TY - JOUR
T1 - Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data
T2 - A demonstration in a population of rhesus macaques (Macaca mulatta)
AU - Petty, Lauren E.
AU - Phillippi-Falkenstein, Kathrine
AU - Kubisch, H. Michael
AU - Raveendran, Muthuswamy
AU - Harris, R. Alan
AU - Vallender, Eric J.
AU - Huff, Chad D.
AU - Bohm, Rudolf P.
AU - Rogers, Jeffrey
AU - Below, Jennifer E.
N1 - Publisher Copyright:
© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
PY - 2021/5
Y1 - 2021/5
N2 - 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.
AB - 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.
KW - bioinfomatics/phyloinfomatics
KW - kinship
KW - mammals
KW - quantitative genetics
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U2 - 10.1111/1755-0998.13317
DO - 10.1111/1755-0998.13317
M3 - Article
C2 - 33386679
AN - SCOPUS:85099966397
SN - 1755-098X
VL - 21
SP - 1333
EP - 1346
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 4
ER -