Open Collections

Delmore, Kira E.; Hübner, Sariel; Kane, Nolan C.; Schuster, Richard; Andrew, Rose L.; Câmara, Francisco; Guigo, Roderic; Irwin, Darren E.

<b>Abstract</b><br/>Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.; <b>Usage notes</b><br /><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">Catharus_ustulatus_draft_assembly_annotation_Feb13_2015.tar</h4><div class="o-metadata__file-description">Folder containing draft genome assembly and annotation. Assembly generated using a reference-based approach and three paired-end 100bp Illumina libraries (one fragment, two mate pair). Annotation generated using the MAKER pipeline.</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry"><h4 class="o-heading__level3-file-title">SNP table</h4><div class="o-metadata__file-description">SNP table generated using snp-frequency-diff.pl in Popoolation2. Includes statistics on the major and minor alleles for all SNPs in coastal (_1) and inland (_2) populations of Swainson's thrushes.</div><div class="o-metadata__file-name">snp_table_coastal_inland.txt</br></div></div>

British Columbia

Dryad version number: 1</p>

Version status: submitted</p>

Dryad curation status: Published</p>

Sharing link: https://datadryad.org/stash/share/UXvepHMjcCYDx25PRmy0PDX8ZEFyOaHxtitQGfeyeOw</p>

Storage size: 771451937</p>

Visibility: public</p>

University of British Columbia Library

10.14288/1.0397882

https://doi.org/10.5683/SP2/QTSUZP; https://doi.org/10.5061/dryad.j631f

Dataverse