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  • Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii) PLOS ONE Ma, X., Kelley, J. L., Eilertson, K., Musharoff, S., Degenhardt, J. D., Martins, A. L., Vinar, T., Kosiol, C., Siepel, A., Gutenkunst, R. N., Bustamante, C. D. 2013; 8 (10)

    Abstract

    To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.

    View details for DOI 10.1371/journal.pone.0077175

    View details for Web of Science ID 000326037000047

    View details for PubMedID 24194868

    View details for PubMedCentralID PMC3806739

  • Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PloS one Ma, X., Kelley, J. L., Eilertson, K., Musharoff, S., Degenhardt, J. D., Martins, A. L., Vinar, T., Kosiol, C., Siepel, A., Gutenkunst, R. N., Bustamante, C. D. 2013; 8 (10)

    Abstract

    To gain insights into evolutionary forces that have shaped the history of Bornean and Sumatran populations of orang-utans, we compare patterns of variation across more than 11 million single nucleotide polymorphisms found by previous mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our analysis of the mitochondrial data yields a far more ancient split time between the two populations (~3.4 million years ago) than estimates based on autosomal data (0.4 million years ago), suggesting a complex speciation process with moderate levels of primarily male migration. We find that the distribution of selection coefficients consistent with the observed frequency spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to the distribution in humans. Our analysis indicates that 35% of genes have evolved under detectable negative selection. Overall, our findings suggest that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.

    View details for DOI 10.1371/journal.pone.0077175

    View details for PubMedID 24194868

    View details for PubMedCentralID PMC3806739

  • Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation AMERICAN JOURNAL OF HUMAN GENETICS Kidd, J. M., Gravel, S., Byrnes, J., Moreno-Estrada, A., Musharoff, S., Bryc, K., Degenhardt, J. D., Brisbin, A., Sheth, V., Chen, R., McLaughlin, S. F., Peckham, H. E., Omberg, L., Chung, C. A., Stanley, S., Pearlstein, K., Levandowsky, E., Acevedo-Acevedo, S., Auton, A., Keinan, A., Acuna-Alonzo, V., Barquera-Lozano, R., Canizales-Quinteros, S., Eng, C., Burchard, E. G., Russell, A., Reynolds, A., Clark, A. G., Reese, M. G., Lincoln, S. E., Butte, A. T., De La Vega, F. M., Bustamante, C. D. 2012; 91 (4): 660-671

    Abstract

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.

    View details for DOI 10.1016/j.ajhg.2012.08.025

    View details for Web of Science ID 000309568500008

    View details for PubMedID 23040495

    View details for PubMedCentralID PMC3484644