Data from: Whole genomes reveal evolutionary relationships and mechanisms underlying gene-tree discordance in Neodiprion sawflies

Rapidly evolving taxa are excellent models for understanding the
mechanisms that give rise to biodiversity. However, developing an accurate
historical framework for comparative analysis of such lineages remains a
challenge due to ubiquitous incomplete lineage sorting and introgression.
Here, we use a whole-genome alignment, multiple locus-sampling strategies,
and summary-tree and SNP-based species-tree methods to infer a species
tree for eastern North American Neodiprion species, a clade of
pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We
recovered a well-supported species tree that—except for three uncertain
relationships—was robust to different strategies for analyzing
whole-genome data. Nevertheless, underlying gene-tree discordance was
high. To understand this genealogical variation, we used multiple linear
regression to model site concordance factors estimated in 50-kb windows as
a function of several genomic predictor variables. We found that site
concordance factors tended to be higher in regions of the genome with more
parsimony-informative sites, fewer singletons, less missing data, lower GC
content, more genes, lower recombination rates, and lower D-statistics
(less introgression). Together, these results suggest that incomplete
lineage sorting, introgression, and genotyping error all shape the genomic
landscape of gene-tree discordance in Neodiprion. More generally, our
findings demonstrate how combining phylogenomic analysis with knowledge of
local genomic features can reveal mechanisms that produce topological
heterogeneity across genomes.