DOI: 10.5061/dryad.fttdz08z0
title: Data from: Phylogenomic perspectives on speciation in a North American biodiversity hotspot: An example using the California sages (Salvia subgenus Audibertia; Lamiaceae)

description: 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
 Mediterranean climate is the underlying cause of extant diversity in
 subgenus Audibertia. Geneflow has largely not facilitated
 speciation. Its signal in the nuclear genome seems to mostly be erased by
 backcrossing, but organellar genomes each capture different events of
 historical geneflow, perhaps characteristic of many lineages in the CA-FP.
 Mechanical reproductive isolation is likely only part of a mosaic of
 factors limiting geneflow.
description: # 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) \##################################### directory "concatenated" \##################################### This directory contains all alignments necessary for the maximum likelihood analyses. "Audibertia_ML_concat_final.nex" and "Audibertia_ML_concat_final.no.mohavensis.nex" are alignments will all loci concatenated, with and without S. mohavensis, respectively. The associated "best_scheme" nexus files are the IQ-Tree selected substitution model for each locus. \##################################### directory "ASTRAL" \##################################### This directory contains all alignments necessary for the ASTRAL analysis, as well as the output. "all.alignments.zip" contains alignments for each locus. "contrees.tgz" contains each RAxML maximum likelihood tree with bipartition support. "ASTRAL.LPP.tre" contains the ASTRAL result with local posterior probabilities with all taxa "ASTRAL.LPP.no.mohavensis.tre" contains the ASTRAL result with local posterior probabilities without S. mohavensis "ASTRAL.POLYTOMY.tre" contains the ASTRAL result of the polytomy test. \##################################### directory "starBEAST" \##################################### This contins the alignments and XML files used in the starBEAST analysis. If you would like to reproduce some of this, particularly for locus selection, see the R script "Audibertia.sequence.stats.alignment.prep.R" "tips.csv" is necessary to generate sequence stats for each tip (justifying their selection in subsetted analyses). "mindist_30.zip" contains 30 alignments for the loci with the minimum distance to the ASTRAL tree "PIS_30.zip" contains 30 alignments for the loci with the greatest number of parsimony informative sites The BEAST XML files for each are "PI30.UCONST.xml" and "min30.UCONST.xml". The tree for the posterior sample of each dataset is present as: "min30.MCC.median.tre" "min30.on.NET.tre" "PI30.MCC.median.tre" "PI30.on.NET.tre" Summarized as either the maximum clade credibility tree or forced to the topology of the best network (and ASTRAL tree) \##################################### directory "SNAq" \##################################### Contains alignments and results for each of the four taxon subsets, broken down by clade. Again, "Audibertia.sequence.stats.alignment.prep.R" will produce alignments for each subset. Terminals selected for each clade are detailed in the spreadsheet "network_subsets.xlsx" The subfolder for each clade contains four files: ".clade.zip" are the input alignments. "mb_output" is the MrBayes output of each genetree. Each "rr.tre" file is the best network, rerooted to the known outgroup with branch lengths in coalescent units. Each "calibratednetworks.tre" file is the best network, rerooted to the known outgroup with branch lengths in absolute time. Networks can be generated using the scripts found here: [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) on the alignments, followed by the "snaq_parallel.jl" script to generate the best network and the "snaq_boostrap.jl" script to conduct a bootstrap analysis. "tree.dists.R" will take the MrBayes genetrees to calculate pairwise distance between taxa, used by the script "calibrate.networks.jl" to generate chronograms. \##################################### directory "HyDe" \##################################### This directory contains the input data needed to run HyDe on quartets for sects. Audibertia and Echinosphahe. "-data.txt" files contains the DNA alignments "-map.txt" files contains species assignment for each tip. \##################################### directory "organelles" \##################################### This directory contains files needed to generate the analyses of organellar data. The nexus alignments are for each organellar genome respectively, and the XML files are for the BEAST analysis of their respective genome. \##################################### directory "hybrids" \##################################### In order to re-run this analysis, this assumes that you have dowloaded coordinate data as described in the Materials and Methods and you also have the crossing data downloaded from the Annals of Botany website. Run "clean.salvia.R" to clean coordinates and generate the overlap statistics yourself. The calculated overlap statistics as used in the paper can be found in "geo.overlap.csv". To conduct all analyses involving hybrids as well as ancestral state reconstructions, run "hybrid.analysis.R".