An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta)

Cody T. Ross, Jessica A. Weise, Sarah Bonnar, David Nolin, Jessica Satkoski Trask, David Glenn Smith, Betsy Ferguson, James Ha, H. Michael Kubisch, Amanda Vinson, Sree Kanthaswamy

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    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.

    Original languageEnglish (US)
    Pages (from-to)313-324
    Number of pages12
    JournalAmerican Journal of Primatology
    Volume76
    Issue number4
    DOIs
    StatePublished - 2014

    Fingerprint

    Macaca mulatta
    relatedness
    single nucleotide polymorphism
    polymorphism
    microsatellite repeats
    primate
    Primates
    pedigree
    genotype
    comparison
    prediction

    Keywords

    • Colony management
    • Kinship
    • Macaca
    • Relatedness estimation
    • SNP
    • STR

    ASJC Scopus subject areas

    • Animal Science and Zoology
    • Ecology, Evolution, Behavior and Systematics

    Cite this

    An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta). / Ross, Cody T.; Weise, Jessica A.; Bonnar, Sarah; Nolin, David; Satkoski Trask, Jessica; Smith, David Glenn; Ferguson, Betsy; Ha, James; Kubisch, H. Michael; Vinson, Amanda; Kanthaswamy, Sree.

    In: American Journal of Primatology, Vol. 76, No. 4, 2014, p. 313-324.

    Research output: Contribution to journalArticle

    Ross, Cody T. ; Weise, Jessica A. ; Bonnar, Sarah ; Nolin, David ; Satkoski Trask, Jessica ; Smith, David Glenn ; Ferguson, Betsy ; Ha, James ; Kubisch, H. Michael ; Vinson, Amanda ; Kanthaswamy, Sree. / An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta). In: American Journal of Primatology. 2014 ; Vol. 76, No. 4. pp. 313-324.
    @article{490a2d7fc60747c7923fdd210c14c2fb,
    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.",
    keywords = "Colony management, Kinship, Macaca, Relatedness estimation, SNP, STR",
    author = "Ross, {Cody T.} and Weise, {Jessica A.} and Sarah Bonnar and David Nolin and {Satkoski Trask}, Jessica and Smith, {David Glenn} and Betsy Ferguson and James Ha and Kubisch, {H. Michael} and Amanda Vinson and Sree Kanthaswamy",
    year = "2014",
    doi = "10.1002/ajp.22235",
    language = "English (US)",
    volume = "76",
    pages = "313--324",
    journal = "American Journal of Primatology",
    issn = "0275-2565",
    publisher = "John Wiley and Sons Inc.",
    number = "4",

    }

    TY - JOUR

    T1 - An empirical comparison of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) for relatedness estimation in Chinese rhesus macaques (Macaca mulatta)

    AU - Ross, Cody T.

    AU - Weise, Jessica A.

    AU - Bonnar, Sarah

    AU - Nolin, David

    AU - Satkoski Trask, Jessica

    AU - Smith, David Glenn

    AU - Ferguson, Betsy

    AU - Ha, James

    AU - Kubisch, H. Michael

    AU - Vinson, Amanda

    AU - Kanthaswamy, Sree

    PY - 2014

    Y1 - 2014

    N2 - 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.

    AB - 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.

    KW - Colony management

    KW - Kinship

    KW - Macaca

    KW - Relatedness estimation

    KW - SNP

    KW - STR

    UR - http://www.scopus.com/inward/record.url?scp=84895930779&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=84895930779&partnerID=8YFLogxK

    U2 - 10.1002/ajp.22235

    DO - 10.1002/ajp.22235

    M3 - Article

    C2 - 24273109

    AN - SCOPUS:84895930779

    VL - 76

    SP - 313

    EP - 324

    JO - American Journal of Primatology

    JF - American Journal of Primatology

    SN - 0275-2565

    IS - 4

    ER -