Contact

  • Academic
    jahemker@stanford.edu
    University - Student Department: Department of Developmental Biology Position: Graduate

All Publications

  • Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming. Proceedings of the National Academy of Sciences of the United States of America Couper, L. I., Dodge, T. O., Hemker, J. A., Kim, B. Y., Exposito-Alonso, M., Brem, R. B., Mordecai, E. A., Bitter, M. C. 2025; 122 (2): e2418199122

    Abstract

    Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, promoting expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in mosquito heat tolerance, and phenotypic trade-offs in tolerance to prolonged versus acute heat exposure. Further, we found genomic variation associated with prolonged heat tolerance was clustered in several regions of the genome, suggesting the presence of larger structural variants such as chromosomal inversions. A simple evolutionary model based on our data estimates that the maximum rate of evolutionary adaptation in mosquito heat tolerance will exceed the projected rate of climate warming, implying the potential for mosquitoes to track warming via genetic adaptation.

    View details for DOI 10.1073/pnas.2418199122

    View details for PubMedID 39772738

  • Evolutionary adaptation under climate change:Aedessp. demonstrates potential to adapt to warming. bioRxiv : the preprint server for biology Couper, L. I., Dodge, T. O., Hemker, J. A., Kim, B. Y., Exposito-Alonso, M., Brem, R. B., Mordecai, E. A., Bitter, M. C. 2024

    Abstract

    Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm edges. However, whether mosquito populations could maintain their warm range edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis , a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and their genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in acute heat tolerance, which phenotypically trades off with tolerance to prolonged heat exposure. A simple evolutionary model based on our data shows that, under most scenarios, the estimated maximum rate of evolutionary adaptation in mosquito heat tolerance exceeds that of projected climate warming. Our findings indicate that natural mosquito populations likely have the potential to track projected warming via genetic adaptation. Prior climate-based projections may thus underestimate the range of mosquito and mosquito-borne disease distributions under future climate conditions.Significance Statement: Global change may have profound impacts on the distribution of mosquito-borne diseases, which collectively cause nearly one million deaths each year. Accurately predicting these impacts is critical for disease control preparedness, and will depend, in part, on whether mosquitoes can adapt to warming-a key open question. Using experimental and genomic data from a relative of major vector species that already experiences a wide thermal gradient, we find that natural mosquito populations have high levels of genetically-based variation in heat tolerance that could enable adaptation on pace with warming. Incorporating the potential for adaptive responses may therefore be necessary for accurate predictions of mosquito-borne disease distributions under warming, which is critical for preparing mosquito control interventions.

    View details for DOI 10.1101/2024.08.23.609454

    View details for PubMedID 39229052

  • Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS biology Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., Dorus, S., Fujichika, T., Hemker, J. A., Hrcek, J., Kankare, M., Katoh, T., Magnacca, K. N., Martin, R. A., Matsunaga, T., Medeiros, M. J., Miller, D. E., Pitnick, S., Schiffer, M., Simoni, S., Steenwinkel, T. E., Syed, Z. A., Takahashi, A., Wei, K. H., Yokoyama, T., Eisen, M. B., Kopp, A., Matute, D., Obbard, D. J., O'Grady, P. M., Price, D. K., Toda, M. J., Werner, T., Petrov, D. A. 2024; 22 (7): e3002697

    Abstract

    Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

    View details for DOI 10.1371/journal.pbio.3002697

    View details for PubMedID 39024225

  • Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. bioRxiv : the preprint server for biology Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., Dorus, S., Fujichika, T., Hemker, J. A., Hrcek, J., Kankare, M., Katoh, T., Magnacca, K. N., Martin, R. A., Matsunaga, T., Medeiros, M. J., Miller, D. E., Pitnick, S., Simoni, S., Steenwinkel, T. E., Schiffer, M., Syed, Z. A., Takahashi, A., Wei, K. H., Yokoyama, T., Eisen, M. B., Kopp, A., Matute, D., Obbard, D. J., O'Grady, P. M., Price, D. K., Toda, M. J., Werner, T., Petrov, D. A. 2023

    Abstract

    Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

    View details for DOI 10.1101/2023.10.02.560517

    View details for PubMedID 37873137

    View details for PubMedCentralID PMC10592941

  • Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference. Genome biology and evolution Schull, J. K., Turakhia, Y., Hemker, J. A., Dally, W. J., Bejerano, G. 2022

    Abstract

    We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared to morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.

    View details for DOI 10.1093/gbe/evac013

    View details for PubMedID 35171243