UBC Research Data

Data from: Genomic islands of divergence are not affected by geography of speciation in sunflowers. Renaut, Sebastien; Grassa, Christopher J.; Yeaman, Sam; Lai, Zhao; Kane, Nolan K.; Moyers, Brook T.; Bowers, John E.; Burke, John M.; Rieseberg, Loren H.

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Abstract
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.; Usage notes
HA412_trinity_noAltSplice_400bpminfasta file. Reference transcriptome described in the study and used for all alignments.ordered_transcriptome_trinity.txtThis is the genetic map used to position genes and SNPs. Column 1 refers to the contig name, column 2 to the chromosome number and column 3 to the position in centimorgansann_pet_fst_mapSNP table for H. annuus - H. petiolaris comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.deb_arg_fst_mapSNP table for H.debilis - H. argophyllus comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.pet_arg_fst_mapSNP table for H. petiolaris -H. argophyllus comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.ann_deb_fst_mapSNP table for H. annuus - H. debilis comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.coverage_per_gene_individualsColumn 1 is the name of the reference contig. Column 2, the length of the reference. Column 3 and after, the number of sequences aligedn to that particular contig (calculated using samtools idxstats).

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