Phylogenetics and demography of the western North American endemic Pacific Laurasian Clade of Isoëtes
Data files
Apr 14, 2025 version files 115.59 MB
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BPP_A00_Exclude_hybrids.zip
9.09 MB
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BPP_A00_Include_hybrids.zip
9.16 MB
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hybpiper_stats.tsv
11.90 KB
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isoetes.goflag.targets.nodups.fasta
149.29 KB
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paralog_report.csv
70.23 KB
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Phased_data_fasta.zip
1.85 MB
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Phased_data_nexus.zip
2.05 MB
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README.md
2.24 KB
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seq_lengths.tsv
132.66 KB
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SVDQ_trees.zip
93.08 MB
Abstract
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.
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 1.3paralog_report.csv
- number of paralogous gene copies identified per sample using HybPiper 1.3isoetes.goflag.targets.nodups.fasta
- custom target file for HybPiper 1.3 in FASTA format, with one ortholog per gene, selected from individualFF290_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
andCR5205
), including the controlA00_GTR_21.ctl
and sequence filebpp.txt
and mapping filebppmap.txt
, as well as the resulting treeBPP_A00_Exclude_hybrids.tre
, log filesmcmc_A00_18.txt
and analytical resultsbpp_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
andCR5205
), including the controlA00_GTR_19.ctl
and sequence filebpp.txt
and mapping filebppmap.txt
, as well as the resulting treeBPP_A00_Include_hybrids.tre
, log filesmcmc_19.txt
and analytical resultsbpp
out19.txt
.SVDQtrees
- Folder containing the results for the SVDQ analysis in PAUP, including the sequence fileseq.nex
, SVDQ control nexus filesvdq.nex
, bootstrap trees fileCombined_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.
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.