title: Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii).
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.
authors.affiliation: Department of Statistics, Stanford University, Stanford, California, United States of America.
authors.forename: Xin
authors.initials: X
authors.lastname: Ma
authors.forename: Joanna L
authors.initials: JL
authors.lastname: Kelley
authors.forename: Kirsten
authors.initials: K
authors.lastname: Eilertson
authors.forename: Shaila
authors.initials: S
authors.lastname: Musharoff
authors.forename: Jeremiah D
authors.initials: JD
authors.lastname: Degenhardt
authors.forename: André L
authors.initials: AL
authors.lastname: Martins
authors.forename: Tomas
authors.initials: T
authors.lastname: Vinar
authors.forename: Carolin
authors.initials: C
authors.lastname: Kosiol
authors.forename: Adam
authors.initials: A
authors.lastname: Siepel
authors.forename: Ryan N
authors.initials: RN
authors.lastname: Gutenkunst
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
mesh_terms: D025041:Animal Migration; D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D001893:Borneo; D019143:Evolution, Molecular; D040961:Genetic Drift; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D007214:Indonesia; D008297:Male; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D057079:Pongo / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity