DOI: 10.5061/dryad.52504
title: Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

description: 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.
description: 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
 (<em>Quercus berberidifolia, Quercus durata, Quercus
 cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa
 </em>and<em> Quercus pacifica</em>) 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 (<em>Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa </em>and<em> Quercus pacifica</em>) 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 (<em>Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa </em>and<em> Quercus pacifica</em>) 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.zip