Phylogenetics and demography of the western North American endemic Pacific Laurasian Clade of Isoëtes

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., 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., , # 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...,