Data from: Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences ...
We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent...
| Main Authors: | , , |
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| Format: | Dataset |
| Language: | English |
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Dryad
2016
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.46fb1 https://datadryad.org/stash/dataset/doi:10.5061/dryad.46fb1 |
| Summary: | We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14–15 Kya were suggested to reflect founding of freshwater populations by marine ... : SNPs_subsetA VCF file containing a random subset (1%) of all SNPs discovered in this study. This file was used for conducting PCA and calculating nucleotide diversity.mtDNA_alignmentsThe zip file contains the three mtDNA alignments used in this study. "mitogenomes.fas" is the alignment of the mitogenomes of the 81 individuals included in this study together with an outgroup. Control Region was removed from the alignment. Based on it, two other alignments, "alignment_with_1994-cytb.fas" and "alignment_with_2008-cytb.fas", were created by incorporating the data from Orti et al. (1994) and Makinen & Merila (2008), respectively. ... |
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