Inference of Gorilla demographic and selective history from whole genome sequence data

Abstract

Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.

Signatures of positive selection and local adaptation to urbanization in white‐footed mice (Peromyscus leucopus)

“…We included the P. leucopus demographic history into our analysis and found 0.019% of the sequenced loci to contain SFS patterns indicative of selective sweeps. This rate is in line with other studies that reported that 0.5% of regions in domesticated rice (Wang et al, 2014), 0.02% of loci in black cottonwood (Zhou, Bawa, & Holliday, 2014) and 0.02% of the gorilla genome (McManus et al, 2014) show evidence of selective sweeps or hitchhiking.…”

Speciation in sympatry with ongoing secondary gene flow and a potential olfactory trigger in a radiation of Cameroon cichlids

“…As g‐phocs models the coalescent process without incorporating recombination, it assumes no recombination within loci, and free recombination between loci. Following several other studies (Choi et al., ; Gronau et al., ; Hung et al., ; McManus et al., ), we picked 1 kb loci separated by at least 50 kb. Following (Gronau et al., ), loci were selected not to contain the following classes of sites within the O. niloticus reference genome—that is, rather than being simply masked, these sites were not allowed to occur in input loci: (a) hard‐masked (N) or soft‐masked (lowercase bases) sites in the publicly available genome assembly; (b) sites that were identified to be prone to ambiguous read mapping using the program SNPable (Li, , using k = 50 and r = 0.5 and excluding rankings 0 and 1); and (c) any site within an exon or <500 bp from an exon boundary.…”

Recurrent loss-of-function mutations reveal costs to OAS1 antiviral activity in primates

“…Western gorillas are estimated to have diverged from eastern gorillas approximately 261 Kya, with some gene flow continuing between the populations until between approximately 77-150 Kya 31,32 .…”