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{7302919dcd754e278198b196e0fcaf88,
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 -