Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models, and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with species distribution models and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.Simple Sequence Repeat Data This file contains the genotypes for 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci and 812 individuals from six Californian scrub oak species (Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa and Quercus pacifica) collected in 87 localities. GenotypicData.xlsx Neighbor-joining phylogenetic trees Neighbor-joining phylogenetic trees based on 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci PhylogeneticTrees.zip Input files used for phylogenetic analyses in POPULATIONS Input files used for neighbor-joining phylogenetic analyses implemented in the program POPULATIONS based on 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci PopulationsInputFiles.zip Input files used for PCAs on genetic and environmental data Input files for PCA analyses based on genetic (16 nuclear simple sequence repeat loci) and climatic data (Bio2, Bio3, Bio8, Bio13, Bio14, Bio15, and Bio18) PCAInputFiles.zip Climate layers used for MAXENT analyses Climate layers (asc. files) for the present and the last glacial maximum (LGM) used for MAXENT analyses. Two climate models (CCSM and MIROC) were used for projections to the LGM. MaxentClimateLayers.zip Occurrence data used for MAXENT and ENMTOOLS analyses Occurrence data for the six studied species (Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa and Quercus pacifica) used for MAXENT and ENMTOOLS analyses. OcurrenceData.xlsx Input files used for STRUCTURE analyses Input files used for Bayesian analyses of genetic structure implemented in the program STRUCTURE. There is one file for each studied species (Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa and Quercus pacifica) and the different hierarchical analyses performed for different subsets of species. StructureInputFiles.zip Input file used for BAPS analyses Input file used for Bayesian analyses of genetic structure implemented in the program BAPS. BAPSInput.txt Input files used for Mantel tests Input files for Mantel tests performed using the program ZT. These files include two indexes of niche overlap (D and I) between each pair of species and different estimates of interspecific genetic differentiation (Fst, Reynolds distance, G`st and Jost`s D) calculated for 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci. MantelTestInputFiles.zi