Genomic approaches to understanding population divergence and speciation in birds

David P L Toews, Leonardo Campagna, Scott A. Taylor, Christopher N. Balakrishnan, Daniel T. Baldassarre, Petra E. Deane-Coe, Michael G. Harvey, Daniel M. Hooper, Darren E. Irwin, Caroline D. Judy, Nicholas A. Mason, John E. McCormack, Kevin McCracken, Carl H. Oliveros, Rebecca J. Safran, Elizabeth S C Scordato, Katherine Faust Stryjewski, Anna Tigano, J. Albert Uy, Benjamin M. Winger

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon secondary contact and hybridization, and (3) quantifying levels of genomic divergence between closely related taxa. We find that in many cases, high-throughput sequencing data confirms previous work from traditional molecular markers, although there are examples in which genome-wide genetic markers provide a different biological interpretation. We also discuss how these new data allow researchers to address entirely novel questions, and conclude by outlining a number of intellectual and methodological challenges as the genomics era moves forward.

Original languageEnglish (US)
Pages (from-to)13-30
Number of pages18
JournalAuk
Volume133
Issue number1
DOIs
StatePublished - Oct 1 2015

Fingerprint

genomics
genome
divergence
bird
birds
researchers
capture method
history
secondary contact
genetic markers
genetic marker
biogeography
transcriptome
gene flow
RNA
hybridization
sequence analysis
loci
methodology
method

Keywords

  • evolution
  • next-generation sequencing
  • population genomics
  • transcriptomics

ASJC Scopus subject areas

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

Cite this

Toews, D. P. L., Campagna, L., Taylor, S. A., Balakrishnan, C. N., Baldassarre, D. T., Deane-Coe, P. E., ... Winger, B. M. (2015). Genomic approaches to understanding population divergence and speciation in birds. Auk, 133(1), 13-30. https://doi.org/10.1642/AUK-15-51.1

Genomic approaches to understanding population divergence and speciation in birds. / Toews, David P L; Campagna, Leonardo; Taylor, Scott A.; Balakrishnan, Christopher N.; Baldassarre, Daniel T.; Deane-Coe, Petra E.; Harvey, Michael G.; Hooper, Daniel M.; Irwin, Darren E.; Judy, Caroline D.; Mason, Nicholas A.; McCormack, John E.; McCracken, Kevin; Oliveros, Carl H.; Safran, Rebecca J.; Scordato, Elizabeth S C; Stryjewski, Katherine Faust; Tigano, Anna; Uy, J. Albert; Winger, Benjamin M.

In: Auk, Vol. 133, No. 1, 01.10.2015, p. 13-30.

Research output: Contribution to journalArticle

Toews, DPL, Campagna, L, Taylor, SA, Balakrishnan, CN, Baldassarre, DT, Deane-Coe, PE, Harvey, MG, Hooper, DM, Irwin, DE, Judy, CD, Mason, NA, McCormack, JE, McCracken, K, Oliveros, CH, Safran, RJ, Scordato, ESC, Stryjewski, KF, Tigano, A, Uy, JA & Winger, BM 2015, 'Genomic approaches to understanding population divergence and speciation in birds', Auk, vol. 133, no. 1, pp. 13-30. https://doi.org/10.1642/AUK-15-51.1
Toews DPL, Campagna L, Taylor SA, Balakrishnan CN, Baldassarre DT, Deane-Coe PE et al. Genomic approaches to understanding population divergence and speciation in birds. Auk. 2015 Oct 1;133(1):13-30. https://doi.org/10.1642/AUK-15-51.1
Toews, David P L ; Campagna, Leonardo ; Taylor, Scott A. ; Balakrishnan, Christopher N. ; Baldassarre, Daniel T. ; Deane-Coe, Petra E. ; Harvey, Michael G. ; Hooper, Daniel M. ; Irwin, Darren E. ; Judy, Caroline D. ; Mason, Nicholas A. ; McCormack, John E. ; McCracken, Kevin ; Oliveros, Carl H. ; Safran, Rebecca J. ; Scordato, Elizabeth S C ; Stryjewski, Katherine Faust ; Tigano, Anna ; Uy, J. Albert ; Winger, Benjamin M. / Genomic approaches to understanding population divergence and speciation in birds. In: Auk. 2015 ; Vol. 133, No. 1. pp. 13-30.
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