Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

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.