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.
sub_c85d6m20p3
xml file used in BEAST analysis
sub_c85d6m20p3b
xml file used in BEAST analysis.
sub_c85d6m20p3c
xml file used in BEAST analysis
Freezing vulnerability
Predicted 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.csv
Tree height (m) for Virentes species
Data show tree height data in meters for mature trees for seven Virentes species, including source locations and geographic coordinates.
Tree.height.csv
Leaf area and shape for Virentes species
Leaf 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.csv
Concatenated alignment of RADseq data: sub_c85d6m20p3.phy
Concatenated 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.phy
Concatenated alignment of RADseq data: virentes_ME_c85d6m20p3.phy
Concatenated 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.phy
Concatenated alignment of RADseq data: virentes_ME_c85d6m4p3
Concatenated 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.phy
All Virentes SSRs in Structure format
Dinucleotide 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.csv
IMa input file
Input file (including chloroplast sequence data, NIA-i3 sequence data, and nuclear SSR data) and command line strings for IMa analyses
BR_FU_IMa_input.txt
Concatenated chloroplast sequence data: Virentes
Concatenated 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.seq
Chloroplast trnD-trnT: all Virentes sequences
Chloroplast trnD-trnT region for 391 individuals from seven Virentes species. Sequence length is 615 bp.
trnD-trnT_all_sequences.seq
Chloroplast rp132 trnL region: all Virentes sequences
Chloroplast sequence data for rp132 trnL for seven Virentes species and 327 individuals. Sequence length is 835 bp.
rp132_trnl_all_sequences.seq