DOI: 10.5061/dryad.21mb45j
title: Data from: Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs

description: Cherax is a genus of 58 species of decapod crustaceans that are widespread
 across Australia and New Guinea. We use single-nucleotide polymorphisms
 (SNPs) to examine phylogeographic patterns in the most widespread species
 of Cherax, namely, C. destructor, and test the distinctiveness of one
 undescribed species, two C. destructor subspecies, previously proposed
 evolutionarily significant units, and management units. Both the
 phylogenetic analyses and the analysis of fixed allelic differences
 between populations support the current species-level taxonomy of C.
 setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of
 C. destructor albidus and C. d. destructor and the existence of one
 undescribed species. The two populations of C. d. albidus from the Glenelg
 and Wimmera rivers were significantly distinct, with eight diagnostic
 differences (&lt;1% fixed differences, null expectation is four fixed
 differences), but this low level of divergence is interpreted as within
 the range that might be expected of management units, that is, among
 allopatric populations of a single species or subspecies. A southern clade
 of C. d. destructor comprising the Murray River and its tributaries
 upstream from its confluence with the Darling River is genetically
 distinct from a northern clade comprising populations from the Lake Eyre
 Basin, the northern half of the Murray–Darling Basin (Darling River
 catchment) and the Lower Murray River below the Darling confluence.
description: Cherax_data_inputR script to read DCra15_Chdes_SNP_2row.csv into genlight objects (CRAN package adegenet) to facilitate analysis. Creates two genlight objects, one for the full dataset and one for the ingroup taxon onlycherax_full_filterScript to filter the full dataset on callrate, repeatability and secondaries, and to combine sampling sites within a single drainage and with very low sample sizes.cherax_ingroup_filterScript to filter the ingroup dataset on callrate, repeatability and secondaries.cherax_recode_ingroup_onlyRecode table to select ingroup taxa only.Cherax_prelim_pop_recodeRecode table to tidy up population labels, and other issues that arose during the sequencing.cherax_prelim_ind_recodeRecode table to tidy up individual labels, duplicates and other issues that arose during the sequencing.cherax_ingroup_onlyThe ingroup dataset saved in compact binary form as a genlight object. Can be read with gl &lt;- readRDS(cherax_ingroup_only.Rdata)cherax_ind_metadataMetadata to assign to individuals when the two genlight objects are constructed. Used by script gl.read.dart() in Cherax_data_input.Rcherax_full_glThe full dataset saved in compact binary form as a genlight object. Can be read with gl &lt;- readRDS(cherax_full_gl.Rdata)DCra15_Chdes_SilicoDArTPresence/Absence data (SilicoDArT) provided by Diversity Arrays Technology (refer to https://www.diversityarrays.com/ for further information on data formats). Zipped.DCra15_Chdes_SNP_2rowSNP dataset (DArTSeq) provided by Diversity Arrays Technology in 2-Row format (refer to https://www.diversityarrays.com/ for further information on data formats)README