebrates. Pelvic reduction in stickleback fish (family Gasterosteidae) provides a striking example of parallel evolution in a genetically tractable system. Previous studies suggest that cis-acting regulatory changes at the Pitx1 locus control pelvic reduction in a population of threespine sticklebacks (Gasterosteus aculeatus). In this study, progeny from intergeneric crosses between pelvic-reduced threespine and ninespine (Pungitius pungitius) sticklebacks also showed severe pelvic reduction, implicating a similar genetic origin for this trait in both genera. Comparative sequencing studies in complete and pelvic-reduced Pungitius revealed no differences in the Pitx1 coding sequences, but Pitx1 expression was absent from the prospective pelvic region of larvae from pelvic-reduced parents. A much more phylogenetically distant example of pelvic reduction, loss of hindlimbs in manatees, shows a similar left-right size bias that is a morphological signature of Pitx1-mediated pelvic reduction in both sticklebacks and mice. These multiple lines of evidence suggest that changes in Pitx1 may represent a key mechanism of morphological evolution in multiple populations, species, and genera of sticklebacks, as well as in distantly related vertebrate lineages.

    View details for DOI 10.1073/pnas.0604706103

    View details for Web of Science ID 000240648300038

    View details for PubMedID 16945911

    View details for PubMedCentralID PMC1564237

  • Mineral formation in joints caused by complete or joint-specific loss of ANK function JOURNAL OF BONE AND MINERAL RESEARCH Gurley, K. A., Chen, H., Guenther, C., Nguyen, E. T., Rountree, R. B., Schoor, M., Kingsley, D. M. 2006; 21 (8): 1238-1247


    To reveal the ANK complete loss of function phenotype in mice, we generated conditional and null alleles. Mice homozygous for the null allele exhibited widespread joint mineralization, similar in severity to animals harboring the original ank allele. A delayed yet similar phenotype was observed in mice with joint-specific loss of ANK function.The ANK pyrophosphate regulator was originally identified and proposed to play a key role in articular cartilage maintenance based on a single spontaneous mouse mutation (ank) that causes severe generalized arthritis. A number of human mutations have subsequently been reported in the human ortholog (ANKH), some of which produce skull and long bone defects with no apparent defects in joints or articular cartilage. None of the currently known mouse or human mutations clearly eliminate the function of the endogenous gene.Two new Ank alleles were generated using homologous recombination in mouse embryonic stem (ES) cells. Joint range of motion assays and muCT studies were used to quantitatively assess phenotypic severity in wildtype, heterozygous, and homozygous mice carrying either the null (Anknull) or original (Ankank) allele. A Gdf5-Cre expressing line was crossed to mice harboring the conditional (Ankfloxp) allele to eliminate ANK function specifically in the joints. Histological stains and beta-galactosidase (LACZ) activity were used to determine the correlation between local loss of ANK function and defective joint phenotypes.Anknull/Anknull mice develop severe ectopic postnatal crystal deposition in almost every joint of the body, leading to eventual joint fusion and loss of mobility. The severity of phenotype in these mice is indistinguishable from that of Ankank/Ankank mice. In addition, despite the widespread expression of Ank in many tissues, the specific deletion of Ank in joints also produces joint mineralization and ankylosis.These studies show that ANK function is required locally in joints to inhibit mineral formation and that the Ank gene plays a key role in postnatal maintenance of joint mobility and function.

    View details for DOI 10.1359/JBMR.060515

    View details for Web of Science ID 000239299400008

    View details for PubMedID 16869722

  • Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer GENOMICS Portnoy, M. E., McDermott, K. J., Antonellis, A., Margulies, E. H., Prasad, A. B., KINGSLEY, D. M., Green, E. D., Mortlock, D. P. 2005; 86 (3): 295-305


    The identification of noncoding functional elements within vertebrate genomes, such as those that regulate gene expression, is a major challenge. Comparisons of orthologous sequences from multiple species are effective at detecting highly conserved regions and can reveal potential regulatory sequences. The GDF6 gene controls developmental patterning of skeletal joints and is associated with numerous, distant cis-acting regulatory elements. Using sequence data from 14 vertebrate species, we performed novel multispecies comparative analyses to detect highly conserved sequences flanking GDF6. The complementary tools WebMCS and ExactPlus identified a series of multispecies conserved sequences (MCSs). Of particular interest are MCSs within noncoding regions previously shown to contain GDF6 regulatory elements. A previously reported conserved sequence at -64 kb was also detected by both WebMCS and ExactPlus. Analysis of LacZ-reporter transgenic mice revealed that a 440-bp segment from this region contains an enhancer for Gdf6 expression in developing proximal limb joints. Several other MCSs represent candidate GDF6 regulatory elements; many of these are not conserved in fish or frog, but are strongly conserved in mammals.

    View details for DOI 10.1016/ygeno.2005.05.003

    View details for Web of Science ID 000231350300005

    View details for PubMedID 15979840

  • Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles SCIENCE Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., KINGSLEY, D. M. 2005; 307 (5717): 1928-1933


    Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling armor plate patterning in wild threespine sticklebacks. Mapping, sequencing, and transgenic studies show that the Ectodysplasin (EDA) signaling pathway plays a key role in evolutionary change in natural populations and that parallel evolution of stickleback low-plated phenotypes at most freshwater locations around the world has occurred by repeated selection of Eda alleles derived from an ancestral low-plated haplotype that first appeared more than two million years ago. Members of this clade of low-plated alleles are present at low frequencies in marine fish, which suggests that standing genetic variation can provide a molecular basis for rapid, parallel evolution of dramatic phenotypic change in nature.

    View details for DOI 10.1126/science.1107239

    View details for Web of Science ID 000227957300048

    View details for PubMedID 15790847

  • BMP receptor signaling is required for postnatal maintenance of articular cartilage PLOS BIOLOGY Rountree, R. B., Schoor, M., Chen, H., Marks, M. E., Harley, V., Mishina, Y., Kingsley, D. M. 2004; 2 (11): 1815-1827


    Articular cartilage plays an essential role in health and mobility, but is frequently damaged or lost in millions of people that develop arthritis. The molecular mechanisms that create and maintain this thin layer of cartilage that covers the surface of bones in joint regions are poorly understood, in part because tools to manipulate gene expression specifically in this tissue have not been available. Here we use regulatory information from the mouse Gdf5 gene (a bone morphogenetic protein [BMP] family member) to develop new mouse lines that can be used to either activate or inactivate genes specifically in developing joints. Expression of Cre recombinase from Gdf5 bacterial artificial chromosome clones leads to specific activation or inactivation of floxed target genes in developing joints, including early joint interzones, adult articular cartilage, and the joint capsule. We have used this system to test the role of BMP receptor signaling in joint development. Mice with null mutations in Bmpr1a are known to die early in embryogenesis with multiple defects. However, combining a floxed Bmpr1a allele with the Gdf5-Cre driver bypasses this embryonic lethality, and leads to birth and postnatal development of mice missing the Bmpr1a gene in articular regions. Most joints in the body form normally in the absence of Bmpr1a receptor function. However, articular cartilage within the joints gradually wears away in receptor-deficient mice after birth in a process resembling human osteoarthritis. Gdf5-Cre mice provide a general system that can be used to test the role of genes in articular regions. BMP receptor signaling is required not only for early development and creation of multiple tissues, but also for ongoing maintenance of articular cartilage after birth. Genetic variation in the strength of BMP receptor signaling may be an important risk factor in human osteoarthritis, and treatments that mimic or augment BMP receptor signaling should be investigated as a possible therapeutic strategy for maintaining the health of joint linings.

    View details for DOI 10.1371/journal.pbio.0020355

    View details for Web of Science ID 000225160300013

    View details for PubMedID 15492776

    View details for PubMedCentralID PMC523229

  • New genomic tools for molecular studies of evolutionary change in threespine sticklebacks 4th International Conference on Stickleback Behaviour and Evolution Kingsley, D. M., Zhu, B. L., Osoegawa, K., de Jong, P. J., Schein, J., Marra, M., Peichel, C., Amamiya, C., Schluter, D., Balabhadra, S., Friedlander, B., Cha, Y. M., Dickson, M., Grimwood, J., Schmutz, J., Talbot, W. S., Myers, R. BRILL ACADEMIC PUBLISHERS. 2004: 1331–1344
  • A simple and efficient microinjection protocol for making transgenic sticklebacks 4th International Conference on Stickleback Behaviour and Evolution Hosemann, K. E., Colosimo, P. E., Summers, B. R., Kingsley, D. M. BRILL ACADEMIC PUBLISHERS. 2004: 1345–1355
  • The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome CURRENT BIOLOGY Peichel, C. L., Ross, J. A., Matson, C. K., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Mori, S., Schluter, D., KINGSLEY, D. M. 2004; 14 (16): 1416-1424


    Many different environmental and genetic sex-determination mechanisms are found in nature. Closely related species can use different master sex-determination switches, suggesting that these developmental pathways can evolve very rapidly. Previous cytological studies suggest that recently diverged species of stickleback fish have different sex chromosome complements. Here, we investigate the genetic and chromosomal mechanisms that underlie sex determination in the threespine stickleback (Gasterosteus aculeatus).Genome-wide linkage mapping identifies a single chromosome region at the distal end of linkage group (LG) 19, which controls male or female sexual development in threespine sticklebacks. Although sex chromosomes are not cytogenetically visible in this species, several lines of evidence suggest that LG 19 is an evolving sex chromosome system, similar to the XX female/XY male system in many other species: (1) males are consistently heterozygous for unique alleles in this region; (2) recombination between loci linked to the sex-determination region is reduced in male meiosis relative to female meiosis; (3) sequence analysis of X- and Y-specific bacterial artificial chromosome (BAC) clones from the sex-determination region reveals many sequence differences between the X- and Y-specific clones; and (4) the Y chromosome has accumulated transposable elements and local duplications.Taken together, our data suggest that threespine sticklebacks have a simple chromosomal mechanism for sex determination based on a nascent Y chromosome that is less than 10 million years old. Further analysis of the stickleback system will provide an exciting window into the evolution of sex-determination pathways and sex chromosomes in vertebrates.

    View details for Web of Science ID 000223586900019

    View details for PubMedID 15324658

  • Evidence for ecology's role in speciation NATURE McKinnon, J. S., Mori, S., Blackman, B. K., David, L., KINGSLEY, D. M., Jamieson, L., Chou, J., Schluter, D. 2004; 429 (6989): 294-298


    A principal challenge in testing the role of natural selection in speciation is to connect the build-up of reproductive isolation between populations to divergence of ecologically important traits. Demonstrations of 'parallel speciation', or assortative mating by selective environment, link ecology and isolation, but the phenotypic traits mediating isolation have not been confirmed. Here we show that the parallel build-up of mating incompatibilities between stickleback populations can be largely accounted for by assortative mating based on one trait, body size, which evolves predictably according to environment. In addition to documenting the influence of body size on reproductive isolation for stickleback populations spread across the Northern Hemisphere, we have confirmed its importance through a new experimental manipulation. Together, these results suggest that speciation may arise largely as a by-product of ecological differences and divergent selection on a small number of phenotypic traits.

    View details for DOI 10.1038/nature02556

    View details for Web of Science ID 000221505900042

    View details for PubMedID 15152252

  • The genetic architecture of parallel armor plate reduction in threespine sticklebacks PLOS BIOLOGY Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., Kingsley, D. M. 2004; 2 (5): 635-641


    How many genetic changes control the evolution of new traits in natural populations? Are the same genetic changes seen in cases of parallel evolution? Despite long-standing interest in these questions, they have been difficult to address, particularly in vertebrates. We have analyzed the genetic basis of natural variation in three different aspects of the skeletal armor of threespine sticklebacks (Gasterosteus aculeatus): the pattern, number, and size of the bony lateral plates. A few chromosomal regions can account for variation in all three aspects of the lateral plates, with one major locus contributing to most of the variation in lateral plate pattern and number. Genetic mapping and allelic complementation experiments show that the same major locus is responsible for the parallel evolution of armor plate reduction in two widely separated populations. These results suggest that a small number of genetic changes can produce major skeletal alterations in natural populations and that the same major locus is used repeatedly when similar traits evolve in different locations.

    View details for DOI 10.1371/journal.pbio.0020109

    View details for Web of Science ID 000221599500013

    View details for PubMedCentralID PMC385219

  • The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS biology Colosimo, P. F., Peichel, C. L., Nereng, K., Blackman, B. K., Shapiro, M. D., Schluter, D., Kingsley, D. M. 2004; 2 (5): E109-?


    How many genetic changes control the evolution of new traits in natural populations? Are the same genetic changes seen in cases of parallel evolution? Despite long-standing interest in these questions, they have been difficult to address, particularly in vertebrates. We have analyzed the genetic basis of natural variation in three different aspects of the skeletal armor of threespine sticklebacks (Gasterosteus aculeatus): the pattern, number, and size of the bony lateral plates. A few chromosomal regions can account for variation in all three aspects of the lateral plates, with one major locus contributing to most of the variation in lateral plate pattern and number. Genetic mapping and allelic complementation experiments show that the same major locus is responsible for the parallel evolution of armor plate reduction in two widely separated populations. These results suggest that a small number of genetic changes can produce major skeletal alterations in natural populations and that the same major locus is used repeatedly when similar traits evolve in different locations.

    View details for PubMedID 15069472

  • Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks NATURE Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jonsson, B., Schluter, D., Kingsley, D. M. 2004; 428 (6984): 717-723


    Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.

    View details for DOI 10.1038/nature02415

    View details for Web of Science ID 000220823800030

    View details for PubMedID 15085123

  • A general approach for identifying distant regulatory elements applied to the Gdf6 gene GENOME RESEARCH Mortlock, D. P., Guenther, C., Kingsley, D. M. 2003; 13 (9): 2069-2081


    Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distant regulatory elements into smaller intervals for detailed study. The mouse Gdf6 gene is expressed in a number of distinct embryonic locations that are involved in the patterning of skeletal and soft tissues. To identify sequences responsible for Gdf6 regulation, we first isolated a series of overlapping bacterial artificial chromosomes (BACs) that extend varying distances upstream and downstream of the gene. A LacZ reporter cassette was integrated into the Gdf6 transcription unit of each BAC using homologous recombination in bacteria. Each modified BAC was injected into fertilized mouse eggs, and founder transgenic embryos were analyzed for LacZ expression mid-gestation. The overlapping segments defined by the BAC clones revealed five separate regulatory regions that drive LacZ expression in 11 distinct anatomical locations. To further localize sequences that control expression in developing skeletal joints, we created a series of BAC constructs with precise deletions across a putative joint-control region. This approach further narrowed the critical control region to an area containing several stretches of sequence that are highly conserved between mice and humans. A distant 2.9-kilobase fragment containing the highly conserved regions is able to direct very specific expression of a minimal promoter/LacZ reporter in proximal limb joints. These results demonstrate that even distant, complex regulatory sequences can be identified using a combination of BAC scanning, BAC deletion, and comparative sequencing approaches.

    View details for DOI 10.1101/gr.1306003

    View details for Web of Science ID 000185085300010

    View details for PubMedID 12915490

    View details for PubMedCentralID PMC403689

  • Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes DEVELOPMENTAL BIOLOGY Settle, S. H., Rountree, R. B., Sinha, A., Thacker, A., Higgins, K., KINGSLEY, D. M. 2003; 254 (1): 116-130


    Growth/differentiation factors 5, 6, and 7 (GDF5/6/7) represent a distinct subgroup within the bone morphogenetic protein (BMP) family of secreted signaling molecules. Previous studies have shown that the Gdf5 gene is expressed in transverse stripes across developing skeletal elements and is one of the earliest known markers of joint formation during embryonic development. Although null mutations in this gene disrupt formation of some bones and joints in the skeleton, many sites are unaffected. Here, we show that the closely related family members Gdf6 and Gdf7 are expressed in different subsets of developing joints. Inactivation of the Gdf6 gene causes defects in joint, ligament, and cartilage formation at sites distinct from those seen in Gdf5 mutants, including the wrist and ankle, the middle ear, and the coronal suture between bones in the skull. Mice lacking both Gdf5 and Gdf6 show additional defects, including severe reduction or loss of some skeletal elements in the limb, additional fusions between skeletal structures, scoliosis, and altered cartilage in the intervertebral joints of the spinal column. These results show that members of the GDF5/6/7 subgroup are required for normal formation of bones and joints in the limbs, skull, and axial skeleton. The diverse effects on joint development and the different types of joints affected in the mutants suggest that members of the GDF family play a key role in establishing boundaries between many different skeletal elements during normal development. Some of the skeletal defects seen in single or double mutant mice resemble defects seen in human skeletal diseases, which suggests that these genes may be candidates that underlie some forms of carpal/tarsal coalition, conductive deafness, scoliosis, and craniosynostosis.

    View details for Web of Science ID 000180731500009

    View details for PubMedID 12606286

  • Cementum: A phosphate-sensitive tissue JOURNAL OF DENTAL RESEARCH Nociti, F. H., Berry, J. E., Foster, B. L., Gurley, K. A., KINGSLEY, D. M., Takata, T., Miyauchi, M., Somerman, M. J. 2002; 81 (12): 817-821


    Ectopic calcification within joints has been reported in humans and rodents exhibiting mutations in genes that regulate the level of extracellular pyrophosphate, e.g., ank and PC-1; however, periodontal effects of these mutations have not previously been examined. These initial studies using ank and PC-1 mutant mice were done to see if such mineral deposition and resulting ankylosis were occurring in the periodontium as well. Surprisingly, results indicated the absence of ankylosis; however, a marked increase in cementum formation on the root surfaces of fully developed teeth of these mutant mice was noted. Examination of ank mutant mice at earlier ages of tooth root formation indicated that this striking observation is apparent from the onset of cementogenesis. These findings suggest that cells within the periodontal region are highly responsive to changes in phosphate metabolism. This information may prove valuable in attempts to design successful therapies for regenerating periodontal tissues.

    View details for Web of Science ID 000179555900005

    View details for PubMedID 12454094

  • Mutations in ANKH cause chondrocalcinosis AMERICAN JOURNAL OF HUMAN GENETICS Pendleton, A., Johnson, M. D., Hughes, A., Gurley, K. A., Ho, A. M., Doherty, M., Dixey, J., Gillet, P., Loeuille, D., McGrath, R., REGINATO, A., Shiang, R., Wright, G., Netter, P., Williams, C., Kingsley, D. M. 2002; 71 (4): 933-940


    Chondrocalcinosis (CC) is a common cause of joint pain and arthritis that is caused by the deposition of calcium-containing crystals within articular cartilage. Although most cases are sporadic, rare familial forms have been linked to human chromosomes 8 (CCAL1) or 5p (CCAL2) (Baldwin et al. 1995; Hughes et al. 1995; Andrew et al. 1999). Here, we show that two previously described families with CCAL2 have mutations in the human homolog of the mouse progressive ankylosis gene (ANKH). One of the human mutations results in the substitution of a highly conserved amino acid residue within a predicted transmembrane segment. The other creates a new ATG start site that adds four additional residues to the ANKH protein. Both mutations segregate completely with disease status and are not found in control subjects. In addition, 1 of 95 U.K. patients with sporadic CC showed a deletion of a single codon in the ANKH gene. The same change was found in a sister who had bilateral knee replacement for osteoarthritis. Each of the three human mutations was reconstructed in a full-length ANK expression construct previously shown to regulate pyrophosphate levels in cultured cells in vitro. All three of the human mutations showed significantly more activity than a previously described nonsense mutation that causes severe hydroxyapatite mineral deposition and widespread joint ankylosis in mice. These results suggest that small sequence changes in ANKH are one cause of CC and joint disease in humans. Increased ANK activity may explain the different types of crystals commonly deposited in human CCAL2 families and mutant mice and may provide a useful pharmacological target for treating some forms of human CC.

    View details for Web of Science ID 000178613800019

    View details for PubMedID 12297987

    View details for PubMedCentralID PMC378546

  • Dysregulated expression of BMP5 in a patient with deformed helices, axial skeletal defects, and heterotopic ossification: A clue from the short-ear mouse. 24th Annual Meeting of the American-Society-for-Bone-and-Mineral-Research FELDMAN, G. J., Patel, R., Billings, P. C., KINGSLEY, D. M., Shore, E. M., Kaplan, F. S. WILEY-BLACKWELL. 2002: S499–S499
  • The genetic architecture of divergence between threespine stickleback species NATURE Peichel, C. L., Nereng, K. S., Ohgi, K. A., Cole, B. L., Colosimo, P. F., Buerkle, C. A., Schluter, D., Kingsley, D. M. 2001; 414 (6866): 901-905


    The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution.

    View details for Web of Science ID 000172813300044

    View details for PubMedID 11780061

  • Reciprocal mouse and human limb phenotypes caused by gain- and loss-of-function mutations affecting Lmbr1 GENETICS Clark, R. M., Marker, P. C., ROESSLER, E., Dutra, A., Schimenti, J. C., Muenke, M., Kingsley, D. M. 2001; 159 (2): 715-726


    The major locus for dominant preaxial polydactyly in humans has been mapped to 7q36. In mice the dominant Hemimelic extra toes (Hx) and Hammertoe (Hm) mutations map to a homologous chromosomal region and cause similar limb defects. The Lmbr1 gene is entirely within the small critical intervals recently defined for both the mouse and human mutations and is misexpressed at the exact time that the mouse Hx phenotype becomes apparent during limb development. This result suggests that Lmbr1 may underlie preaxial polydactyly in both mice and humans. We have used deletion chromosomes to demonstrate that the dominant mouse and human limb defects arise from gain-of-function mutations and not from haploinsufficiency. Furthermore, we created a loss-of-function mutation in the mouse Lmbr1 gene that causes digit number reduction (oligodactyly) on its own and in trans to a deletion chromosome. The loss of digits that we observed in mice with reduced Lmbr1 activity is in contrast to the gain of digits observed in Hx mice and human polydactyly patients. Our results suggest that the Lmbr1 gene is required for limb formation and that reciprocal changes in levels of Lmbr1 activity can lead to either increases or decreases in the number of digits in the vertebrate limb.

    View details for Web of Science ID 000171744900024

    View details for PubMedID 11606546

    View details for PubMedCentralID PMC1461845

  • The BMP family member Gdf7 is required for seminal vesicle growth, branching morphogenesis, and cytodifferentiation DEVELOPMENTAL BIOLOGY Settle, S., Marker, P., Gurley, K., Sinha, A., Thacker, A., Wang, Y. Z., Higgins, K., Cunha, G., Kingsley, D. M. 2001; 234 (1): 138-150


    Epithelial-mesenchymal interactions play an important role in the development of many different organs and tissues. The secretory glands of the male reproductive system, including the prostate and seminal vesicles, are derived from epithelial precursors. Signals from the underlying mesenchyme are required for normal growth, branching, and differentiation of the seminal vesicle epithelium. Here, we show that a member of the BMP family, Gdf7, is required for normal seminal vesicle development. Expression and tissue recombination experiments suggest that Gdf7 is a mesenchymal signal that acts in a paracrine fashion to control the differentiation of the seminal vesicle epithelium.

    View details for DOI 10.1006/dbio.2001.0244

    View details for Web of Science ID 000169059300011

    View details for PubMedID 11356025

  • A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens DEVELOPMENTAL BIOLOGY Thut, C. J., Rountree, R. B., Hwa, M., KINGSLEY, D. M. 2001; 231 (1): 63-76


    The anterior segment of the vertebrate eye includes the cornea, iris, ciliary body, trabecular meshwork, and lens. Although malformations of these structures have been implicated in many human eye diseases, little is known about the molecular mechanisms that control their development. To identify genes involved in anterior segment formation, we developed a large-scale in situ hybridization screen and examined the spatial and temporal expression of over 1000 genes during eye development. This screen identified 62 genes with distinct expression patterns in specific eye structures, including several expressed in novel patterns in the anterior segment. Using these genes as developmental markers, we tested for the presence of inductive signals that control the differentiation of anterior segment tissues. Organ culture recombination experiments showed that a chick lens is capable of inducing the expression of markers of the presumptive iris and ciliary body in the developing mouse neural retina. The inducing activity from the lens acts only over short ranges and is present at multiple stages of eye development. These studies provide molecular evidence that an evolutionarily conserved signal from the lens controls tissue specification in the developing optic cup.

    View details for Web of Science ID 000167271000005

    View details for PubMedID 11180952

  • Sequence interpretation - Functional annotation of mouse genome sequences SCIENCE Nadeau, J. H., Balling, R., Barsh, G., Beier, D., Brown, S. D., Bucan, M., Camper, S., Carlson, G., Copeland, N., Eppig, J., Fletcher, C., Frankel, W. N., Ganten, D., Goldowitz, D., Goodnow, C., Guenet, J. L., Hicks, G., de Angelis, M. H., Jackson, I., Jacob, H. J., Jenkins, N., Johnson, D., Justice, M., Kay, S., Kingsley, D., Lehrach, H., Magnuson, T., Meisler, M., Poustka, A. M., Rinchik, E. M., Rossant, J., Russell, L. B., Schimenti, J., Shiroishi, T., Skarnes, W. C., Soriano, P., Stanford, W., Takahashi, J. S., Wurst, W., Zimmer, A. 2001; 291 (5507): 1251-?

    View details for Web of Science ID 000166993400028

    View details for PubMedID 11233449

  • Genetic control of bone and joint formation. Novartis Foundation symposium KINGSLEY, D. M. 2001; 232: 213-222


    The form and pattern of the vertebrate skeleton is thought to be strongly influenced by several fundamental morphogenetic behaviours of mesenchymal cells during embryonic development. Recent genetic and developmental studies have identified some of the genes that play an important role in controlling both the aggregation of mesenchymal cells into rough outlines of future skeletal elements (condensations), and in controlling where skeletal precursors cleave or segment to produce separate skeletal elements connected by joints. Members of the bone morphogenetic protein (BMP) family appear to play an important role in both processes. Mouse and human mutations in these genes lead to defects in formation of specific bones and joints, with striking specificity for particular anatomical locations. Results from a range of experiments suggest that these molecules may have multiple functions during normal skeletal development and patterning. A major challenge for the future is to identify genes and pathways that can maintain, repair, or stimulate the regeneration of bone and joint structures at later developmental stages.

    View details for PubMedID 11277082

  • Role of the mouse ank gene in control of tissue calcification and arthritis SCIENCE Ho, A. M., Johnson, M. D., Kingsley, D. M. 2000; 289 (5477): 265-270


    Mutation at the mouse progressive ankylosis (ank) locus causes a generalized, progressive form of arthritis accompanied by mineral deposition, formation of bony outgrowths, and joint destruction. Here, we show that the ank locus encodes a multipass transmembrane protein (ANK) that is expressed in joints and other tissues and controls pyrophosphate levels in cultured cells. A highly conserved gene is present in humans and other vertebrates. These results identify ANK-mediated control of pyrophosphate levels as a possible mechanism regulating tissue calcification and susceptibility to arthritis in higher animals.

    View details for Web of Science ID 000088169400033

    View details for PubMedID 10894769

  • A novel candidate gene for mouse and human preaxial polydactyly with altered expression in limbs of Hemimelic extra-toes mutant mice GENOMICS Clark, R. M., Marker, P. C., KINGSLEY, D. M. 2000; 67 (1): 19-27


    Polydactyly is a common malformation of vertebrate limbs. In humans a major locus for nonsyndromic pre-axial polydactyly (PPD) has been mapped previously to 7q36. The mouse Hemimelic extra-toes (Hx) mutation maps to a homologous chromosome segment and has been proposed to affect a homologous gene. To understand the molecular changes underlying PPD, we used a positional cloning approach to identify the gene or genes disrupted by the Hx mutation and a closely linked limb mutation, Hammertoe (Hm). High resolution genetic mapping identified a small candidate interval for the mouse mutations located 1.2 cM distal to the Shh locus. The nonrecombinant interval was completely cloned in bacterial artificial chromosomes and searched for genes using a combination of exon trapping, sample sequencing, and mapping of known genes. Two novel genes, Lmbr1 and Lmbr2, are entirely within the candidate interval we defined genetically. The open reading frame of both genes is intact in mutant mice, but the expression of the Lmbr1 gene is dramatically altered in developing limbs of Hx mutant mice. The correspondence between the spatial and temporal changes in Lmbr1 expression and the embryonic onset of the Hx mutant phenotype suggests that the mouse Hx mutation may be a regulatory allele of Lmbr1. The human ortholog of Lmbr1 maps within the recently described interval for human PPD, strengthening the possibility that both mouse and human limb abnormalities are due to defects in the same highly conserved gene.

    View details for Web of Science ID 000088195500003

    View details for PubMedID 10945466

  • Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA DiLeone, R. J., Marcus, G. A., Johnson, M. D., KINGSLEY, D. M. 2000; 97 (4): 1612-1617


    The regulatory regions surrounding many genes may be large and difficult to study using standard transgenic approaches. Here we describe the use of bacterial artificial chromosome clones to rapidly survey hundreds of kilobases of DNA for potential regulatory sequences surrounding the mouse bone morphogenetic protein-5 (Bmp5) gene. Simple coinjection of large insert clones with lacZ reporter constructs recapitulates all of the sites of expression observed previously with numerous small constructs covering a large, complex regulatory region. The coinjection approach has made it possible to rapidly survey other regions of the Bmp5 gene for potential control elements, to confirm the location of several elements predicted from previous expression studies using regulatory mutations at the Bmp5 locus, to test whether Bmp5 control regions act similarly on endogenous and foreign promoters, and to show that Bmp5 control elements are capable of rescuing phenotypic effects of a Bmp5 deficiency. This rapid approach has identified new Bmp5 control regions responsible for controlling the development of specific anatomical structures in the vertebrate skeleton. A similar approach may be useful for studying complex control regions surrounding many other genes important in embryonic development and human disease.

    View details for Web of Science ID 000085409600060

    View details for PubMedID 10677507

    View details for PubMedCentralID PMC26483

  • GDF5 coordinates bone and joint formation during digit development DEVELOPMENTAL BIOLOGY Storm, E. E., KINGSLEY, D. M. 1999; 209 (1): 11-27


    A functional skeletal system requires the coordinated development of many different tissue types, including cartilage, bones, joints, and tendons. Members of the Bone morphogenetic protein (BMP) family of secreted signaling molecules have been implicated as endogenous regulators of skeletal development. This is based on their expression during bone and joint formation, their ability to induce ectopic bone and cartilage, and the skeletal abnormalities present in animals with mutations in BMP family members. One member of this family, Growth/differentiation factor 5 (GDF5), is encoded by the mouse brachypodism locus. Mice with mutations in this gene show reductions in the length of bones in the limbs, altered formation of bones and joints in the sternum, and a reduction in the number of bones in the digits. The expression pattern of Gdf5 during normal development and the phenotypes seen in mice with single or double mutations in Gdf5 and Bmp5 suggested that Gdf5 has multiple functions in skeletogenesis, including roles in joint and cartilage development. To further understand the function of GDF5 in skeletal development, we assayed the response of developing chick and mouse limbs to recombinant GDF5 protein. The results from these assays, coupled with an analysis of the development of brachypodism digits, indicate that GDF5 is necessary and sufficient for both cartilage development and the restriction of joint formation to the appropriate location. Thus, GDF5 function in the digits demonstrates a link between cartilage development and joint development and is an important determinant of the pattern of bones and articulations in the digits.

    View details for Web of Science ID 000079924400002

    View details for PubMedID 10208739

  • An extensive 3 ' regulatory region controls expression of Bmp5 in specific anatomical structures of the mouse embryo GENETICS DiLeone, R. J., Russell, L. B., Kingsley, D. M. 1998; 148 (1): 401-408


    Bone morphogenetic proteins (BMPs) are secreted signaling molecules that control important developmental events in many different organisms. Previous studies have shown that BMPs are expressed at the earliest stages of skeletal development, and are required for formation of specific skeletal features, strongly suggesting that they are endogenous signals used to control formation of skeletal tissue. Despite the importance of BMP signaling in normal development, very little is known about the mechanisms that control the synthesis and distribution of BMP signals in vertebrates. Here, we identify a large array of cis-acting control sequences that lay out expression of the mouse Bmp5 gene in specific skeletal structures and soft tissues. Some of these elements show striking specificity for particular anatomical features within the skeleton, rather than for cartilage and bone in general. These data suggest that the vertebrate skeleton is built from the sum of many independent domains of BMP expression, each of which may be controlled by separate regulatory elements driving expression at specific anatomical locations. Surprisingly, some of the regulatory sequences in the Bmp5 gene map over 270 kb from the Bmp5 promoter, making them among the most distant elements yet identified in studies of eukaryotic gene expression.

    View details for Web of Science ID 000071494000037

    View details for PubMedID 9475750

    View details for PubMedCentralID PMC1459806

  • Bone morphogenetic proteins in the formation and repair of cartilage, bone, and joints Workshop on Skeletal Growth and Development - Clinical Issues and Basic Science Advances KINGSLEY, D. M. AMER ACAD ORTHOPAEDIC SURGEONS. 1998: 87–98
  • The Bmp8 gene is expressed in developing skeletal tissue and maps near the Achondroplasia locus on mouse chromosome 4 GENOMICS DiLeone, R. J., King, J. A., Storm, E. E., Copeland, N. G., Jenkins, N. A., KINGSLEY, D. M. 1997; 40 (1): 196-198

    View details for Web of Science ID A1997WJ33600032

    View details for PubMedID 9070944

  • Spectrum of Bmp5 mutations from germline mutagenesis experiments in mice GENETICS Marker, P. C., Seung, K. J., Bland, A. E., Russell, L. B., KINGSLEY, D. M. 1997; 145 (2): 435-443


    Over 40 years of mutagenesis experiments using the mouse specific-locus test have produced a large number of induced germline mutations at seven loci, among them the short ear locus. We have previously shown that the short ear locus encodes bone morphogenetic protein 5 (BMP5), a member of a large family of secreted signaling molecules that play key roles in axis formation, tissue differentiation, mesenchymalepithelial interactions, and skeletal development. Here we examine 24 chemical- and radiation-induced mutations at the short ear locus. Sequence changes in the Bmp5 open reading frame confirm the importance of cysteine residues in the function of TGF beta superfamily members. The spectrum of N-ethyl-N-nitrosourea-induced mutations also provides new information about the basepair, sequence context, and strand specificity of germline mutations in mammals.

    View details for Web of Science ID A1997WM59900019

    View details for PubMedID 9071596

    View details for PubMedCentralID PMC1207807

  • Joint patterning defects caused by single and double mutations in members of the bone morphogenetic protein (BMP) family DEVELOPMENT Storm, E. E., KINGSLEY, D. M. 1996; 122 (12): 3969-3979


    The mouse brachypodism locus encodes a bone morphogenetic protein (BMP)-like molecule called growth/differentiation factor 5 (GDF5). Here we show that Gdf5 transcripts are expressed in a striking pattern of transverse stripes within many skeletal precursors in the developing limb. The number, location and time of appearance of these stripes corresponds to the sites where joints will later form between skeletal elements. Null mutations in Gdf5 disrupt the formation of more than 30% of the synovial joints in the limb, leading to complete or partial fusions between particular skeletal elements, and changes in the patterns of repeating structures in the digits, wrists and ankles. Mice carrying null mutations in both Gdf5 and another BMP family member, Bmp5, show additional abnormalities not observed in either of the single mutants. These defects include disruption of the sternebrae within the sternum and abnormal formation of the fibrocartilaginous joints between the sternebrae and ribs. Previous studies have shown that members of the BMP family are required for normal development of cartilage and bone. The current studies suggest that particular BMP family members may also play an essential role in the segmentation process that cleaves skeletal precursors into separate elements. This process helps determine the number of elements in repeating series in both limbs and sternum, and is required for normal generation of the functional articulations between many adjacent structures in the vertebrate skeleton.

    View details for Web of Science ID A1996WC55400028

    View details for PubMedID 9012517

  • Mechanical and geometric changes in the growing femora of BMP-5 deficient mice BONE Mikic, B., VANDERMEULEN, M. C., KINGSLEY, D. M., Carter, D. R. 1996; 18 (6): 601-607


    We examined the growth-related changes in femoral geometry and torsional strength in BMP-5 deficient short-ear mice over a 22-week time interval ("long-term" changes). Four groups of female mice (n = 6 per group) were examined: short-ear animals and their heterozygous control littermates at 4 and 26 weeks of age. In agreement with findings previously observed in a mixed-gender group of adult mice (26 weeks), the femora of short-ear animals were significantly smaller in length and cross section at both ages. The magnitudes of the differences between genotypes were comparable at each age, indicating that the overall rates of appositional and endochondral growth were similar for both genotypes over the 22-week period. In the adult animals, short-ear femora were 27 +/- 7% weaker in torsional strength due to their smaller cross-sectional geometry. However, bone strength in adult short-ear mice appeared to be adequate for animal size: No significant difference was detected in maximum femoral torque when normalized by body mass. In 4-week old animals, BMP-5 deficiency was associated with a 27 +/- 6% lower body mass, but the torsional strength of the femur was not significantly different from that of controls. Cross-sectional geometry was smaller in 4-week old short-ear mice, but the apparent bone material ultimate shear stress was elevated by 33 +/- 10%, thereby resulting in a whole bone torsional strength equivalent to that of the larger control mice. While the data suggest a higher material strength in the 4-week-old short-ear animals, no significant difference in the level of bone mineralization was detectable between genotypes at either age.

    View details for Web of Science ID A1996UT99700017

    View details for PubMedID 8806002

  • The role of BMPs and GDFs in development of region-specific skeletal structures Conference on Molecular and Developmental Biology of Cartilage King, J. A., Storm, E. E., Marker, P. C., DiLeone, R. J., KINGSLEY, D. M. NEW YORK ACAD SCIENCES. 1996: 70–79

    View details for Web of Science ID A1996BF92H00009

    View details for PubMedID 8702185



    The mouse represents an excellent model system for the study of genetic deafness in humans. Many mouse deafness mutants have been identified and the anatomy of the mouse and human ear is similar. Here we report the use of a positional cloning approach to identify the gene encoded by the mouse recessive deafness mutation, Snell's waltzer (sv). We show that sv encodes an unconventional myosin heavy chain, myosin VI, which is expressed within the sensory hair cells of the inner ear, and appears to be required for maintaining their structural integrity. The requirement for myosin VI in hearing makes this gene an excellent candidate for a human deafness disorder.

    View details for Web of Science ID A1995TH62900012

    View details for PubMedID 7493015



    Murine Bmp7 has been assigned to distal Chromosome 2 by interspecific backcross mapping. The map location suggests close linkage to classical mouse mutations and places Bmp7 within a chromosome region thought to contain one or more unidentified imprinted genes. A direct test suggests that Bmp7 is not imprinted. An examination of embryonic RNA expression patterns shows that Bmp7 is expressed in a variety of skeletal and nonskeletal tissues. Both embryonic expression patterns and the human chromosomal sublocalization inferred from its mouse location make Bmp7 a candidate for the gene affected in some patients with Holt-Oram syndrome.

    View details for Web of Science ID A1995RQ98900030

    View details for PubMedID 7490098



    Bone morphogenetic proteins (BMPs) play a critical role in early skeletal development. BMPs are also potential mediators of bone response to mechanical loading, but their role in later stages of bone growth and adaptation has yet to be studied. We characterized the postcranial skeletal defects in mature mice with BMP deficiency by measuring hind-limb muscle mass and long bone geometric, material, and torsional mechanical properties. The animals studied were 26-week-old short ear mice (n = 10) with a homozygous deletion of the BMP-5 gene and their heterozygous control litter mates (n = 15). Gender-related effects, which were found to be independent of genotype, were also examined. The femora of short ear mice were 3% shorter than in controls and had significantly lower values of many cross-sectional geometric and structural strength parameters (p < 0.05). No significant differences in ash content or material properties were detected. Lower femoral whole bone torsional strength was due to the smaller cross-sectional geometry (16% smaller section modulus) in the short ear mice. The diminished cross-sectional geometry may be commensurate with lower levels of in vivo loading, as reflected by body mass (-8%) and quadriceps mass (-11%). While no significant gender differences were found in whole bone strength or cross-sectional geometry, males had significantly greater body mass (+18%) and quadriceps mass (+15%) and lower tibio-fibular ash content (-3%). The data suggest that adult female mice have a more robust skeleton than males, relative to in vivo mechanical demands. Furthermore, although the bones of short ear mice are smaller and weaker than in control animals, they appear to be biomechanically appropriate for the in vivo mechanical loads that they experience.

    View details for Web of Science ID A1995RB63900005

    View details for PubMedID 7605705



    Mutations at the mouse short ear (se) locus alter the formation and repair of skeletal structures and the development of several soft tissues. Most of the developmental effects of the gene have been studied using a spontaneous mutation reported over 70 years ago. Here we show that this mutation consists of a nonsense mutation in a secreted signaling molecule called bone morphogenetic protein 5 (BMP5). This small sequence alteration, in combination with previously reported translocation and deletion mutations, provides strong genetic evidence that BMP5 is the normal product of the se locus. Transcripts from the Bmp5 gene are expressed at the earliest stages of normal skeletal development in patterns that closely resemble the shapes of forming skeletal elements. The gene is also expressed at several sites of soft tissue abnormalities previously reported in se animals, including lungs, liver, ureter, bladder, and intestines. The combined genetic, biochemical, and expression data suggest that BMP5 is a key signal used to initiate formation of particular skeletal elements and is required for normal development of several soft tissues as well.

    View details for Web of Science ID A1994PT49200009

    View details for PubMedID 7958439



    The mutation brachypodism (bp) alters the length and number of bones in the limbs of mice but spares the axial skeleton. It illustrates the importance of specific genes in controlling the morphogenesis of individual skeletal elements in the tetrapod limb. We now report the isolation of three new members of the transforming growth factor-beta (TGF-beta) superfamily (growth/differentiation factors (GDF) 5,6 and 7) and show by mapping, expression patterns and sequencing that mutations in Gdf5 are responsible for skeletal alterations in bp mice. GDF5 and the closely related GDF6 and GDF7 define a new subgroup of factors related to known bone- and cartilage-inducing molecules, the bone morphogenetic proteins (BMPs). Studies of Bmp5 mutations in short ear mice have shown that at least one other BMP gene is also required for normal skeletal development. The highly specific skeletal alterations in bp and short ear mice suggest that different members of the BMP family control the formation of different morphological features in the mammalian skeleton.

    View details for PubMedID 8145850


    View details for Web of Science ID A1994MU12700001

    View details for PubMedID 8299934


    View details for Web of Science ID A1994QD08500009

    View details for PubMedID 7719002



    Bone morphogenetic proteins (BMPs) are a family of secreted signaling molecules that were originally isolated on the basis of their remarkable ability to induce the formation of ectopic bones when implanted into adult animals. The first mutations identified in a mammalian BMP gene suggest that members of this family induce the formation, patterning and repair of particular morphological features in higher animals.

    View details for Web of Science ID A1994MR68900007

    View details for PubMedID 8146910

  • Encyclopedia of the mouse genome III. October 1993. Mouse chromosome 9. Mammalian genome KINGSLEY, D. M. 1993; 4: S136-53

    View details for PubMedID 8268669



    The mouse short ear gene is required for normal growth and patterning of skeletal structures, and for repair of bone fractures in adults. We have carried out an extensive chromosome walk in the chromosome region that surrounds this locus. Here we show that the short ear region contains the gene for a TGF beta-related protein called bone morphogenetic protein 5 (Bmp-5). This gene is deleted or rearranged in several independent mutations at the short ear locus. Mice homozygous for large deletions of the Bmp-5 coding region are viable and fertile. Mutations at the short ear locus provide an important new tool for defining the normal functions of BMPs in mammals. The specific skeletal defects seen in short-eared animals, which occur against a background of otherwise normal skeletal structures, suggest that particular aspects of skeletal morphology may be determined by individual members of a family of signaling factors that can induce the formation of cartilage and bone in vivo.

    View details for Web of Science ID A1992JW43500007

    View details for PubMedID 1339316


    View details for Web of Science ID A1992JT43900009

    View details for PubMedID 1498428

  • Mouse chromosome 9. Mammalian genome KINGSLEY, D. M. 1991; 1: S127-45

    View details for PubMedID 1799796

  • CHROMOSOMAL LOCATION OF MURINE AND HUMAN IL-1 RECEPTOR GENES GENOMICS Copeland, N. G., SILAN, C. M., KINGSLEY, D. M., Jenkins, N. A., Cannizzaro, L. A., Croce, C. M., Huebner, K., Sims, J. E. 1991; 9 (1): 44-50


    The gene for the type I interleukin-1 (IL-1) receptor has been mapped in both mouse and human. In the human genome, a combination of segregation analysis of rodent-human hybrid cells and chromosomal in situ hybridization has placed the gene on the long arm of chromosome 2, at band 2q12. This is near the reported map position of the loci for IL-1 alpha and IL-1 beta (2q13----2q21). The murine gene has been mapped by analysis of restriction fragment length polymorphisms in interspecific backcrosses to the centromeric end of chromosome 1, in a region that is syntenic to a portion of human chromosome 2. The murine Il-1r1 gene has thus been separated from the IL-1 genes, which lie on murine chromosome 2.

    View details for Web of Science ID A1991EP97200006

    View details for PubMedID 1672292



    Scavenger receptors have been implicated in the development of atherosclerosis and other macrophage-associated functions. The bovine type I and type II scavenger receptors are multidomain transmembrane proteins that differ only by the presence in the type I receptor of an additional, extracellular cysteine-rich C-terminal domain. The isolation of type I and type II receptor cDNAs from a murine macrophage cell line, P388D1, establishes the presence of mRNAs encoding both receptor types in a single cell. Their sequences are highly similar to the bovine cDNAs. Receptor type-specific cDNA probes map to a common locus on murine chromosomes 8, suggesting that a single gene encodes both mRNAs. The type I-specific scavenger receptor cysteine-rich (SRCR) domain helps define a previously unrecognized family of remarkably well-conserved domains. Highly homologous SRCR domains (one, three, or four per polypeptide chain) are found in diverse secreted and cell-surface proteins from humans (e.g., CD5, complement factor I), mice (Ly-1), and sea urchins (speract receptor).

    View details for Web of Science ID A1990EJ60700026

    View details for PubMedID 1978939



    We have generated a 30-cM molecular genetic linkage map of the proximal half of mouse chromosome 14 by interspecific backcross analysis. Loci that were mapped in this study include Bmp-1, Ctla-1, Hap, hr, Plau, Psp-2, Rib-1, and Tcra. A region of homology between mouse chromosome 14 and human chromosome 10 was identified by the localization of Plau to chromosome 14. This interspecific backcross map will be valuable for establishing linkage relationships of additional loci to mouse chromosome 14.

    View details for Web of Science ID A1990CW56300012

    View details for PubMedID 1971251

  • Chromosomal localization of seven members of the murine TGF-beta superfamily suggests close linkage to several morphogenetic mutant loci. Genomics Dickinson, M. E., KOBRIN, M. S., SILAN, C. M., KINGSLEY, D. M., JUSTICE, M. J., MILLER, D. A., CECI, J. D., LOCK, L. F., Lee, A., BUCHBERG, A. M. 1990; 6 (3): 505-520


    Chromosomal locations have been assigned to seven members of the TGF-beta superfamily using an interspecific mouse backcross. Probes for the Tgfb-1, -2, and -3, Bmp-2a and -3, and Vgr-1 genes recognized only single loci, whereas the Bmp-2b probe recognized two independently segregating loci (designated Bmp-2b1 and Bmp-2b2). The results show that the seven members of the TGF-beta superfamily map to eight different chromosomes, indicating that the TGF-beta family has become widely dispersed during evolution. Five of the eight loci (Tgfb-1, Bmp-2a, Bmp-2b1, Bmp-2b2, Vgr-1) mapped near mutant loci associated with connective tissue and skeletal disorders, raising the possibility that at least some of these mutations result from defects in TGF-beta-related genes.

    View details for PubMedID 1970330

  • GENETIC ABLATION OF A MOUSE GENE EXPRESSED SPECIFICALLY IN BRAIN EMBO JOURNAL KINGSLEY, D. M., Rinchik, E. M., Russell, L. B., Ottiger, H. P., Sutcliffe, J. G., Copeland, N. G., Jenkins, N. A. 1990; 9 (2): 395-399


    The 1B1075 gene was initially identified from a cDNA clone of a rat brain messenger RNA expressed in particular subsets of CNS neurons and pituitary cells. Although the protein encoded by this gene is of unknown function, its sequence suggests that it may be related to secretogranin proteins, which are found in association with secretory granules in a variety of peptidergic endocrine and neuronal cells. Here we show that the mouse 1B1075 gene is located between the dilute (d) and short ear (se) genes on chromosome 9. Many different deletion mutations have previously been isolated in the genetic region that includes these genes. By producing mice carrying two deletions that overlap at the 1B1075 locus, the gene for this brain-specific message can be completely eliminated from otherwise viable animals. The animals missing the 1B1075 gene provide an important new tool for determining the function of this gene in the brain. In addition, these results provide a new molecular entry point for detailed characterization of other genes in the d-se region.

    View details for Web of Science ID A1990CN55700012

    View details for PubMedID 2303033



    A 64-centiMorgan linkage map of mouse chromosome 9 was developed using cloned DNA markers and an interspecific backcross between Mus spretus and the C57BL/6J inbred strain. This map was compared to conventional genetic maps using six markers previously localized in laboratory mouse strains. These markers included thymus cell antigen-1, cytochrome P450-3, dilute, transferrin, cholecystokinin, and the G-protein alpha inhibitory subunit. No evidence was seen for segregation distortion, chromosome rearrangements, or altered genetic distances in the results from interspecific backcross mapping. Regional map locations were determined for four genes that were previously assigned to chromosome 9 using somatic cell hybrids. These genes were glutathione S-transferase Ya subunit (Gsta), the T3 gamma subunit, the low density lipoprotein receptor, and the Ets-1 oncogene. The map locations for these genes establish new regions of synteny between mouse chromosome 9 and human chromosomes 6, 11, and 19. In addition, the close linkage detected between the dilute and Gsta loci suggests that the Gsta locus may be part of the dilute/short ear complex, one of the most extensively studied genetic regions of the mouse.

    View details for Web of Science ID A1989AN07000015

    View details for PubMedID 2572508

  • IDENTIFICATION OF 2 MURINE LOCI HOMOLOGOUS TO THE V-CBL ONCOGENE JOURNAL OF VIROLOGY REGNIER, D. C., Kozak, C. A., KINGSLEY, D. M., Jenkins, N. A., Copeland, N. G., Langdon, W. Y., Morse, H. C. 1989; 63 (9): 3678-3682


    The virally transduced oncogene v-cbl transforms fibroblasts in vitro and induces early B-cell-lineage lymphomas in vivo. A series of probes derived from a molecular clone of v-cbl were used to map related sequences in the mouse genome. Analyses of Chinese hamster x mouse somatic-cell hybrids showed that two related genes, cbl-1 and cbl-2, were located on chromosomes 6 and 9, respectively. Restriction enzyme studies of DNA from hybrid cells containing either chromosome 6 or 9 suggested that cbl-1 resembles v-cbl and may be a processed gene, whereas cbl-2 has a complex genomic structure. Analyses of Mus domesticus/M. spretus interspecific backcross mice showed that Cbl-1 maps between the immunoglobulin kappa light chain and T-cell receptor beta chain loci and that Cbl-2 is tightly linked to Thy-1.

    View details for Web of Science ID A1989AK28400014

    View details for PubMedID 2760978


    View details for Web of Science ID A1989AM04200016

    View details for PubMedID 2544008


    View details for Web of Science ID A1989AV40700003

    View details for PubMedID 2691861



    A rapidly reversible defect in protein O-glycosylation exhibited by a line of mutant Chinese hamster ovary (CHO) cells was used to study the kinetics and function of O-glycosylation of the low density lipoprotein (LDL) receptor. The mutant line, genotype LDLD, cannot synthesize UDP-N-acetylgalactosamine under normal culture conditions and, therefore, cannot add mucin-type O-linked oligosaccharides to proteins. The UDP-N-acetylgalactosamine pools in LDLD cells can be filled rapidly when N-acetylgalactosamine is added to the culture medium, thus restoring normal synthesis of O-linked carbohydrates. Pulse-chase metabolic labeling experiments were used to show that (i) the first step in the O-glycosylation of LDL receptors can occur posttranslationally; (ii) after O-linked sugar-deficient LDL receptors reach the cell surface, they are not subject to subsequent O-linked sugar addition, suggesting that they do not return to compartments in which O-glycosylation takes place; (iii) O-linked carbohydrate chains on the LDL receptor itself are required for normal stability and function; and (iv) the instability of the O-linked sugar-deficient LDL receptor is due to proteolytic cleavage and the release into the medium of the bulk of the NH2-terminal extracellular domain of the receptor. It appears that O-glycosylation of the LDL receptor and several other cell surface glycoproteins permits stable cell-surface expression by preventing proteolytic cleavage of the extracellular domains of these proteins.

    View details for Web of Science ID A1988N986900048

    View details for PubMedID 3380796



    Exchange of small molecules between cells through intercellular junctions is a widespread phenomenon implicated in many physiological and developmental processes. This type of intercellular communication can restore the activity of low-density lipoprotein (LDL) receptors in mammalian cells that are deficient in the enzyme UDP-Gal/UDP-GalNAc 4-epimerase. Pure cultures of the 4-epimerase mutant are unable to synthesize normal carbohydrate chains on LDL receptors and many other glycoproteins and therefore do not express LDL receptor activity. When these cells are cocultivated with cells expressing normal 4-epimerase activity, the structure and function of LDL receptors are restored to normal by the transfer of this enzyme's products through intercellular junctions. The formation of functional junctions does not require normal glycosylation of membrane proteins. Because many convenient assays and selections for LDL receptor activity are available, this mutant can provide a powerful new tool for biochemical and genetic studies of intercellular junctional communication.

    View details for Web of Science ID A1987F457300038

    View details for PubMedID 3798096



    Biochemical, immunological, and genetic techniques were used to investigate the genetic defects in three types of low density lipoprotein (LDL) receptor-deficient hamster cells. The previously isolated ldlB, ldlC, and ldlD mutants all synthesized essentially normal amounts of a 125,000-D precursor form of the LDL receptor, but were unable to process this receptor to the mature form of 155,000 D. Instead, these mutants produced abnormally small, heterogeneous receptors that reached the cell surface but were rapidly degraded thereafter. The abnormal sizes of the LDL receptors in these cells were due to defective processing of the LDL receptor's N- and O-linked carbohydrate chains. Processing defects in these cells appeared to be general since the ldlB, ldlC, and ldlD mutants also showed defective glycosylation of a viral glycoprotein, alterations in glycolipid synthesis, and changes in resistance to several toxic lectins. Preliminary structural studies suggested that these cells had defects in multiple stages of the Golgi-associated processing reactions responsible for synthesis of glycolipids and in the N-linked and O-linked carbohydrate chains of glycoproteins. Comparisons between the ldl mutants and a large number of previously isolated CHO glycosylation defective mutants showed that the genetic defects in ldlB, ldlC, and ldlD cells were unique and that only very specific types of carbohydrate alteration could dramatically affect LDL receptor function.

    View details for Web of Science ID A1986C223500005

    View details for PubMedID 3700466



    We previously isolated an unusual hamster cell mutant (ldlD) that does not express LDL receptor activity unless it is cocultivated with other cells or grown in high concentrations of serum. We now show that ldlD cells are deficient in the enzyme UDP-galactose and UDP-N-acetylgalactosamine (GalNAc) 4-epimerase. When ldlD cells are grown in glucose-based media, they cannot synthesize enough UDP-galactose and UDP-GalNAc to allow normal synthesis of glycolipids and glycoproteins. The 4-epimerase deficiency accounts for all glycosylation defects previously observed in ldlD cells, including production of abnormal LDL receptors. All abnormal phenotypes of ldlD cells can be fully corrected by exogenous galactose and GalNAc. The separate effects of these sugars on LDL receptor activity suggest that O-linked carbohydrate chains are crucial for receptor stability. ldlD cells may be useful for structural and functional studies of many proteins, proteoglycans, and glycolipids containing galactose or GalNAc.

    View details for Web of Science ID A1986A542800010

    View details for PubMedID 3948246

  • GENETIC-ANALYSIS OF RECEPTOR-MEDIATED ENDOCYTOSIS TRENDS IN BIOCHEMICAL SCIENCES Krieger, M., Kingsley, D., Sege, R., Hobbie, L., Kozarsky, K. 1985; 10 (11): 447-452


    We have used cell fusion and mutant reversion analysis to study a collection of Chinese hamster ovary (CHO) cell mutants that are unable to bind and internalize low density lipoprotein (LDL). Pairwise cell fusions show that these LDL receptor-deficient mutants fall into three recessive complementation groups, ldlA, ldlB, and ldlC. Complementation was detected by observing the uptake of fluorescent LDL and was quantitated by measuring the degradation of 125I-labeled LDL by isolated hybrid cells. Previous studies had defined a fourth recessive complementation group, ldlD. Complementation tests between CHO cells and human fibroblasts suggested that the defects in mutants of the ldlA complementation group are analogous to those in a patient with homozygous familial hypercholesterolemia. A revertant of an ldlA mutant was isolated and appeared to be heterozygous at the ldlA locus. The phenotype of this revertant was similar to that of cells from patients with the heterozygous form of familial hypercholesterolemia. Together with recent DNA transfection studies, these results suggest that the ldlA locus is the structural gene for the LDL receptor in CHO cells. Mutants in the ldlB, ldlC, and ldlD complementation groups must have defects in genes that are required for either the regulation, synthesis, transport, recycling, or turnover of LDL receptors.

    View details for Web of Science ID A1984TK56500037

    View details for PubMedID 6089204



    This paper describes a rapid and efficient two-step procedure for the isolation of mutant cells with defects in receptor-mediated endocytosis. The procedure takes advantage of two fungal metabolites, compactin (ML236B), a potent inhibitor of cholesterol biosynthesis, and amphotericin B, a polyene antibiotic that forms toxic complexes with sterols in membranes. Mutagen-treated Chinese hamster ovary cells were preincubated overnight in a medium containing mevalonate, low density lipoprotein (LDL), and compactin (Mev/LDL/Com). At the end of the preincubation period, wild-type cells were cholesterol replete while mutant cells that could not utilize the cholesterol in LDL were cholesterol deficient. Subsequent incubation with amphotericin B for 6 hr killed most of the wild-type cells. After a second round of Mev/LDL/Com-amphotericin B selection, endocytosis-defective clones appeared at a frequency of approximately equal to 2.6 X 10(-5). Some of these clones expressed LDL receptor-defective phenotypes and fell into one of two previously defined classes of mutation. Sensitivity of the mutants to infection by vesicular stomatitis virus suggested that the mutations do not disrupt the coated pit-coated vesicle pathway of endocytosis. Minor modifications in the Mev/LDL/Com-amphotericin B selection permit the isolation of cholesterol auxotrophs and might allow the isolation of conditional-lethal mutations. Because LDL can be coupled to ligands that bind to receptors other than the LDL receptor, Mev/LDL/Com-amphotericin B selection may permit the isolation of mutant cells with defects that specifically disrupt other endocytic pathways.

    View details for Web of Science ID A1983RH33500032

    View details for PubMedID 6310583