Stanford Advisors


All Publications


  • The impact of identity by descent on fitness and disease in dogs. Proceedings of the National Academy of Sciences of the United States of America Mooney, J. A., Yohannes, A., Lohmueller, K. E. 2021; 118 (16)

    Abstract

    Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.

    View details for DOI 10.1073/pnas.2019116118

    View details for PubMedID 33853941

  • Understanding the Hidden Complexity of Latin American Population Isolates. American journal of human genetics Mooney, J. A., Huber, C. D., Service, S., Sul, J. H., Marsden, C. D., Zhang, Z., Sabatti, C., Ruiz-Linares, A., Bedoya, G., Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer, N., Lohmueller, K. E., Fears, S. C., Service, S. K., Kremeyer, B., Lic, C. A., Lic, X. A., Bejarano, J., Lic, M. R., Castrillon, G., Lopez, M. C., Montoya, G., Montoya, P., Teshiba, T. M., Altshuler, L., Bartzokis, G., Escobar, J., Ospina-Duque, J., Risch, N., Ruiz-Linares, A., Cantor, R. M., Lopez-Jaramillo, C., Macaya, G., Molina, J., Reus, V. I., Sabatti, C., Freimer, N. B., Bearden, C. E., Sul, J. H., Huang, A. Y., Ramensky, V., Hwang, S., Park, Y., Zhang, Z., Olde Loohuis, L. M., Spesny, M., Gomez-Makhinson, J., Bedoya, G., Coppola, G. 2018; 103 (5): 707–26

    Abstract

    Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36*. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.

    View details for PubMedID 30401458

  • Understanding the Hidden Complexity of Latin American Population Isolates AMERICAN JOURNAL OF HUMAN GENETICS Mooney, J. A., Huber, C. D., Service, S., Sul, J., Marsden, C. D., Zhang, Z., Sabatti, C., Ruiz-Linares, A., Bedoya, G., Freimer, N., Lohmueller, K. E., Costa Rica Colombia Consortium 2018; 103 (5): 707–26