DOI: 10.5061/dryad.4b8gtht9v
title: Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)

description: Adaptation to environmental change requires that populations harbor the
 necessary genetic variation to respond to selection. However,
 dispersal-limited species with fragmented populations and reduced genetic
 diversity may lack this variation and are at an increased risk of local
 extinction. In freshwater fish species, environmental change in the form
 of increased stream temperatures places many cold-water species at-risk.
 We present a study of rainbow darters (Etheostoma caeruleum) in which we
 evaluated the importance of genetic variation on adaptive potential and
 determined responses to extreme thermal stress. We compared fine-scale
 patterns of morphological and thermal tolerance differentiation across
 eight sites, including a unique lake habitat. We also inferred
 contemporary population structure using genomic data and characterized the
 relationship between individual genetic diversity and stress tolerance. We
 found site-specific variation in thermal tolerance that generally matched
 local conditions and morphological differences associated with lake-stream
 divergence. We detected patterns of population structure on a highly local
 spatial scale that could not be explained by isolation by distance or
 stream connectivity. Finally, we showed that individual thermal tolerance
 was positively correlated with genetic variation, suggesting that sites
 with increased genetic diversity may be better at tolerating novel stress.
 Our results highlight the importance of considering intraspecific
 variation in understanding population vulnerability and stress response.
description: <b>Variant file in VCF format</b>
 7,906 SNPs in 119 individuals aligned to a draft of the
 orangethroat darter genome used for population genomic analyses.
 Individual IDs correspond to sites sampled in Table 1.
 VCF_RDarters.vcf <b>Critical thermal
 maximum model </b> Critical thermal maximum of
 119 individuals used in modeling thermal tolerance. CTM refers to critical
 thermal maximum. Cup and batch correspond to a location within the
 insulated cooler and trial number, respectively. Obs_Het and Exp_Het
 correspond to individual observed and expected heterozygosity,
 respectively. CTM_Model_RDarters.xlsx
 <strong>Critical thermal maximum
 values</strong> Critical thermal maximum of all
 153 individuals used to investigate significant pairwise site differences
 and the relationship between thermal tolerance, water temperature, and
 average maximum air temperature. CTM refers to critical thermal maximum.
 Cup and batch correspond to a location within the insulated cooler and
 trial number, respectively. tmax_JunetoAugust and tmax_EntireYear refer to
 the average maximum air temperature collected using Daymet at a given site
 from June to August and the entire year, respectively. Temp is the water
 temperature collected at each site. 
 CTM_RDarters.xlsx <b>Morphology
 canonical variate scores </b> Canonical variate
 scores for 154 individuals calculated using MorphoJ software. Individual
 and population IDs refer to sites in Table 1. Location refers to the
 position of the site within tributary.
 CVA_Scores_RDarters.txt <b>Morphology
 discriminant function scores</b> Discriminant
 function scores for 154 individuals calculated using MorphoJ software to
 explore lake versus stream divergence. Individual IDs refer to sites
 sampled in Table 1. DF_Scores_RDarters.txt
 <b>Isolation by distance file </b>
 Geographic (km) and genetic distance (F<sub>ST</sub>
 from Stacks output) between all sites sampled in Table 1.
 IBD_RDarters.xlsx <b>MorphoJ project
 file </b> Project file containing morphological
 analyses conducted in 154 individuals. Requires the MorphoJ software for
 visualization. MorphoJ_RDarters.morphoj
 <b>Identity by descent results </b>
 Pairwise genetic relatedness between 119 individuals computed
 using identity by descent in Plink. PI_HAT corresponds to the relatedness
 of two individuals (proportion of shared alleles).
 Relatedness_RDarters.xlsx <b>StreamTree
 input file</b> Input file for StreamTree
 analysis. Samples correspond to sites sampled in Table 1, while sections
 refer to the total number of stream sections between sample sites. Genetic
 distance is represented by F<sub>ST</sub> calculated from
 Stacks. StreamTree_RDarters.txt