Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird

Understanding the patterns and processes that contribute to phenotypic
diversity and speciation is a central goal of evolutionary biology.
Recently, high-throughput sequencing has provided unprecedented
phylogenetic resolution in many lineages that have experienced rapid
diversification. The Holarctic redpoll finches (Genus: Acanthis) provide
an intriguing example of a recent, phenotypically diverse lineage;
traditional sequencing and genotyping methods have failed to detect any
genetic differences between currently recognized species, despite marked
variation in plumage and morphology within the genus. We examined
variation among 20 712 anonymous single nucleotide polymorphisms (SNPs)
distributed throughout the redpoll genome in combination with 215 825 SNPs
within the redpoll transcriptome, gene expression data and ecological
niche modelling to evaluate genetic and ecological differentiation among
currently recognized species. Expanding upon previous findings, we present
evidence of (i) largely undifferentiated genomes among currently
recognized species; (ii) substantial niche overlap across the North
American Acanthis range; and (iii) a strong relationship between polygenic
patterns of gene expression and continuous phenotypic variation within a
sample of redpolls from North America. The patterns we report may be
caused by high levels of ongoing gene flow between polymorphic
populations, incomplete lineage sorting accompanying very recent or
ongoing divergence, variation in cis-regulatory elements, or phenotypic
plasticity, but do not support a scenario of prolonged isolation and
subsequent secondary contact. Together, these findings highlight ongoing
theoretical and computational challenges presented by recent, rapid bouts
of phenotypic diversification and provide new insight into the
evolutionary dynamics of an intriguing, understudied non-model system.