Abstract
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.
Highlights
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)
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]
Summary
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]. Twelve western lowland samples were sequenced, Effie, Kaja and Snowflake were excluded from this comparison because their low depths of sequence coverage would have limited the number of sites callable across all individuals, given the calling thresholds used Several genes are located there, including some associated with immune response: the BTN2 subfamily, which forms part of the immunoglobulin superfamily, and PRSS16, which encodes for thymusspecific serine protease, thought to be involved in the prevention of auto-immunity [21] We note that both the density of called sites and the depth of coverage in this region are not unusually high or low relative to the rest of the chromosome (Figure S4 in File S2), suggesting that the signal of reduced diversity there is not an artefact of the sequencing method. In the second component both Matadi and Bikira are separately isolated from the others; given the number of samples and BiKira’s inbred status, this structure may not be significant
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