• Libraries
    • Log in to:
    View Item 
    •   MSpace Home
    • University of Manitoba Researchers
    • University of Manitoba Scholarship
    • View Item
    •   MSpace Home
    • University of Manitoba Researchers
    • University of Manitoba Scholarship
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Sequence differences at orthologous microsatellites inflate estimates of human-chimpanzee differentiation

    Thumbnail
    View/Open
    1471-2164-15-990.xml (175.2Kb)
    1471-2164-15-990.pdf (2.061Mb)
    1471-2164-15-990-S1.xlsx (51.75Kb)
    1471-2164-15-990-S2.pdf (537.7Kb)
    1471-2164-15-990-S3.xlsx (58.15Kb)
    1471-2164-15-990-S4.pdf (318.1Kb)
    1471-2164-15-990-S5.zip (1.008Mb)
    1471-2164-15-990-S6.pdf (1.166Mb)
    1471-2164-15-990-S7.xlsx (51.75Kb)
    1471-2164-15-990-S8.pdf (115.1Kb)
    1471-2164-15-990-S9.pdf (270.4Kb)
    Date
    2014-11-18
    Author
    Kwong, Michelle
    Pemberton, Trevor J
    Metadata
    Show full item record
    Abstract
    Abstract Background Microsatellites---contiguous arrays of 2–6 base-pair motifs---have formed the cornerstone of population-genetic studies for over two decades. Their genotype data typically takes the form of PCR fragment lengths obtained using locus-specific primer pairs to amplify the genomic region encompassing the microsatellite. Recently, we reported a dataset of 5,795 human and 84 chimpanzee individuals with genotypes at 246 human-derived autosomal microsatellites as a resource to facilitate interspecies comparisons. A major assumption underlying this dataset is that PCR amplicons at orthologous microsatellites are commensurable between species. Results We find this assumption to be frequently incorrect owing to discordance in microsatellite organization and variability, as well as nontrivial length imbalances caused by small species-specific indels in microsatellite flanking sequences. Converting PCR fragment lengths into the repeat numbers they represent at 138 microsatellites whose organization and variability was found to be highly similar in both species, we show that interspecies incommensurability among PCR amplicons can inflate F ST and D PS estimates by up to 10.6%. Separate investigations of determinants of microsatellite variability in humans and chimpanzees uncover similar patterns with mean and maximum numbers of repeats, as well as numbers and ranges of distinct alleles, all important factors in predicting heterozygosity. In contrast, across microsatellites, numbers of repeats were significantly smaller in chimpanzees than in humans, while numbers and ranges of distinct alleles were instead larger. Conclusions Our findings have fundamental implications for interspecies comparisons using microsatellites and offer new opportunities for more accurate comparisons of patterns of human and chimpanzee genetic variation in numerous areas of application.
    URI
    http://hdl.handle.net/1993/30069
    DOI
    10.1186/1471-2164-15-990
    Collections
    • Rady Faculty of Health Sciences Scholarly Works [1296]
    • University of Manitoba Scholarship [1952]

    DSpace software copyright © 2002-2016  DuraSpace
    Contact Us | Send Feedback
    Theme by 
    Atmire NV
     

     

    Browse

    All of MSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

    My Account

    Login

    Statistics

    View Usage Statistics

    DSpace software copyright © 2002-2016  DuraSpace
    Contact Us | Send Feedback
    Theme by 
    Atmire NV