Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)

The California Floristic Province (CA-FP) is the most species-rich region of North American north of Mexico. Several hypotheses have been proposed to explain why this region is exceptionally diverse, including that it harbors many recently diverged clades with weak or no barriers to reproduction.
Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple species often occurring in sympatry. Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of geneflow and mechanical reproductive isolation.
Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades and species are generally not mechanically isolated.
Rapid, recent speciation with some horizontal geneflow during the rise of Medit..., , , # Data from: Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)

This Dryad data repository is meant to accompany the paper:

Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)

by Jeffrey P. Rose, Ricardo Kriebel, Kenneth J. Sytsma, and Bryan T. Drew

The archive is arranged in several folders according to each analysis. Scripts needed to run analyses are also available.
Please also consult scripts available from: [https://github.com/crsl4/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors](https://github.com/crsl4/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors)

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This directory contains all alignments necessary for the...