DOI: 10.5061/dryad.9cnp5hqv5
title: Pleistocene glaciation drove shared population coexpansion in eastern North American snakes

description: Glacial cycles during the Pleistocene had profound impacts on local
 environments and climatic conditions. In North America, some regions that
 currently support diverse biomes were entirely covered by ice sheets,
 while other regions were environmentally unsuitable for the organisms that
 live there now. Organisms that occupy these regions in the present day
 must have expanded or dispersed into these regions since the last glacial
 maximum, leading to the possibility that species with similar geographic
 distributions may show temporally concordant population size changes
 associated with these warming trends. We examined 17 lineages from 9
 eastern North American snake species and species complexes to test for a
 signal of temporally concordant coexpansion using a machine learning
 approach. We found that the majority of lineages show population size
 increases towards the present, with evidence for coexpansion in five out
 of fourteen lineages, while expansion in others was idiosyncratic. We also
 examined relationships between genetic distance and current environmental
 predictors and showed that genomic responses to environmental predictors
 are not consistent among species. We therefore conclude that Pleistocene
 warming resulted in population size increases in most eastern North
 American snake species, but variation in environmental preferences and
 other species-specific traits results in variance in the exact timing of
 expansion.
description: # Data accompanying: Pleistocene glaciation drove shared population
 coexpansion in eastern North American snakes ### Harrington, Overcast,
 Myers, and Burbrink All scripts used to analyze these data are available
 in the Github repository accompanying this paper:
 [https://github.com/seanharrington256/Coexp_scripts](https://github.com/seanharrington256/Coexp_scripts). Raw sequence reads generated for this study are available on the NCBI Sequence Read Archive under BioProject ID PRJNA1189052. Note that data for L. getula and L. traingulum complexes were obtained from previous publications as described in the Methods section of the manuscript. ## Information about individual samples: * `Appendix_1.xlsx` - Geographic coordinates, species/complex designation, population designation, and number of sequencing reads for samples in this study, excluding the previously published milk snake data. In the case of specimens of *Farancia*, museum numbers are included as a separate column, as the numbers we used throughout our study for these samples are mostly field numbers. ## Data for population structure, gdm, isolation-by-distance These are files that were used for R analyses, i.e., all analyses excluding stairway plot 2 and PTA. For each species/complex, there are files containing unlinked SNPs as output from ipyrad in structure (`.ustr`) and geno (`.ugeno`) format and vcf files containing all SNPs (`.vcf`). Note that milk snakes were handled differently in these analyses, and relied only on a vcf file: `Milks_filtered_snps_taxa.vcf` included here. geno formatted genetic data files: * `abacura_only.ugeno` data for *Farancia abacura* * `Acontortrix_p123_v2_25miss.ugeno` data for *Agkistrodon contortrix* * `Dpunctatus_p123_v3_25missEAST.ugeno` data for *Diadophis punctatus* * `erytro.ugeno` data for *Farancia erytrogramma* * `Lgetula_p123_v4_25miss.ugeno` data for *Lampropeltis getula* complex * `Mflagellum_p123_v3_25missEast.ugeno` data for *Masticophis flagellum* * `Pguttatus_p123_v2_25miss.ugeno` data for *Pantherophis guttatus* complex * `Sdekayi_p123_v4_25miss.ugeno` data for *Storeria dekayi* structure formatted genetic data files: * `abacura_only.ustr` data for *Farancia abacura* * `Acontortrix_p123_v2_25miss.ustr` data for *Agkistrodon contortrix* * `Dpunctatus_p123_v3_25missEAST.ustr` data for *Diadophis punctatus* * `erytro.ustr` data for *Farancia erytrogramma* * `Lgetula_p123_v4_25miss.ustr` data for *Lampropeltis getula* complex * `Mflagellum_p123_v3_25missEast.ustr` data for *Masticophis flagellum* * `Pguttatus_p123_v2_25miss.ustr` data for *Pantherophis guttatus* complex * `Sdekayi_p123_v4_25miss.ustr` data for *Storeria dekayi* vcf formatted genetic data files: * `abacura_only.vcf` data for *Farancia abacura* * `Acontortrix_p123_v2_25miss.vcf` data for *Agkistrodon contortrix* * `Dpunctatus_p123_v3_25missEAST.vcf` data for *Diadophis punctatus* * `erytro.vcf` data for *Farancia erytrogramma* * `Lgetula_p123_v4_25miss.vcf` data for *Lampropeltis getula* complex * `Mflagellum_p123_v3_25missEast.vcf` data for *Masticophis flagellum* * `Pguttatus_p123_v2_25miss.vcf` data for *Pantherophis guttatus* complex * `Sdekayi_p123_v4_25miss.vcf` data for *Storeria dekayi* * `Milks_filtered_snps_taxa.vcf` data for *Lampropeltis triangulum* complex ## Data for stairway plot 2 and PTA * `pop_files.zip` is a zip archive containing the population files used in stairway plot 2 and PTA. Each file is a populations file formatted for input to Stairwayplot2 and simple contains the sample number and population designation of each sample to be included in a single Stairwayplot2 analysis. * `stairway_PTA_vcf.zip` is a zip archive containing the vcf files for each population that were used as stairway plot 2 and PTA input. Population designations match the population files. ## Environmental data * `all_coords_requested.csv` - File of geographic coordinates read into R for spatial analyses and plotting. Includes sample ID number (`number`), species/complex (`species`), longitude (`lon`), and latitude (`lat`). * `Coexp_coords_altitude.csv` - Altitude/elevation extracted from altitude also from [Worldclim database](https://www.worldclim.org/data/worldclim21.html) (or [direct download link](https://biogeo.ucdavis.edu/data/worldclim/v2.1/base/wc2.1_30s_elev.zip)) for each sample in the `all_coords_requested.csv` file. Columns are sample number and meters above sea level (`alt`). * `Coexp_coords_present_bioclim.csv` - Bioclim climatic variables extracted at 30 seconds resolution for each sample in the `all_coords_requested.csv` file downloaded from [https://www.worldclim.org/data/worldclim21.html](https://www.worldclim.org/data/worldclim21.html) (Bioclimatic variables section) or [download link](https://biogeo.ucdavis.edu/data/worldclim/v2.1/base/wc2.1_30s_bio.zip). * `Coexp_coords_present_envirem.csv` - Envirem environmental variables described and downloaded from [http://envirem.github.io/](http://envirem.github.io/) at 30 seconds resolution extracted for each sample in the `all_coords_requested.csv` file. Note that several samples not used in this study are included in these environmental data files.