Application of the geographic population structure (GPS) algorithm for biogeographical analyses of wild and captive gorillas

Ranajit Das,Priyanka Upadhyai

doi:10.1186/s12859-018-2568-5

Abstract

BackgroundThe utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their population biology and facilitate the geo-localization of individuals to promote their efficacious management, particularly when bred in captivity. The Geographic Population Structure (GPS) algorithm is an admixture based tool for inference of biogeographical affinities and has been employed for the geo-localization of various human populations worldwide. Here, we applied the GPS tool for biogeographical analyses and localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project (GAGP), employing Gorillas with known ancestral origin as the reference data.ResultsOur findings suggest that GPS was successful in recapitulating the population history and estimating the geographic origins of all gorilla genomes queried and localized the wild gorillas with unknown geographical origin < 150 km of National Parks/Wildlife Reserves within the political boundaries of countries, considered as prominent modern-day abode for gorillas in the wild. Further, the GPS localization of most captive-born gorillas was congruent with their previously presumed ancestral homes.ConclusionsCurrently there is limited knowledge of the ancestral origins of most North American captive gorillas, and our study highlights the usefulness of GPS for inferring ancestry of captive gorillas. Determination of the native geographical source of captive gorillas can provide valuable information to guide breeding programs and ensure their appropriate management at the population level. Finally, our findings shine light on the broader applicability of GPS for protecting the genetic integrity of other endangered non-human species, where controlled breeding is a vital component of their conservation.

Highlights

The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species
We investigated the whole genome sequence (WGS) information from 31 gorilla genomes available in Great Ape Genome Project (GAGP) [7] corresponding to two subspecies of western gorillas (Gorilla gorilla), namely western lowland gorilla (Gorilla gorilla gorilla) and Cross River gorilla (Gorilla gorilla dielhi), as well as the eastern lowland gorilla (Gorilla beringei graueri); using the Geographic Population Structure (GPS) tool we localized the ancestral origins of both wild and captive gorillas of unknown geographic origins, employing those with a known provenance, as reference
Clustering of populations and admixture analysis Principal Component Analysis (PCA) was performed in PLINK v1.9 and the top two principal components (PCs) were plotted in R v3.2.3

Summary

Introduction

The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. We applied the GPS tool for biogeographical analyses and localization of the ancestral origins of wild and captive gorilla genomes, of unknown geographic source, available in the Great Ape Genome Project (GAGP), employing Gorillas with known ancestral origin as the reference data. At least 283 wild gorillas have been imported to North America [4] Since their inclusion under the protection of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in 1975 there have been no wild born gorillas added to the captive population. The limited availability of information regarding the biogeographic ancestry of gorillas has likely constrained their management pertaining to maximizing genetic diversity at the species level, which can be achieved by preventing inbreeding among related individuals. It is noteworthy that unlike in the wild, captive gorillas have been revealed as significantly more admixed from two or more genetically distinct wild born populations [1, 4, 7]

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