title: An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta).
abstract: We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller & Goodnight [1989] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management.
authors.affiliation: Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, California; California National Primate Research Center, University of California, Davis, California.
authors.forename: Cody T
authors.initials: CT
authors.lastname: Ross
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Weise
authors.forename: Sarah
authors.initials: S
authors.lastname: Bonnar
authors.forename: David
authors.initials: D
authors.lastname: Nolin
authors.forename: Jessica
authors.initials: J
authors.lastname: Satkoski Trask
authors.forename: David Glenn
authors.initials: DG
authors.lastname: Smith
authors.forename: Betsy
authors.initials: B
authors.lastname: Ferguson
authors.forename: James
authors.initials: J
authors.lastname: Ha
authors.forename: H Michael
authors.initials: HM
authors.lastname: Kubisch
authors.forename: Amanda
authors.initials: A
authors.lastname: Vinson
authors.forename: Sree
authors.initials: S
authors.lastname: Kanthaswamy
mesh_terms: D000465:Algorithms; D000818:Animals; D000830:Animals, Laboratory; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000592:standards; D007756:Laboratory Animal Science; D008253:Macaca mulatta / Q000235:genetics*; D018895:Microsatellite Repeats; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide
keywords: Macaca; SNP; STR; colony management; kinship; relatedness estimation