Data from: Inferring responses to climate dynamics from historical demography in neotropical forest lizards

We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.datafiles_SFS_aSFS_genoUnlinked SNP data used in population-level (SFS) and multi-population (aSFS) demographic analyses, in .geno format.datafiles_SFS_aSFS_phylipUnlinked SNP data used in population-level (SFS) and multi-population (aSFS) demographic analyses, in .phy format.datafiles_SVDQ_sNMF_genoUnlinked SNP data used in phylogenetic (SVD Quartets) and genetic clustering (sNMF) analyses, in .geno format.datafiles_SVDQ_sNMF_phylipUnlinked SNP data used in phylogenetic (SVD Quartets) and genetic clustering (sNMF) analyses, in .phy format.Dataset S1Phylogenetic tree of A. punctatus, including outgroups and support values.Dataset_S1_Apunctatus.treDataset S2Phylogenetic tree of A. ortonii, including outgroups and support values.Dataset_S2_Aortonii.treDataset S3Phylogenetic tree of P. marmoratus, including outgroups and support valuesDataset_S3_Pmarmoratus.treDataset S4Sampling schemes used in population-level and aSFS analyses (columns A–E) and posterior estimates of the populationlevel analyses (columns F–AL).Dataset_S4.xlsxDataset S5Posterior estimates of ζ, DI, time of population size change among populations responding synchronously, and corresponding cross-validation results based on hABC analyses and the aSFS.Dataset_S5.xlsxDataset S6Voucher numbers, locality information, and genetic cluster assignment of sampled specimens.Dataset_S6.xlsxDataset S7Distribution records used in species distribution models of A. punctatus and A. ortonii.Dataset_S7.xlsxDataset S8Atlantic Forest specimens used in spatial demographic models.Dataset_S8.xlsxTable S1Posterior distributions of parameters estimated in spatial demographic models.Table_S1.docxFig S1Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (Atlantic Forest I).Fig_S1.pdfFig S2Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (Atlantic Forest II).Fig_S2.pdfFig S3Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (eastern Amazonia).Fig_S3.pdfFig S4Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (western Amazonia).Fig_S4.pdfFig S5Plots of the posterior distributions of parameters and PCA from multi-population demographic analyses based on the aSFS.Fig_S5.pdfFig S6Plots of the posterior distributions of parameters estimated in spatial demographic models.Fig_S6.ti