TY - JOUR
T1 - Comparing divergence landscapes from reduced-representation and whole genome resequencing in the yellow-rumped warbler (Setophaga coronata) species complex
AU - Szarmach, Stephanie J.
AU - Brelsford, Alan
AU - Witt, Christopher C.
AU - Toews, David P.L.
N1 - Funding Information:
The authors would like to thank the Museum of Southwestern Biology and the Cornell Museum of Vertebrates (Charles Dardia, curator) for tissue loans. We thank C. Gregory Schmitt, C. Jonathan Schmitt, Cole J. Wolf, Nicholas K. Fletcher, and Borja Milá for facilitating the sample collection. The authors also thank Darren Irwin and the Irwin Laboratory at the University of British Columbia, where the original GBS data were generated; and Irby Lovette and the Lovette laboratory at the Cornell Laboratory of Ornithology, where the original ddRAD and WGS data were generated. The authors would also like to thank Andrew Foote, Evelyn Jensen, Rebecca Taylor, and David Coltman for the invitation to contribute to this special issue of , as well as three anonymous reviewers whose comments greatly improved the manuscript. Funding was supported by Pennsylvania State University and startup funds from the Eberly College of Science and the Huck Institutes of the Life Sciences. Molecular Ecology
Funding Information:
The authors would like to thank the Museum of Southwestern Biology and the Cornell Museum of Vertebrates (Charles Dardia, curator) for tissue loans. We thank C. Gregory Schmitt, C. Jonathan Schmitt, Cole J. Wolf, Nicholas K. Fletcher, and Borja Mil? for facilitating the sample collection. The authors also thank Darren Irwin and the Irwin Laboratory at the University of British Columbia, where the original GBS data were generated; and Irby Lovette and the Lovette laboratory at the Cornell Laboratory of Ornithology, where the original ddRAD and WGS data were generated. The authors would also like to thank Andrew Foote, Evelyn Jensen, Rebecca Taylor, and David Coltman for the invitation to contribute to this special issue of Molecular Ecology, as well as three anonymous reviewers whose comments greatly improved the manuscript. Funding was supported by Pennsylvania State University and startup funds from the Eberly College of Science and the Huck Institutes of the Life Sciences.
Publisher Copyright:
© 2021 John Wiley & Sons Ltd
PY - 2021/12
Y1 - 2021/12
N2 - Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers’ ability to accurately characterize certain genomic features, such as landscapes of divergence—how FST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-FST peaks were not detected in the ddRAD data set, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10–20 kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.
AB - Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers’ ability to accurately characterize certain genomic features, such as landscapes of divergence—how FST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-FST peaks were not detected in the ddRAD data set, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10–20 kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.
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U2 - 10.1111/mec.15940
DO - 10.1111/mec.15940
M3 - Article
C2 - 33934424
AN - SCOPUS:85106292111
SN - 0962-1083
VL - 30
SP - 5994
EP - 6005
JO - Molecular ecology
JF - Molecular ecology
IS - 23
ER -