Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Geographic variation in insect coloration is among the most intriguing
examples of rapid phenotypic evolution and provides opportunities to study
mechanisms of phenotypic change and diversification in closely related
lineages. The bumble bee Bombus bifarius comprises two geographically
disparate color groups characterized by red-banded and black-banded
abdominal pigmentation, but with a range of spatially and phenotypically
intermediate populations across western North America. Microsatellite
analyses have revealed that B. bifarius in the USA are structured into two
major groups concordant with geography and color pattern, but also suggest
ongoing gene flow among regional populations. In this study, we better
resolve the relationships among major color groups to better understand
evolutionary mechanisms promoting and maintaining such polymorphism. We
analyze >90,000 and >25,000 single-nucleotide polymorphisms
derived from transcriptome (RNAseq) and double digest restriction site
associated DNA sequencing (ddRAD), respectively, in representative samples
from spatial and color pattern extremes in B. bifarius as well as
phenotypic and geographic intermediates. Both ddRAD and RNAseq data
illustrate substantial genome-wide differentiation of the red-banded
(eastern) color form from both black-banded (western) and intermediate
(central) phenotypes and negligible differentiation among the latter
populations, with no obvious admixture among bees from the two major
lineages. Results thus indicate much stronger background differentiation
among B. bifarius lineages than expected, highlighting potential
challenges for revealing loci underlying color polymorphism from
population genetic data alone. These findings will have significance for
resolving taxonomic confusion in this species and in future efforts to
investigate color-pattern evolution in B. bifarius and other polymorphic
bumble bee species.