DOI: 10.5061/dryad.15rk0
title: Data from: Differentially expressed genes match bill morphology and plumage despite largely homogenous genomes in a Holarctic songbird

description: 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.
description: rpba_trim_noogmiss_200lociSNAPP input file for species delimitation analyses based on 200 locirpba_trim_nomiss_35lociSNAPP input file for species delimitation analyses based on 35 loci with no missing dataredpoll_wOG_1587SNPsGenepop formatted file for 1587 SNPs for redpolls and two outgroup (Loxia) individuals. SNPs were assembled using the stacks pipeline.RedpollFilteredStructureTranscriptomeStructure file generated by calling SNPs from the de novo transcriptome presented in Mason and Taylor using the GATKRedpollOnly_m5M5n5r0.8_20kSNPsGenepop formatted file that contains information for 20,712 SNPs generated using Stacks with a ddRAD-Seq pipeline. Stacks was run with -m 5, -M 5, -n 5m5M5n5r0.8_20kSNPs.genRNASeqShellScriptsThis zip file contains shell scripts used in the RNA-Seq portion of this study.ddRADShellScriptsThis file contains shell scripts associated with the ddRAD-Seq portion of this studyRScriptsThis file contains R Scripts used to analyze the ddRAD-Seq and RNA-Seq portions of this study.RedpollSNAPP_200lociOutput of SNAPP species tree analysis run using 200 loci.TPM1.0.genes.counts.matrix.TMM_normalizedFPKM read counts of contigs from RNA-Seq portion of study. This file is referenced in the R scripts also included in this Dryad accession.README.txtREADME file that explains the contents of this submission.