All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. Whole genome assembly projects have provided an invaluable foundation for understanding genetics in all four genera, but to date genetic studies of multiple individuals within great ape species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,006,670 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.

Copyright: © 2013 Scally et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Introduction

Two species of gorilla are currently recognized, based on morphology and geographical distribution within equatorial Africa: western gorillas (Gorilla gorilla), in tropical forest north of the Congo river on the west side of the continent, and eastern gorillas (Gorilla beringei) ∼1000 km to the east, extending to the slopes of the central African mountains [1], [2]. Estimates of when the two species diverged have varied, but recent calculations based on genomic data suggest an initial divergence time of at least 500,000 years ago [3] with gene flow continuing until as recently as 80,000 years ago [4] [5]. Both species are further classified into two subspecies: within the western species, western lowland gorillas (Gorilla gorilla gorilla) and Cross River gorillas (Gorilla gorilla diehli); within the eastern gorillas, mountain gorillas (Gorilla beringei beringei) and eastern lowland gorillas (Gorilla beringei graueri).

Western gorillas are classified as critically endangered and eastern gorillas as endangered on the IUCN Red List of Threatened Species [6]. Accurate census statistics are difficult to obtain, but current estimates indicate that wild population levels are rapidly declining, and gorillas of both species generally live in small isolated populations. The major causes of gorilla population decline are thought to be habitat loss, hunting for the bushmeat trade and outbreaks of the Ebola virus [7], and habitat fragmentation in particular has been proposed to have played a role in structuring gorilla genetic diversity [8], [9]. In light of these pressures, an understanding of present day genetic variation in gorilla populations, and of their demography, is relevant for conservation efforts. Genetic information is increasingly used, in combination with morphological and ecological data, to classify wild populations and to define (and redefine) taxonomic units for conservation. On longer timescales, understanding the association between past population bottlenecks and inferred climatic or habitat changes may provide valuable insights into the long-term forces affecting gorilla survival [10].

To date, most population-scale studies of genetic variation in gorillas have relied on mtDNA [8], [11], [12], [13] and a limited number of autosomal loci [4]. However, ancestry at individual loci is sensitive to sampling variance, and the mtDNA locus, being enriched with functional sites, has been found to be under selection in other species and therefore susceptible to introgression of haplotypes between populations [14]. Therefore such loci may not be representative of genetic diversity and ancestry across the genome.

Here we present a genome-wide survey of gorilla genetic variation, using a reduced representation sequencing approach to analyse polymorphic loci in twelve western lowland and two eastern lowland gorillas. Using over 3 million SNPs across multiple samples, the largest catalogue of gorilla genetic polymorphism presented to date, we consider the demography of western lowland gorillas, comparing levels of heterozygosity in different individuals and studying the genome-wide distribution of polymorphism and the frequency spectrum of variant alleles. We also use principal component analysis (PCA) and haplotype clustering methods to identify structure within the western lowland population.

Samples We analysed DNA from 14 gorilla individuals (Table 1): 12 western lowland and two eastern lowland gorillas. All gorillas were living in zoos at the time of sampling, and all but three wild-born individuals (Snowflake, Guy and Mukisi) were also born in captivity. For 12 of the individuals, some information about geographical origins was obtained by tracing information about the capture locations of their wild-born ancestors, based on their available family trees (File S1). PPT PowerPoint slide

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larger image TIFF original image Download: Table 1. Gorillas sampled in this study. https://doi.org/10.1371/journal.pone.0065066.t001