DOI: 10.5061/dryad.j424f07
title: Data from: Environment but not geography explains genetic variation in the invasive and largely panmictic European starling in North America

description: Populations of invasive species that colonize and spread in novel
 environments may differentiate both through demographic processes and
 local selection throughout the genome. European starlings (Sturnus
 vulgaris) were introduced to New York in 1890 and subsequently spread
 throughout North America, becoming one of the most widespread and numerous
 bird species on the continent. Genome-wide comparisons across starling
 individuals and populations can identify demographic and/or selective
 factors that facilitated this rapid and successful expansion. We
 investigated patterns of genomic diversity and differentiation using
 reduced-representation genome sequencing (ddRADseq) of 17 starling
 populations. Consistent with this species’ high dispersal rates and rapid
 expansion history, we found low genome-wide differentiation and few FST
 outliers even at a continental scale. Despite starting from a founding
 population of approximately 180 individuals, North American starlings do
 not seem to have undergone a detectable genetic bottleneck: they have
 maintained an extremely large effective population size since
 introduction. We find more than 200 variants that correlate with
 temperature and/or precipitation. Genotype-environment associations (but
 not outlier scans) identify these SNPs against a background of negligible
 genome- and range-wide divergence. Such variants fall in the coding
 regions of genes associated with metabolism, stress, and neurological
 function. This evidence for incipient local adaptation in North American
 starlings suggests that it can evolve rapidly even in wide-ranging and
 evolutionarily young populations. This survey of genomic signatures of
 expansion in North American starlings is the most comprehensive to date
 and complements ongoing studies of world-wide local adaptation in these
 highly dispersive and invasive birds.
description: Variant call file of
 Stacks/Populations output This file contains all
 SNPs found in more than 80% of the population. EUSTallSNPr8.vcf
 
 Index Groups for
 Individuals These files contain the
 index group labels for each individual, which can be used to process the
 raw sequencing data in the SRA accompanying this manuscript.
 Indices.zip
description: Breast muscle tissue was sampled using biopsy punches (Integra
 Miltex) and frozen in 95% ethanol. Samples were shipped on dry ice, and
 DNA was extracted using a Qiagen DNeasy kit following the
 manufacturer's protocol (Qiagen). DNA concentration of each sample
 was quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific).
 Following the protocol of Peterson et al. (2012), we generated a
 reduced-representation genomic data set of doubledigested,
 restriction-site associated DNA (RAD) markers as described in Thrasher et
 al. (2017) using the restriction enzymes SbfI and MspI and adaptors P1 and
 P2. We sequenced 100-bp, single-end reads of the 160 best-quality
 libraries on an Illumina HiSeq 2500. We trimmed and filtered for quality
 using the fastx-toolkit (http:// hannonlab.cshl.edu/fastx_toolkit). We
 then used the process_radtags commands in stacks version 1.19 (Catchen et
 al., 2013) to demultiplex the remaining sequences. In subsequent filtering
 steps, we retained reads only if the following conditions were met: reads
 passed the Illumina chastity filter, contained an intact SbfI RAD site,
 contained one of the unique barcodes, and did not contain Illumina
 indexing adaptors. Individual reads were mapped to a
 Sturnis vulgaris reference genome (Hofmeister, Rollins et al., in prep)
 using bowtie2 version 2.2.8 (Langmead & Salzberg, 2012) using the
 “very sensitive local” set of alignment presets, and then assembled
 sequences into “stacks” using the ref-map option in stacks. Compared to a
 reference-free approach, the bioinformatics pipeline used for the
 reference-based assembly has the advantage of using fewer similarity
 thresholds to build loci. We required that a single-nucleotide
 polymorphism (SNP) be present in a minimum of 80% of the individuals (-r
 0.8) with a minimum stack depth of 10 reads at a locus within an
 individual (-m 10) for it to be called. We removed two individuals, one
 with &gt;50% missing data and one with &gt;50% relatedness
 (measured using the unadjusted AJK statistic and calculated within
 vcftools), leaving 158 individuals remaining in the study. A total of
 15,038 SNPs were identified. We used the VCFTOOLS –hwe option to remove
 any SNPs out of Hardy–Weinberg equilibrium (HWE) (e.g., an exact test that
 compared expected and observed heterozygosity in polymorphic sites only
 gave a p-value less than .001). About 6% of sequenced variants (904
 variants) were out of HWE across all sampling sites; given that (i) we are
 particularly interested in SNPs that may be specific to certain
 populations, and (ii) filtering for HWE did not change the results
 described in sections (1) and (2) below, we retain all 15,038 SNPs for the
 VCF file included in this upload.