DOI: 10.5061/dryad.2j1d35d
title: Data from: Deconstructing an infamous extinction crisis: Survival of Partula species on Moorea and Tahiti

description: Eleven of eighteen Society Island Partula species endemic to the Windward
 Island subgroup (Moorea and Tahiti) have been extirpated by an ill-advised
 biological control program. The conservation status of this critically
 endangered tree snail radiation is of considerable import, but is clouded
 by taxonomic uncertainty due to the extensive lack of congruence among
 species designations, diagnostic morphologies and molecular markers. Using
 a combination of museum, captive, and remnant wild snails, we obtained the
 first high-resolution nuclear genomic perspective of the evolutionary
 relationships and survival of fourteen Windward Island Partula species,
 totaling 93 specimens. We analyzed ~1,607-28,194 nuclear genomic loci
 collected with the double digest Restriction-site Associated sequencing
 method. Results from phylogenomic trees, species estimation, and
 population assignment tests yielded monophyly of the Windward Island
 subgroup. Within this group, two well-supported clades encompassing five
 species complexes were recovered. Clade 1 was restricted to Tahiti and
 contained two species complexes: “P. affinis” (three species) and “P.
 otaheitana” (five species). Clade 2 occurred on Moorea and on Tahiti and
 consisted of three species complexes: one Tahitian, “P. clara/P. hyalina”;
 the other two, “P. taeniata” (three species) and “P. suturalis” (six
 species), Moorean. Our genomic results largely corroborated previous
 mitochondrial DNA survival estimates for Moorea and Tahiti, with all five
 species complexes having members surviving in captivity and/or as remnant
 wild populations, although the details vary in each case. Continued,
 proactive conservation and management may yet ensure a
 phylogenetically-representative survival of the fabled Partula species of
 Moorea and Tahiti.
description: RAxML-matricesThe file contains the nine .phy formatted data matrices for use in RAxML to construct the phylogenomic trees. The nine matrices were generated using ipyrad. Files are named by the similarity threshold (85, 90, or 95%) and taxon coverage used (75, 50, or 25%).ipyrad-parameter-filesThe file contains the nine parameter files used by ipyrad to generate all data matrices for downstream analyses. We used three similarity threshold values (85, 90, and 95%) and three different taxon coverages (75, 50, and 25% of individuals).mrbayes-data-matrixThis file contains the data matrix from the 90% similarity threshold including 75% of individuals used for analysis in MrBayes. The nexus file was generated by ipyrad.SI-AATTC-90-75.nex.gzSingle SNP VCF fileThis is the single SNP file in vcf format that was used to generate inputs for Structure, treemix, and DAPC analyses in the manuscript. File was created using the python code vcf_single_snp.py (Bongaerts 2018).SI-90-75-sSNP-2169snp.vcfSVDquartets input fileThis is the file used to generate the species estimation tree in SVDquartetsSI-90-75-SVDquartets.nexTreemix inputThis is the input file used to conduct the f3 admixture tests. The file contains seven "populations" based on the structure analyses.SI-90-75-sSNP-treemix.tmix.gzDAPC input filesThis file contains all of the input files used for the DAPC analyses in the manuscript. They are in genepop format and were generated from the single SNP vcf file.DAPC-input.zipstructure-inputThis file contains all of the inputs used for the five different structure analyses. The input files were generated from the single SNP vcf and converted to the structure format using PGDspider.