Data from: Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers

Detecting positive selection using genomic data is critical to
understanding the role of adaptive evolution. Of particular interest in
this context is sex chromosomes since they are thought to play a special
role in local adaptation and speciation. We sought to circumvent the
challenges associated with statistical phasing when using haplotype-based
statistics in sweep scans by benefitting from that whole-chromosome
haplotypes of the sex chromosomes can be obtained by re-sequencing of
individuals of the hemizygous sex. We analyzed whole Z chromosome
haplotypes from 100 females from several populations of four black and
white flycatcher species (in birds, females are ZW and males ZZ). Based on
integrated haplotype score (iHS) and number of segregating sites by length
(nSL) statistics, we found strong and frequent haplotype structure in
several regions of the Z chromosome in each species. Most of these sweep
signalswere population-specific, with essentially no evidence for regions
under selection shared among species. Some completed sweeps were revealed
by the cross-population extended haplotype homozygosity (XP-EHH)
statistic. Importantly, by using statistically phased Z chromosome data
from re-sequencing of males, we failed to recover the signals of selection
detected in analyses based on whole-chromosome haplotypes from females;
instead, what likely represent false signals of selection were frequently
seen. This highlights the power issues in statistical phasing and cautions
against conclusions from selection scans using such data. The detection of
frequent selective sweeps on the avian Z chromosome supports a large role
of sex chromosomes in adaptive evolution.