10.5061/DRYAD.RR78S
Toivainen, Tuomas
University of Oulu
Pyhäjärvi, Tanja
University of Oulu
Niittyvuopio, Anne
University of Oulu
Savolainen, Outi
University of Oulu
Data from: A recent local sweep at the PHYA locus in the Northern European
Spiterstulen population of Arabidopsis lyrata
Dryad
dataset
2014
selective sweep
Arabidopsis lyrata
2014-01-22T21:02:25Z
2014-01-22T21:02:25Z
en
https://doi.org/10.1111/mec.12682
440061 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Northern and central European Arabidopsis lyrata ssp. petraea populations
are locally adapted to prevailing climatic conditions through differences
in timing of life history events. The timing of flowering, and in
perennials, the timing of growth cessation influence fitness. Phytochrome
A may have an important role in regulating these life-history traits as it
perceives changes in daylength. We asked, whether PHYA has contributed to
local adaptation to the northern conditions in A. l. petraea. To search
for signals of directional selection at the PHYA locus, we resequenced
PHYA and 9 short fragments around PHYA from a 57 kb region from a German
(Plech) and a Norwegian (Spiterstulen) population and compared patterns of
differentiation and diversity to a set of 19 reference loci around the
genome. First, we found that the populations were highly differentiated:
there were three nonsynonymous fixed differences at the PHYA locus, which
was in stark contrast with the total four fixed differences in the 19
reference loci. Compatible with a sweep hypothesis, variation was almost
completely removed from the 9.4 kb region around PHYA in the northern
Spiterstulen population. The overall level of linkage disequilibrium (LD)
was higher in Spiterstulen, but there was no LD across the PHYA locus in
the population, which is also a known consequence of a selective sweep.
The sweep has likely occurred after the last glacial maximum, which
suggests that it has contributed to adaptation to the northern conditions.
Input files (and output file) for sweep testingssw_clsw.zipAlignment files
for fragments 1-11Alignment_files.zipLinkage disequilibrium patterns
across 57 kb region (figures 2A and 2B)LD_across 57 kb region.fasLinkage
disequilibrium patterns between flanking loci (2 and 9, figure 2D)LD_2 and
9_loci.fasFragment and sample specific Accession nosFile includes table of
Accession nos for each sample in each sequenced fragment