Recent Loss of Genetic Diversity in Eastern Gorillas

Abstract

Many primate populations are declining as a result of human activities. Eastern gorillas are the most affected of all great apes. Understanding the genomic consequences of rapid declines is important for assessing conservation needs. Genomic analyses of museum specimens that predate the most recent changes allow for quantification of the genomic effects of population declines and extinctions. Grauer's gorillas, one of the two Eastern gorilla subspecies, have declined by almost 80% in the last two decades. Comparisons of genomic changes over the last 100 years revealed severe reduction in genetic diversity and increase in inbreeding and frequency of deleterious mutations. The other subspecies, the Mountain gorilla, has experienced little genomic change, possibly as a result of both long‐term evolutionary history and recent conservation efforts over the last 60 years. There is thus hope for the critically endangered species if appropriate conservation actions are taken.

Key Concepts

  • Wild animal populations are declining as a result of human activities.
  • Eastern gorillas have experienced a drastic decline in population size and are now critically endangered.
  • Severe declines in population size leave genomic signatures in the affected populations and can lead to population extinctions.
  • Samples from historical specimens can inform about genomic changes that have happened in the last few centuries.
  • Temporal comparisons of genome‐wide diversity and functional profiles can be used to direct conservation actions.

Keywords: conservation genetics; Grauer's gorilla; Mountain gorilla; ancient DNA; population decline; mitochondria; whole‐genome sequencing; genetic diversity

Figure 1. Gorilla distribution ranges and conservation status. The insert shows gorilla evolutionary relationships with divergence dates as estimated by McManus et al. , Thalmann et al. and Roy et al. . Note that although the distribution plots tend to show continuous distribution within the outlined blocks, the actual distribution of gorillas is extremely fragmented. The two mountain gorilla populations (Bwindi and Virunga Massif) are shown larger for clarity. CR, critically endangered; EN, endangered.
Figure 2. Inferred demographic history of gorillas using PSMC. Genomes for two Western Lowland, two Grauer's and two Mountain gorillas were mapped against the long‐read Western Lowland gorilla assembly (Gordon et al., ). PSMC analysis, which inferred changes in effective population size through time, was conducted for all autosomes, excluding sites within highly repetitive regions and those below depth 1/3X and above depth 2X of genome‐wide coverage. Trajectories between the Western Lowland and Eastern (Grauer's + Mountain) gorillas start diverging 1–2 million years ago, with the most prominent change starting ∼200 000 years ago (using a generation‐time of 19.3 years and a mutation rate of 1.25 × 10−8). Source: Adapted from van der Valk et al. .
Figure 3. Temporal changes in Eastern gorilla genetic diversity and its functional consequences. (a) Mitochondrial haplotype diversity (Hd) of historical and present‐day Grauer's and Mountain gorillas. Present‐day Grauer's gorillas show significantly lower haplotype diversity than the historical samples. (b) Mitochondrial haplotype diversity of historical Grauer's gorillas from extinct populations outside of the current distribution range, and historical and present‐day Grauer's gorilla populations inside the current distribution range. Extinct peripheral populations were significantly more diverse than historical and present‐day populations from within the range. (c) Genome‐wide heterozygosity as estimated from historical and present‐day samples. Each black dot represents one individual genome. (d) Fraction of the genomes in ROH above 100 kb (open bars), and long ROH between 2.5 and 10 Mb indicative of inbreeding within the last 10 generations (solid bars). (e) Ratio of nonreference (derived) alleles between historical and present‐day genomes at loss‐of‐function and missense sites in protein‐coding genes. Loss‐of‐function sites include for instance premature stop codons, nucleotide deletions that change the protein sequence, etc.; missense sites consist of mutations that change the encoded protein. Both types of changes are likely to have negative effects. This ratio is significantly different from 1 in Grauer's gorillas, indicating a higher frequency in deleterious mutations in present‐day compared to historical populations. Error bars in a and b depict 95% CI. Error bars in c–e depict ±1 SD. *p < 0.05, **p < 0.01; ***p < 0.001; NS, not significant. (a,b) From van der Valk et al. CC BY 4.0. Public Domain. (c–e) From van der Valk et al. .
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How to Cite close
Guschanski, Katerina(Jul 2020) Recent Loss of Genetic Diversity in Eastern Gorillas. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0029016]