Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)
Xin Ma,Joanna L. Kelley,Kirsten Eilertson,Shaila Musharoff,Jeremiah D. Degenhardt,André L. Martins,Tomas Vinar,Carolin Kosiol,Adam Siepel,Ryan N. Gutenkunst,Carlos Bustamante +10 more
TLDR
It is suggested that purifying natural selection, genetic drift, and a complex demographic history are the dominant drivers of genome evolution for the two orang-utan populations.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.read more
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Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples.
TL;DR: A flexible and computationally tractable method, called Fit∂a∂i, is presented to estimate the DFE of new mutations using the site frequency spectrum from a large number of individuals, suggesting that nearly neutral forces play a larger role in human evolution than previously thought.
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Accelerated Diversification of Nonhuman Primate Malarias in Southeast Asia: Adaptive Radiation or Geographic Speciation?
Michael P. Muehlenbein,M. Andreína Pacheco,Jesse E. Taylor,Sean P. Prall,Laurentius Ambu,Senthilvel K. S. S. Nathan,Sylvia Alsisto,Diana Ramirez,Ananias A. Escalante +8 more
TL;DR: It is hypothesized that the diversification of this group of parasites has been facilitated by the diversity, geographic distributions, and demographic histories of their primate hosts, and phylogenetic analysis of data suggests that the malaria parasites infecting Southeast Asian macaques and their relatives are speciating three to four times more rapidly than those with other mammalian hosts such as lemurs and African apes.
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Two to Tango: Co-evolution of Hominid Natural Killer Cell Receptors and MHC.
TL;DR: The hominid lineage presents a choreographed co-evolution of KIR with their MHC class I ligands, with chimpanzee KIR exhibit strong binding and, compared to humans, smaller differences between binding levels of activating and inhibitory KIR.
Journal ArticleDOI
Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog
TL;DR: In this review, genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation are summarized and synthesized.
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ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.
Champak Reddy Beeravolu,Champak Reddy Beeravolu,Michael J. Hickerson,Michael J. Hickerson,Michael J. Hickerson,Laurent A. F. Frantz,Laurent A. F. Frantz,Konrad Lohse +7 more
TL;DR: ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination, is introduced.
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