DOI: 10.5061/dryad.5hqbzkhdv
title: Phylogenetics and demography of the western North American endemic Pacific Laurasian Clade of Isoëtes

description: The hydrophilic lycopod genus Isoëtes L. has a naturally patchy
 distribution, made more extreme due to anthropogenic habitat degradation.
 We used a combination of population genetic and multi-locus molecular
 phylogenetic approaches to understand the effects of this patchiness on
 the evolution and demography of the Pacific Laurasian Clade (PLC) species,
 to decipher the relationships among the three PLC species, and to
 determine the degree of isolation of the different populations. We
 discovered that the populations studied are highly structured and that two
 of the species, as currently circumscribed, are not monophyletic. Instead,
 our phylogenetic results suggest that there are eight species within the
 PLC; of these eight, five appear to have been the result of a rapid
 radiation that was followed by a prolonged period of stasis.
description: Targeted DNA sequencing using the GOFLAG probes to enrich
 Illumina sequencing libraries for 408 exon regions. Data analyzed using
 standard procedures for high-throughput DNA sequencing, phylogenetics, and
 admixture analysis.
description: # Data for: "Phylogenetics and demography of the western North
 American endemic Pacific Laurasian Clade of Isoëtes" *
 `hybpiper_stats.tsv` - tabular file of statistics for gene recovery of
 targeted sequences with HybPiper (v1.3) * `seq_lengths.tsv` - tabular file
 of gene recovery lengths for each sample at each gene using HybPiper 1.3 *
 `paralog_report.csv` - number of paralogous gene copies identified per
 sample using HybPiper 1.3 * `isoetes.goflag.targets.nodups.fasta` - custom
 target file for HybPiper 1.3 in FASTA format, with one ortholog per gene,
 selected from individual `FF290_10` (*Isoetes nuttalii*) *
 `Phased_data_fasta` - Folder containing all alligned and trimmed FASTA
 sequence files used in the analysis. * `Phased_data_nexus` - Folder
 containing all alligned and trimmed NEXUS files used to generate the FASTA
 files in Phased_data_fasta, while retaining all exluded sequence elements.
 * `BPP_A00_Exclude_hybrids` - Folder containing files needed to run the
 Bayseian Phylogenetic and Phylogeography analysis program on the
 subsampled dataset excluding the putative hybrid sites (`FF290` and
 `CR5205`), including the control `A00_GTR_21.ctl` and sequence
 file `bpp.txt`  and mapping file `bppmap.txt`, as well as the resulting
 tree `BPP_A00_Exclude_hybrids.tre`, log files `mcmc_A00_18.txt` and
 analytical results `bpp_out_A00_21.txt`. * `BPP_A00_Include_hybrids` -
 Folder containing files needed to run the Bayseian Phylogenetic and
 Phylogeography analysis program on the subsampled dataset including the
 putative hybrid sites (`FF290` and `CR5205`), including the control
 `A00_GTR_19.ctl` and sequence file `bpp.txt` and mapping file
 `bppmap.txt`, as well as the resulting tree `BPP_A00_Include_hybrids.tre`,
 log files `mcmc_19.txt` and analytical results `bpp``out19.txt`. *
 `SVDQtrees` - Folder containing the results for the SVDQ analysis in PAUP,
 including the sequence file `seq.nex`, SVDQ control nexus file `svdq.nex`,
 bootstrap trees file `Combined_Boot_Trees.tre`, and summary tree with
 bootstrap support file `[analysis]_Bootstraps.tre`. Each sub-folder
 contains a different set of analyses: one for the ancestral groups
 analysis, one for the individuals analysis, and one for the sites
 analysis.