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Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)

Citation

Oliveira, Daniel; Reid, Brendan; Fitzpatrick, Sarah (2020), Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum), Dryad, Dataset, https://doi.org/10.5061/dryad.4b8gtht9v

Abstract

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.

Usage Notes

Variant file in VCF format

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

Critical thermal maximum model

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

Critical thermal maximum values

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

Morphology canonical variate scores

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

Morphology discriminant function scores

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

Isolation by distance file

Geographic (km) and genetic distance (FST from Stacks output) between all sites sampled in Table 1.

IBD_RDarters.xlsx

MorphoJ project file

Project file containing morphological analyses conducted in 154 individuals. Requires the MorphoJ software for visualization.

MorphoJ_RDarters.morphoj

Identity by descent results

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

StreamTree input file

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 FST calculated from Stacks.

StreamTree_RDarters.txt

Funding

National Science Foundation, Award: DBI-1460569

National Science Foundation, Award: DBI-1757530

National Science Foundation, Award: FSML-1722621

Michigan State University