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The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake

Citation

Hallas, Joshua; Parchman, Thomas; Feldman, Chris (2022), The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake, Dryad, Dataset, https://doi.org/10.5061/dryad.wh70rxwks

Abstract

Aim: A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity.

Location: Western North America.

Taxon: Western terrestrial garter snake, Thamnophis elegans.

Methods: We used double-digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies of T. elegans: T. e. vagrans (wandering garter snake), T. e. elegans (mountain garter snake) and T. e. terrestris (coast garter snake). We assessed patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction (AAR) and deviations from isolation-by-distance across the landscape using estimated effective migration surfaces (EEMS). We identified environmental variables potentially shaping local adaptation in regional lineages using genetic-environment association (GEA) analyses.

Results: We recovered three well-differentiated genetic groups that correspond to the three subspecies. AAR analyses inferred the eastern Cascade Range as the ancestral area, with dispersal to both the east and west across western North America. Populations of T. e. elegans displayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations of T. e. terrestris show discrete genetic breaks consistent with well-known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in both T. e. elegans and T. e. terrestris.

Main Conclusion: T. elegans is composed of distinct evolutionary lineages, each with its own geographic range and history of diversification. T. e. elegans and T. e. terrestris show unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation in T. elegans.

Usage Notes

thamnophis_elegans_fastqs.txt
Directory containing .fastq files for all Thamnophis species individuals analyzed in the paper. This directory has been compressed as a tar archive. To uncompress from the command line:$ tar -zxvf thamnophis_elegans_fastqs.tar.gz

thamnophis_elegans_specimen_information.txt
This text file contains information on each Thamnophis specimen analyzed with GBS data.  This file contains identification numbers for voucher specimens and their corresponding barcode identification.
 
Basic_VCF_filtering.txt
This file contains basic commands for calling variants.

Funding

National Science Foundation, Award: IOS-1355221