This archive contains supplemental data described in the publication "Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes". Specifically: 1) Extended Data Table 1.csv - List of individual samples used in this study. Species = Purported species as original identified by collector or institution. Institution/Source = Origin of specimen. SampleID = Sample name, as referenced in text and on NCBI SRA where applicable. popID = Population shorthand name (see Extended Data Table 2). accessionID = Museum accession number, if applicable. Sequenced = Indicates whether the individual was sequenced (Y) or not (N). 2) Extended Data Table 2.csv - All population names, shorthand names, and coordinates used in this study, either for phenotyping and/or genotyping. Population = Population name. popID = Shorthand name used throughout the manuscript and analyses. Lat = latitude. Lon = longitude. 3) Extended Data Table 3.csv - Geographic coordinates used in ENMs for Peromyscus maniculatus throughout its known range in North America. Lat = latitude. Lon = longitude. 4) Extended Data Table 4.csv - Spatially thinned geographic coordinates used in ENMs for Peromyscus maniculatus throughout its known range in North America. Lat = latitude. Lon = longitude. 5) Extended Data Video 1.mp4 - Ecological niche models of P. maniculatus throughout its range in North America over the last 21 thousand years, at 500 year intervals. 6) Extended Data Files - Phylogenetic reconstructions at the individual level: 6a) sample_ALL.tree (all samples) 6b) sample_NOADMIX.tree (removed admixed individuals >.70 admixture scores) 6c) pop_ALL.tree (all samples) 6d) pop_NOADMIX.tree (removed admixed individuals >.70 admixture scores) 6) Supplementary Data - Quantitative and qualitative ecotype classifications of each population. pop_ecotypes.txt