Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

Detailed information about the geographic distribution of genetic and
genomic variation is necessary to better understand the organization and
structure of biological diversity. In particular, spatial isolation within
species and hybridization between them can blur species boundaries and
create evolutionary relationships that are inconsistent with a strictly
bifurcating tree model. Here we analyze genome-wide DNA sequence and
genetic ancestry variation in Lycaeides butterflies to quantify the
effects of admixture and spatial isolation on how biological diversity is
organized in this group. We document geographically widespread and
pervasive historic admixture, with more restricted recent hybridization.
This includes evidence supporting previously known and unknown instances
of admixture. The genome composition of admixed individuals varies much
more among than within populations, and tree- and genetic ancestry-based
analyses indicate that multiple distinct admixed lineages or populations
exist. We find that most genetic variants in Lycaeides are rare (minor
allele frequency < 0.5%). Because the spatial and taxonomic
distributions of alleles reflect demographic and selective processes since
mutation, rare alleles, which are presumably younger than common alleles,
were spatially and taxonomically restricted compared to common variants.
Thus, we show patterns of genetic variation in this group are
multifaceted, and we argue that this complexity challenges simplistic
notions concerning the organization of biological diversity into discrete,
easily delineated, and hierarchically structured entities.