Using Ancestry Informative Markers (AIMs) to Detect Fine Structures Within Gorilla Populations.

Ranajit Das,Neha Venkatesh,Ria Roy

doi:10.3389/fgene.2019.00043

Ranajit Das, Neha Venkatesh + Show 1 more

Open Access

https://doi.org/10.3389/fgene.2019.00043

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Abstract

The knowledge of ancestral origin is monumental in conservation of endangered animals since it can aid in preservation of population level genetic integrity and prevent inbreeding among related individuals. Despite maintenance of studbook, the biogeographical affiliation of most captive gorillas is largely unknown, which has constrained management of captive gorillas aiming at maximizing genetic diversity at the population level. In recent years, ancestry informative markers (AIMs) has been successfully employed for the inference of genomic ancestry in a wide range of studies in evolutionary genetics, biomedical research, genetic stock identification, and introgression analysis and forensic analyses. In this study, we sought to derive the AIMs yielding the most cohesive and faithful understanding of biogeographical affiliation of query gorillas. To this end, we compared three commonly used AIMs-determining methods namely, Infocalc, FST, and Smart Principal Component Analysis (SmartPCA) with ADMIXTURE, using gorilla genome data available through Great Ape Genome Project database. Our findings suggest that the SNPs that were detected by at least three of the four AIMs-determining approaches (N = 1,531), is likely most suitable for delineation of gorilla AIMs. It recapitulated the finer structure within western lowland gorilla genomes with high degree of precision. We further have validated the robustness of our results using a randomized negative control containing the same number of SNPs. To the best of our knowledge, this is the first report of an AIMs panel for gorillas that may aid in developing cost-effective resources for large-scale demographic analyses, and greatly help in conservation of this charismatic mega-fauna.

Highlights

Effective conservation of endangered animals with unknown ancestral origin entails delineation of the biogeographic affinities of their ancestors in order to facilitate preservation of the population level integrity of genomic signal
In this study we sought to compare three strategies previously used for ancestry informative markers (AIMs) determination, namely Infocalc algorithm (Paschou et al, 2007; Kosoy et al, 2009), Wright’s FST (Tian et al, 2007; Kidd et al, 2011; Nievergelt et al, 2013), and Smart Principal Component Analysis (SmartPCA) (Patterson et al, 2006) with a novel ADMIXTURE based approach (Alexander et al, 2009) to delineate an AIMs panel that can reproducibly capture the genomic ancestry of gorillas at the population level and aid in identification of gorillas at the individual level
Our results indicate that this AIMs panel can recapitulate the ancestry information of query gorillas with high precision and can help in population level identification of gorillas, which can be monumental in the preservation of unique gorilla gene pools and selection of individuals for captive breeding program

Summary

Introduction

Effective conservation of endangered animals with unknown ancestral origin entails delineation of the biogeographic affinities of their ancestors in order to facilitate preservation of the population level integrity of genomic signal. The knowledge of ancestral origin could be relevant for planned re-introduction of animals to wild habitats and management of captive breeding programs in order to avoid inbreeding depression. Since the gorilla population is rapidly dwindling in the wild as a Ancestry Informative Markers for Gorilla result of severe habitat encroachment and the illegal bushmeat trade, effective management of captive breeding programs has become monumental in order to both increase their numbers and to protect them from inbreeding. Proper knowledge of ancestry is of great importance in captive breeding programs of gorillas in order to avoid inbreeding depression and at the same time to conserve the genomic integrity of the native gorilla populations

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