Demographic changes and marker properties affect detection of human population differentiation

Jennifer B. Listman, Robert T. Malison, Atapol Sughondhabirom, Bao Zhu Yang, Ryan L. Raaum, Nuntika Thavichachart, Kittipong Sanichwankul, Henry R. Kranzler, Sookjaroen Tangwonchai, Apiwat Mutirangura, Todd Disotell, Joel Gelernter

    Research output: Contribution to journalArticle

    Abstract

    Background: Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese) using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats). Results: Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African) while both successfully distinguished Hmong from Thai and Chinese. Conclusion: Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

    Original languageEnglish (US)
    Article number21
    JournalBMC Genetics
    Volume8
    DOIs
    StatePublished - May 11 2007

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    Demography
    Population
    Dinucleotide Repeats
    Microsatellite Repeats
    Genetic Drift
    Chromosome Mapping
    Mutation Rate
    Gene Frequency
    Genotype

    ASJC Scopus subject areas

    • Genetics
    • Genetics(clinical)

    Cite this

    Listman, J. B., Malison, R. T., Sughondhabirom, A., Yang, B. Z., Raaum, R. L., Thavichachart, N., ... Gelernter, J. (2007). Demographic changes and marker properties affect detection of human population differentiation. BMC Genetics, 8, [21]. https://doi.org/10.1186/1471-2156-8-21

    Demographic changes and marker properties affect detection of human population differentiation. / Listman, Jennifer B.; Malison, Robert T.; Sughondhabirom, Atapol; Yang, Bao Zhu; Raaum, Ryan L.; Thavichachart, Nuntika; Sanichwankul, Kittipong; Kranzler, Henry R.; Tangwonchai, Sookjaroen; Mutirangura, Apiwat; Disotell, Todd; Gelernter, Joel.

    In: BMC Genetics, Vol. 8, 21, 11.05.2007.

    Research output: Contribution to journalArticle

    Listman, JB, Malison, RT, Sughondhabirom, A, Yang, BZ, Raaum, RL, Thavichachart, N, Sanichwankul, K, Kranzler, HR, Tangwonchai, S, Mutirangura, A, Disotell, T & Gelernter, J 2007, 'Demographic changes and marker properties affect detection of human population differentiation', BMC Genetics, vol. 8, 21. https://doi.org/10.1186/1471-2156-8-21
    Listman JB, Malison RT, Sughondhabirom A, Yang BZ, Raaum RL, Thavichachart N et al. Demographic changes and marker properties affect detection of human population differentiation. BMC Genetics. 2007 May 11;8. 21. https://doi.org/10.1186/1471-2156-8-21
    Listman, Jennifer B. ; Malison, Robert T. ; Sughondhabirom, Atapol ; Yang, Bao Zhu ; Raaum, Ryan L. ; Thavichachart, Nuntika ; Sanichwankul, Kittipong ; Kranzler, Henry R. ; Tangwonchai, Sookjaroen ; Mutirangura, Apiwat ; Disotell, Todd ; Gelernter, Joel. / Demographic changes and marker properties affect detection of human population differentiation. In: BMC Genetics. 2007 ; Vol. 8.
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    abstract = "Background: Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese) using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats). Results: Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African) while both successfully distinguished Hmong from Thai and Chinese. Conclusion: Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.",
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    AU - Raaum, Ryan L.

    AU - Thavichachart, Nuntika

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