The Auk 133(1):13-30. 2016
Genomic approaches to understanding population divergence and speciation in birds
David P. L. Toews1,2*#, Leonardo Campagna1,2#, Scott A. Taylor1,2#, Christopher N. Balakrishnan3, Daniel T. Baldassarre4, Petra E. Deane-Coe1,2, Michael G. Harvey5, Daniel M. Hooper6, Darren E. Irwin7, Caroline D. Judy5,8, Nicholas A. Mason1,2, John E. McCormack9, Kevin G. McCracken10, Carl H. Oliveros11, Rebecca J. Safran12, Elizabeth S. C. Scordato12, Katherine Faust Stryjewski13, Anna Tigano14, J. Albert C. Uy4, and Benjamin M. Winger6,15
1Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, USA
2Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
3Department of Biology, East Carolina University, Greenville, North Carolina, USA
4Department of Biology, University of Miami, Coral Gables, Florida, USA
5Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
6Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
7Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
8Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
9Moore Laboratory of Zoology, Occidental College, Los Angeles, California, USA
10Department of Biology, University of Miami, Coral Gables, Florida, USA
11Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
12Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, Colorado, USA
13Department of Biology, Boston University, Boston, Massachusetts, USA
14Department of Biology, Queen's University, Kingston, Ontario, Canada
15Integrative Research Center, The Field Museum, Chicago, Illinois, USA
*Corresponding author: firstname.lastname@example.org
#These authors contributed equally to the paper.
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.
The widespread application of methods of high-throughput sequencing to study evolutionary processes and patterns of diversification has led to many important discoveries. However, use of these technologies and the interpretation of the resulting data can be intimidating for those researchers without previous experience. This paper presents a summary and a brief introduction to relevant methods (eg, whole-genome sequencing, sequencing of reduced representation libraries, methods of capture sequences and RNA sequencing), and important steps in the analysis protocols (eg, grouping of loci, allelic variants allocation, assembly of complete genomes and transcriptomes). We also present examples of applications in which researchers have used these technologies to answer questions related to the evolution of birds. We highlight how genomic tools help the advancement of science to discuss their contributions in three major aspects of the evolutionary history of birds. We focus on 1) general inferences about biogeography and biogeographic history, 2) patterns of gene flow and genetic isolation after secondary contact and hybridization, and 3) quantifying the levels of genomic divergence between closely related taxa. We found that in many cases the data of high-throughput sequencing confirmed the results of previous studies with traditional molecular markers, although there are examples where sampling of markers at the genomic level provides a different biological interpretation. Finally, we discuss how these new data can address completely new questions and conclude by outlining a series of methodological and intellectual challenges for the future in the age of genomics.
Keywords: evolution, population genomics, next generation sequencing, transcriptomics.
Received: March 8, 2015; Accepted: July 29, 2015; Published: October 21, 2015
Keywords: evolution, next-generation sequencing, population genomics, transcriptomics
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