DOI: 10.5061/dryad.rjdfn2z7t
title: Data from: Change in sexual signalling traits outruns morphological divergence across an ecological gradient in the post‐glacial radiation of the songbird genus Junco

description: The relative roles of natural and sexual selection in promoting
 evolutionary lineage divergence remains controversial and difficult to
 assess in natural systems. Local adaptation through natural selection is
 known to play a central role in promoting evolutionary divergence, yet
 secondary sexual traits can vary widely among species in recent
 radiations, suggesting that sexual selection may also be important in the
 early stages of speciation. Here we compare rates of divergence in
 ecologically relevant traits (morphology) and sexually selected signaling
 traits (coloration) relative to neutral structure in genome-wide molecular
 markers, and examine patterns of variation in sexual dichromatism to
 explore the roles of natural and sexual selection in the diversification
 of the songbird genus Junco (Aves: Passerellidae). Juncos include
 divergent lineages in Central America and several dark-eyed junco (J.
 hyemalis) lineages that diversified recently as the group recolonized
 North America following the last glacial maximum (c.a. 18,000 years ago).
 We found an accelerated rate of divergence in sexually selected characters
 relative to ecologically relevant traits. Moreover, sexual dichromatism
 measurements suggested a positive relationship between the degree of color
 divergence and the strength of sexual selection when controlling for
 neutral genetic distance. We also found a positive correlation between
 dichromatism and latitude, which coincides with the geographic axis of
 decreasing lineage age in juncos but also with a steep ecological
 gradient. Finally, we found significant associations between genome-wide
 variants linked to functional genes and proxies of both sexual and natural
 selection. These results suggest that the joint effects of sexual and
 ecological selection have played a prominent role in the junco radiation.
description: Population sampling Territorial male juncos
 were sampled across their breeding range using mist nets in order to
 obtain phenotypic data and blood samples for DNA extraction. Each captured
 individual was aged, sexed, and marked with a numbered aluminum band. A
 blood sample was collected by venipuncture of the sub-brachial vein and
 stored in Queen’s lysis buffer (Seutin, 1991) or absolute ethanol at -80ºC
 in the laboratory. After processing, birds were released at the site of
 capture. All sampling activities were conducted in compliance with Animal
 Care and Use Program regulations at the University of California Los
 Angeles, and with state and federal scientific collecting permits in the
 USA and Mexico. Genomic DNA was extracted from blood and tissue samples
 using a Qiagen DNeasy kit (Qiagen<sup>TM</sup>, Valencia, CA)
 for downstream analyses.
 Genotyping-by-sequencing We used
 genotyping-by-sequencing (Elshire<i> et al.</i> 2011) to
 obtain individual genotypes from 216 juncos belonging to the following
 taxa (with sample sizes in parentheses): <i>hyemalis</i> (14),
 <i>carolinensis</i> (22), <i>aikeni</i> (12),
 <i>mearnsi</i> (12), <i>oreganus</i> (16),
 <i>thurberi</i> (34), <i>caniceps </i>(42),
 <i>dorsalis</i> (48), <i>palliatus</i> (8) and
 <i>phaeonotus</i> (8). GBS libraries were prepared and
 sequenced at Cornell University’s Institute for Genomic Diversity, using
 the restriction enzyme PstI for digestion. Sequencing of the
 individually-barcoded libraries was carried out in different lanes of an
 Illumina HiSeq 2000, resulting in an average of 243.2 million good
 barcoded single-end reads 100 bp in length per lane.
 SNP dataset production A high quality genome
 of <i>Junco hyemalis</i> sequenced and assembled by Dovetail™
 by means of Hi-C (Belton et al., 2012) libraries based on Chromosome
 Conformation Capture to be used as reference (BioProject accession number
 PRJNA493001). To recover the chromosomal coordinates of the obtained
 scaffolds we mapped and oriented them against the zebra finch
 (<i>Taeniopygia guttata</i>) genome v87 available in Ensembl
 (Yates et al., 2016). We used the Chromosembler tool available in Satsuma
 (Grabherr et al., 2010) resulting in a final genome assembly of 955.9 Mb
 in length and a N50 of 71.46 Mb. Final read coverage was 290x. For unknown
 technical reasons, the Hi-C approach did not provide sufficient coverage
 for the sexual chromosome Z, so we recovered it from a draft consensus
 genome assembled by combining low-coverage genomes of eight different
 junco individuals intended for a parallel study, once again using
 Chromosembler and the Z chromosome of the zebra finch. We evaluated GBS
 read quality using FASTQC (Andrews, 2010) after sorting them by individual
 with AXE (Murray & Borevitz, 2017) and performed the trimming and
 quality filtering treatment using Trim Galore (Krueger, 2015), for a final
 set of reads ranging from 40 to 90 bp long. Adapter removal stringency was
 set to 1 and the quality parameter ‘q’ to 20. GBS reads were then mapped
 using the mem algorithm in the Burrows-Wheeler Aligner (BWA, Li &
 Durbin, 2009). Read groups assignment and BAM files generation was carried
 out with Picard Tools version 2 (http://broadinstitute.github.io/picard).
 We used the Genome Analysis Toolkit (GATK, McKenna et al., 2010) version
 3.6-0 to call the individual genotypes with the HaplotypeCaller tool. We
 finally used the GenotypeGVCFs tool to gather all the per-sample GVCFs
 files generated in the previous step and produce a set of jointly-called
 SNPs and indels (GATK Best Practices, DePristo et al., 2011, Auwera et
 al., 2013) in the variant call format (<i>vcf</i>).
 FILE: Junco_SNPdataset.vcf Morphometric
 data We obtained morphometric data from 531 museum
 specimens representing all main junco forms, deposited at various natural
 history museums. A wing ruler was used to measure unflattened wing length
 to the nearest 0.5 mm, and dial calipers of 0.1-mm precision were used to
 measure tail length, tarsus length, exposed bill culmen, and bill width
 and depth. All measurements were taken by a single observer.
 FILE: DataMuseums_morphometrics.xlsx Colorimetric data
 and divergence analysis We obtained colorimetric data
 from the same 531 museum specimens measured for morphometric analysis. To
 collect reflectance spectra we used a JAZ-EL200 spectrophotometer with a
 deuterium-tungsten light source via a bifurcate optical fiber probe (Ocean
 Optics<sup>TM</sup>). The reflectance captor probe was mounted
 on a black rubber holder which excluded all external light and maintained
 the probe fixed at a distance of 3 mm from the feather surface at a 90°
 angle (e.g. Schmitz-Ornes, 2006, Chui & Doucet, 2009). The
 spectrum of each measurement ranged from 300 to 700 nm and consisted of
 three replicate measurements of three different readings per replicate,
 taken on each of six plumage patches: crown, nape, back, breast, flank and
 belly. Replicates were averaged before analysis. All reflectance data are
 expressed as the percentage of reflectance from a white standard (WS-1,
 Ocean OpticsTM). The white standard was measured after each specimen and
 the spectrophotometer was recalibrated regularly. All measurements were
 taken by a single observer. FILE: CompleteSpectra_bypatch.xlsx
 Coordinates and environmental data
 Environmental data consisted of the 19 variables available in the
 BioClim database (Hijmans et al., 2005). We also included two vegetation
 variables from the Moderate Resolution Imaging Spectroradiometer (MODIS)
 satellites as available in https://modis.gsfc.nasa.gov: Normalized
 Difference Vegetation Index (NDVI, a measure of canopy greenness); and
 NDVI’s annual standard deviation (std_NDVI). All ecological variables were
 centered and standardized. Occurrence points consisted of our own field
 sampling coordinates, complemented with GBIF accessions for each junco
 form. FILE: ClimCoordinates_All.xlsx