Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).

TitlePedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).
Publication TypeJournal Article
Year of Publication2021
AuthorsPetty, LE, Phillippi-Falkenstein, K, H Kubisch, M, Raveendran, M, Harris, RA, Vallender, EJ, Huff, CD, Bohm, RP, Rogers, J, Below, JE
JournalMol Ecol Resour
Date Published2021 Jan 01
ISSN1755-0998
Abstract

A primary challenge in the analysis of free-ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome-wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third-degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity-by-descent-based methods for pedigree reconstruction and shared segment-based inference of more distant relatedness. We compared the genotype-based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth-degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low-coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

DOI10.1111/1755-0998.13317
Alternate JournalMol Ecol Resour
PubMed ID33386679
Grant ListP51 OD01104 / / NIH Office of the Director /
R24 OD011173 / CD / ODCDC CDC HHS / United States
U42 OD010568 / CD / ODCDC CDC HHS / United States
U42 OD024282 / CD / ODCDC CDC HHS / United States
R01 GM133169 / GM / NIGMS NIH HHS / United States