Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone

Joseph D. Manthey, Stephane Boissinot, Robert G. Moyle

    Research output: Contribution to journalArticle

    Abstract

    Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall's Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

    Original languageEnglish (US)
    Article numberukz015
    JournalAuk
    Volume136
    Issue number2
    DOIs
    StatePublished - Apr 16 2019

    Fingerprint

    woodpeckers
    contact zone
    gene flow
    genomics
    biodiversity
    sequence analysis
    DNA
    ladders
    genome
    introgression
    single nucleotide polymorphism
    biologists
    effective population size
    population size
    hybridization
    range size
    polymorphism
    transect
    sampling

    Keywords

    • contact zone
    • Dryobates
    • genomics
    • hybrid zone
    • Picoides
    • RAD-seq
    • woodpeckers

    ASJC Scopus subject areas

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

    Cite this

    Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone. / Manthey, Joseph D.; Boissinot, Stephane; Moyle, Robert G.

    In: Auk, Vol. 136, No. 2, ukz015, 16.04.2019.

    Research output: Contribution to journalArticle

    @article{0701e0f5b4e04029a60b8933e0889693,
    title = "Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone",
    abstract = "Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall's Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.",
    keywords = "contact zone, Dryobates, genomics, hybrid zone, Picoides, RAD-seq, woodpeckers",
    author = "Manthey, {Joseph D.} and Stephane Boissinot and Moyle, {Robert G.}",
    year = "2019",
    month = "4",
    day = "16",
    doi = "10.1093/auk/ukz015",
    language = "English (US)",
    volume = "136",
    journal = "Auk",
    issn = "0004-8038",
    publisher = "Ornithological Societies of North America",
    number = "2",

    }

    TY - JOUR

    T1 - Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii x D. scalaris contact zone

    AU - Manthey, Joseph D.

    AU - Boissinot, Stephane

    AU - Moyle, Robert G.

    PY - 2019/4/16

    Y1 - 2019/4/16

    N2 - Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall's Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

    AB - Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall's Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.

    KW - contact zone

    KW - Dryobates

    KW - genomics

    KW - hybrid zone

    KW - Picoides

    KW - RAD-seq

    KW - woodpeckers

    UR - http://www.scopus.com/inward/record.url?scp=85068499214&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=85068499214&partnerID=8YFLogxK

    U2 - 10.1093/auk/ukz015

    DO - 10.1093/auk/ukz015

    M3 - Article

    VL - 136

    JO - Auk

    JF - Auk

    SN - 0004-8038

    IS - 2

    M1 - ukz015

    ER -