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

Frontiers in Genetics
Ranajit DasNeha Venkatesh

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, F ST , 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...Continue Reading

References

Feb 13, 2003·Human Genetics·Mark D ShriverRick A Kittles
Nov 25, 2003·American Journal of Human Genetics·Noah A RosenbergJonathan K Pritchard
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Jun 15, 2007·American Journal of Human Genetics·Chao TianMichael F Seldin
Sep 26, 2007·PLoS Genetics·Peristera PaschouPetros Drineas
Aug 4, 2009·Genome Research·David H AlexanderKenneth Lange
Feb 14, 2013·Ecology and Evolution·Noah D SimonsJoseph G Lorenz
Jul 5, 2013·Nature·Javier Prado-MartinezTomas Marques-Bonet
Jul 26, 2013·Proceedings of the National Academy of Sciences of the United States of America·Fereydoun HormozdiariEvan E Eichler
Feb 20, 2014·European Journal of Human Genetics : EJHG·Laura M HuckinsUNKNOWN WTCCC3
Jun 5, 2016·Methods in Molecular Biology·Chris PhillipsMaria Victoria Lareu

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Citations

Apr 11, 2021·Proceedings of the National Academy of Sciences of the United States of America·Cheng ZouJason P Londo

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Methods Mentioned

BETA
PCA
genotyping

Software Mentioned

ADMIXTURE
Infocalc
SmartPCA
R
Inforcalc
EIG
ST
GAGP
AIMs
PLINK

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