A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology

Christina M. Bergey, Luca Pozzi, Todd Disotell, Andrew S. Burrell

    Research output: Contribution to journalArticle

    Abstract

    Over the last two decades primatologists have benefited from the use of numerous molecular markers to study various aspects of primate behavior and evolutionary history. However, most of the studies to date have been based on a single locus, usually mitochondrial DNA, or a few nuclear markers, e. g., microsatellites. Unfortunately, the use of such markers not only is unable to address successfully important questions in primate population genetics and phylogenetics (mainly because of the discordance between gene tree and species tree), but also their development is often a time-consuming and expensive task. The advent of next-generation sequencing allows researchers to generate large amounts of genomic data for nonmodel organisms. However, whole genome sequencing is still cost prohibitive for most primate species. We here introduce a second-generation sequencing technique for genotyping thousands of genome-wide markers for nonmodel organisms. Restriction site-associated DNA sequencing (RAD-seq) reduces the complexity of the genome and allows inexpensive and fast discovery of thousands of markers in many individuals. Here, we describe the principles of this technique and we demonstrate its application in five primates, Microcebus sp., Cebus sp., Theropithecus gelada, Pan troglodytes, and Homo sapiens, representing some of the major lineages within the order. Despite technical and bioinformatic challenges, RAD-seq is a promising method for multilocus phylogenetic and population genetic studies in primates, particularly in young clades in which a high number of orthologous regions are likely to be found across populations or species.

    Original languageEnglish (US)
    Pages (from-to)303-314
    Number of pages12
    JournalInternational Journal of Primatology
    Volume34
    Issue number2
    DOIs
    StatePublished - 2013

    Fingerprint

    primate
    genotyping
    Primates
    genome
    population genetics
    sequence analysis
    Microcebus
    phylogenetics
    DNA
    methodology
    bioinformatics
    Cebus
    phylogeny
    organisms
    Pan troglodytes
    mitochondrial DNA
    genomics
    researchers
    method
    marker

    Keywords

    • Genotyping
    • Nonmodel organisms
    • Phylogenetics
    • Population genetics
    • Restriction site-associated DNA sequencing
    • Second-generation DNA sequencing
    • Single-nucleotide polymorphisms

    ASJC Scopus subject areas

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

    Cite this

    A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology. / Bergey, Christina M.; Pozzi, Luca; Disotell, Todd; Burrell, Andrew S.

    In: International Journal of Primatology, Vol. 34, No. 2, 2013, p. 303-314.

    Research output: Contribution to journalArticle

    Bergey, Christina M. ; Pozzi, Luca ; Disotell, Todd ; Burrell, Andrew S. / A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology. In: International Journal of Primatology. 2013 ; Vol. 34, No. 2. pp. 303-314.
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