Pleistocene glaciation drove shared population coexpansion in eastern North American snakes
Data files
Nov 25, 2024 version files 495.12 MB
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abacura_only.ugeno
234.94 KB
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abacura_only.ustr
1.01 MB
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abacura_only.vcf
10.37 MB
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Acontortrix_p123_v2_25miss.ugeno
706.96 KB
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Acontortrix_p123_v2_25miss.ustr
3.01 MB
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Acontortrix_p123_v2_25miss.vcf
43.37 MB
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all_coords_requested.csv
62.16 KB
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Appendix_1.xlsx
25.43 KB
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Coexp_coords_altitude.csv
18.08 KB
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Coexp_coords_present_bioclim.csv
257.73 KB
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Coexp_coords_present_envirem.csv
257.77 KB
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Dpunctatus_p123_v3_25missEAST.ugeno
471.20 KB
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Dpunctatus_p123_v3_25missEAST.ustr
2.03 MB
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Dpunctatus_p123_v3_25missEAST.vcf
69.40 MB
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erytro.ugeno
34.74 KB
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erytro.ustr
145.53 KB
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erytro.vcf
864.40 KB
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Lgetula_p123_v4_25miss.ugeno
944.35 KB
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Lgetula_p123_v4_25miss.ustr
4.02 MB
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Lgetula_p123_v4_25miss.vcf
95.14 MB
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Mflagellum_p123_v3_25missEast.ugeno
517.19 KB
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Mflagellum_p123_v3_25missEast.ustr
1.99 MB
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Mflagellum_p123_v3_25missEast.vcf
17.33 MB
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Milks_filtered_snps_taxa.vcf
7.18 MB
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Pguttatus_p123_v2_25miss.ugeno
1.75 MB
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Pguttatus_p123_v2_25miss.ustr
7.43 MB
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Pguttatus_p123_v2_25miss.vcf
139.46 MB
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pop_files.zip
13.07 KB
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README.md
5.19 KB
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Sdekayi_p123_v4_25miss.ugeno
195.22 KB
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Sdekayi_p123_v4_25miss.ustr
826.22 KB
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Sdekayi_p123_v4_25miss.vcf
18.92 MB
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stairway_PTA_vcf.zip
67.14 MB
Abstract
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.
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.
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.ugenodata for Farancia abacuraAcontortrix_p123_v2_25miss.ugenodata for Agkistrodon contortrixDpunctatus_p123_v3_25missEAST.ugenodata for Diadophis punctatuserytro.ugenodata for Farancia erytrogrammaLgetula_p123_v4_25miss.ugenodata for Lampropeltis getula complexMflagellum_p123_v3_25missEast.ugenodata for Masticophis flagellumPguttatus_p123_v2_25miss.ugenodata for Pantherophis guttatus complexSdekayi_p123_v4_25miss.ugenodata for Storeria dekayi
structure formatted genetic data files:
abacura_only.ustrdata for Farancia abacuraAcontortrix_p123_v2_25miss.ustrdata for Agkistrodon contortrixDpunctatus_p123_v3_25missEAST.ustrdata for Diadophis punctatuserytro.ustrdata for Farancia erytrogrammaLgetula_p123_v4_25miss.ustrdata for Lampropeltis getula complexMflagellum_p123_v3_25missEast.ustrdata for Masticophis flagellumPguttatus_p123_v2_25miss.ustrdata for Pantherophis guttatus complexSdekayi_p123_v4_25miss.ustrdata for Storeria dekayi
vcf formatted genetic data files:
abacura_only.vcfdata for Farancia abacuraAcontortrix_p123_v2_25miss.vcfdata for Agkistrodon contortrixDpunctatus_p123_v3_25missEAST.vcfdata for Diadophis punctatuserytro.vcfdata for Farancia erytrogrammaLgetula_p123_v4_25miss.vcfdata for Lampropeltis getula complexMflagellum_p123_v3_25missEast.vcfdata for Masticophis flagellumPguttatus_p123_v2_25miss.vcfdata for Pantherophis guttatus complexSdekayi_p123_v4_25miss.vcfdata for Storeria dekayiMilks_filtered_snps_taxa.vcfdata for Lampropeltis triangulum complex
Data for stairway plot 2 and PTA
pop_files.zipis 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.zipis 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 (or direct download link) for each sample in theall_coords_requested.csvfile. 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 theall_coords_requested.csvfile downloaded from https://www.worldclim.org/data/worldclim21.html (Bioclimatic variables section) or download link.Coexp_coords_present_envirem.csv- Envirem environmental variables described and downloaded from http://envirem.github.io/ at 30 seconds resolution extracted for each sample in theall_coords_requested.csvfile.
Note that several samples not used in this study are included in these environmental data files.
