![]() Diversity patterns at polymorphic CNVs also resembled those seen in SNPs ( fig. ![]() S3).Ĭopy number variation (CNV) among gorillas was assessed with a read depth–based approach ( 17), and the number of fixed loss and gain events between populations reflects the accepted taxonomy ( table S5), although eastern lowland and mountain gorillas showed an excess of shared fixed deletions relative to western lowland gorillas, potentially reflecting a small ancestral population prior to their divergence. Similar patterns are also found in a genetic structure analysis using the program ADMIXTURE ( fig. 1D) revealed no substructure within the mountain gorillas sampled here, but did show a separation of eastern lowland gorillas into two subgroups, which may reflect structure within the subspecies as a whole or may only be a feature of the individuals we have sampled. Another PCA focusing on the eastern species only ( Fig. In particular, the separation between eastern lowland and mountain gorilla samples confirms them as genetically distinct populations. 1C) showed a hierarchical structure consistent with the accepted Gorilla taxonomy and the geographical distribution of these populations. A similar situation was observed on the Y chromosome, with only two sites differentiating the three male mountain gorillas ( 15).Ī principal components analysis (PCA) of 11,743,407 single-nucleotide polymorphisms (SNPs) across all samples ( Fig. A detailed analysis of variation in mitochondrial DNA (mtDNA) showed little diversity in mountain gorillas, with only three haplotypes in total differing by just one to three mutations ( 15). These values are consistent with the small reported census population sizes of eastern gorillas relative to those in the west ( 2). Comparing populations, we found that genetic diversity was lower in the eastern species than in the western by a factor of 2 to 3 ( table S3), with mean autosomal heterozygosity (frequency of between-chromosomal differences) of 6.5 × 10 −4 per base pair in mountain and eastern lowland gorillas, versus 1.9 × 10 −3 per base pair in the western lowland population. Sequences were aligned to the gorilla reference genome ( 16), and several tools were used to call variants across samples ( 15). Sequencing was performed to an average 26×depth ( table S1), and combining these data with published gorilla genome sequences ( 12) yielded a total data set of 44 samples spanning all four gorilla subspecies ( table S2). The mountain gorillas originate from both sides of the Virunga massif, including from three groups spanning a densely populated sector on the Rwandan side, and plausibly represent genetic variation and ancestry in the Virunga population at large ( 15). ![]() We performed whole-genome sequencing and analysis for 13 eastern gorillas, comprising seven mountain gorillas from the Virunga volcanoes region and six eastern lowland gorillas. Additionally, the severe population bottleneck experienced by mountain gorillas provides an opportunity to study processes that may have played a recurring role in hominin evolution and extinction. Phenotypic indicators of inbreeding such as syndactyly have been reported ( 13, 14), but the full genetic impact of their decline is unknown. It is also important in assessing their current status and in forming strategies for future conservation efforts. Unlike the other great apes ( 12), mountain gorillas have not been studied on a genome-wide scale, which is key to understanding their biology, evolution, and relationship to sister taxa ( Fig. Node heights are in units of substitutions per base pair each tree is drawn to a separate scale.ĭespite extensive study of mountain gorillas in the field, few genetic analyses have been carried out, and these have been confined to mitochondrial sequences and a limited number of autosomal loci ( 9– 11). ![]() ( E) mtDNA and Y-chromosomal phylogenies. ( D) PCA plot of SNP data from mountain and eastern lowland gorilla samples only. ( C) PCA plot of SNP data for all four gorilla subspecies. ![]() ( A) Distribution of gorilla subspecies ( 2). Geography, taxonomy and genetic structure of gorilla species ![]()
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