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

Ortego J, Noguerales V, Gugger PF, Sork VL

Date Published: November 4, 2015

DOI: http://dx.doi.org/10.5061/dryad.52504

 

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Title Simple Sequence Repeat Data
Downloaded 18 times
Description 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.
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Title Neighbor-joining phylogenetic trees
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Description Neighbor-joining phylogenetic trees based on 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci
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Title Input files used for phylogenetic analyses in POPULATIONS
Downloaded 6 times
Description 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
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Title Input files used for PCAs on genetic and environmental data
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Description 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)
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Title Climate layers used for MAXENT analyses
Downloaded 42 times
Description 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.
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Title Occurrence data used for MAXENT and ENMTOOLS analyses
Downloaded 28 times
Description 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.
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Title Input files used for STRUCTURE analyses
Downloaded 6 times
Description 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.
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Title Input file used for BAPS analyses
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Description Input file used for Bayesian analyses of genetic structure implemented in the program BAPS.
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Title Input files used for Mantel tests
Downloaded 5 times
Description 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.
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When using this data, please cite the original publication:

Ortego J, Noguerales V, Gugger PF, Sork VL (2015) Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Molecular Ecology 24(24): 6188–6208. http://dx.doi.org/10.1111/mec.13457

Additionally, please cite the Dryad data package:

Ortego J, Noguerales V, Gugger PF, Sork VL (2015) Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.52504
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