DOI: 10.5061/dryad.855pg
title: Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

description: The nature and timing of evolution of niche differentiation among closely
 related species remains an important question in ecology and evolution.
 The American live oak clade, Virentes, which spans the unglaciated
 temperate and tropical regions of North America and Mesoamerica, provides
 an instructive system in which to examine speciation and niche evolution.
 We generated a fossil-calibrated phylogeny of Virentes using RADseq data
 to estimate divergence times and used nuclear microsatellites, chloroplast
 sequences and an intron region of nitrate reductase (NIA-i3) to examine
 genetic diversity within species, rates of gene flow among species and
 ancestral population size of disjunct sister species. Transitions in
 functional and morphological traits associated with ecological and
 climatic niche axes were examined across the phylogeny. We found the
 Virentes to be monophyletic with three subclades, including a southwest
 clade, a southeastern US clade and a Central American/Cuban clade. Despite
 high leaf morphological variation within species and transpecific
 chloroplast haplotypes, RADseq and nuclear SSR data showed genetic
 coherence of species. We estimated a crown date for Virentes of 11 Ma and
 implicated the formation of the Sea of Cortés in a speciation event ~5 Ma.
 Tree height at maturity, associated with fire tolerance, differs among the
 sympatric species, while freezing tolerance appears to have diverged
 repeatedly across the tropical–temperate divide. Sympatric species thus
 show evidence of ecological niche differentiation but share climatic
 niches, while allopatric and parapatric species conserve ecological
 niches, but diverge in climatic niches. The mode of speciation and/or
 degree of co-occurrence may thus influence which niche axis plants diverge
 along.
description: sub_c85d6m20p3xml file used in BEAST analysissub_c85d6m20p3bxml file used in BEAST analysis.sub_c85d6m20p3cxml file used in BEAST analysisFreezing vulnerabilityPredicted vulnerability to freezing at -15oC are given as a percentage between 0 and 100 for individuals of each of seven Virentes species based on Bioclim 6 data (mean minimum temperature of the coldest month) for each geographic location. The equation for predicting vulnerability to freezing (FV) was based on empirical relationships from Koehler, Center and Cavender Bares 2012 using the electrolyte leakage method of freezing injury to stems at -15oC: FV =100-[81.202 - 1.4075*X], where X is the mean minimum temperature in the coldest month. Any negative values were assumed to indicate zero vulnerability to freezing at -15oC.Freezing.vulnerability.csvTree height (m) for Virentes speciesData show tree height data in meters for mature trees for seven Virentes species, including source locations and geographic coordinates.Tree.height.csvLeaf area and shape for Virentes speciesLeaf laminar area (mm2) and shape variables based on the first six principal components from analysis of leaf shape for 5,818 scanned leaves from 695 individual trees of seven Virentes species. The approach is based on a quantitative evaluation of the contour shape of each leaf with elliptic Fourier descriptors using the Shape 1.2 imaging software (Iwata & Ukai 2002). The data file also includes source location information of each tree, geographic coordinates, and Bioclim variables associated with each location.PCA_All_Virentes.csvConcatenated alignment of RADseq data: sub_c85d6m20p3.phyConcatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (25 samples total) used to infer phylogenetic trees. The sub_c85d6m20p3.phy alignment is 817673 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.virentes_ME_sub_c85d6m20p3.phyConcatenated alignment of RADseq data: virentes_ME_c85d6m20p3.phyConcatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The c85d6m20p3.phy alignment is 1,703,783 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.virentes_ME_c85d6m20p3.phyConcatenated alignment of RADseq data: virentes_ME_c85d6m4p3Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The virentes_ME_c85d6m4p3.phy alignment is 6,252,421 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 4.virentes_ME_c85d6m4p3.phyAll Virentes SSRs in Structure formatDinucleotide nuclear microsatellites (ZAG36, ZAG11, ZAG1/5, ZAG1/2, ZAG102, ZAG9, ZAG15, ZAG30, ZAG46, ZAG16, ZAG110) for seven Virentes species and 672 individuals, including source location information and geographic coordinates. This is the input file used for the Structure analysis.All live oak microsats_Structure.csvIMa input fileInput file (including chloroplast sequence data, NIA-i3 sequence data, and nuclear SSR data) and command line strings for IMa analysesBR_FU_IMa_input.txtConcatenated chloroplast sequence data: VirentesConcatenated chloroplast DNA sequences from trnD-trnT and rpl32–trnL(UAG) regions or seven Virentes species, 215 individuals. Source information and geographic coordinates are in the ReadMe file.CP.CONCAT.seqChloroplast trnD-trnT: all Virentes sequencesChloroplast trnD-trnT region for 391 individuals from seven Virentes species. Sequence length is 615 bp.trnD-trnT_all_sequences.seqChloroplast rp132 trnL region: all Virentes sequencesChloroplast sequence data for rp132 trnL for seven Virentes species and 327 individuals. Sequence length is 835 bp.rp132_trnl_all_sequences.seq