DOI: 10.5061/dryad.6q6sq
title: Data from: Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae)

description: Molecular data have greatly influenced our concepts of species and their
 relationships in the last few decades, and as a consequence the taxonomy
 of most vertebrate clades has been repeatedly revised to reflect
 phylogeny. However, as larger and more complete molecular data sets become
 available, the sometimes striking disparities between taxonomic revisions
 based on individual gene trees (particularly those based on mitochondrial
 DNA) and species trees has become increasingly apparent. Here, we present
 data from 13 nuclear and one mitochondrial gene. Our results demonstrate
 that the recent taxonomic proposal erecting the new Australian chelid
 genus Flaviemys (Testudines: Chelidae) was an unnecessary action, and that
 recognition of Flaviemys confuses, rather than clarifies, a
 phylogeny-based taxonomy of the group. Taxonomic actions have many broad
 repercussions, and we recommend that taxonomic changes should be proposed
 cautiously and only when they are based on the strongest possible data and
 analyses.
description: Shortnecks_starBEASTxml file for the *BEAST analyses of the nuclear DNAshortnecks_nuDNANexus file of the concatenated nuclear lociShortneck_COINexus file of the COI mitochondrial DNA data.FigureS4Majority rule consensus of the posterior distribution of trees from Bayesian analysis of the AHR (panel A), AIING (B), BDNF (C), and BMP2 (D) loci generated under the HKY+I, K80+G, K80+I, and K80+I model of nucleotide sequence evolution, respectively. Bayesian posterior probabilities (BPP) as indicated. Myuchelys including M. purvisi was monophyletic with strong support (BPP = 1.0) at the AHR locus only. The outgroups were removed for clarity of presentation.FigureS5Majority rule consensus of the posterior distribution of trees from Bayesian analysis of the HMGB2 (panel A), HNFL (B), P26s4 (C) and PAX (D) loci generated under the HKY+I, HKY+I, HKY and HKY+G model of nucleotide sequence evolution, respectively. Bayesian posterior probabilities (BPP) as indicated. Myuchelys including M. purvisi was monophyletic with strong support (BPP = 1.0) at all four loci. The outgroups were removed for clarity of presentation.FigureS6Majority rule consensus of the posterior distribution of trees from Bayesian analysis of the R35 (panel A), RAG (B), TB01 (C) and TB73 (D) loci generated under the HKY, K80+I, K80+G, and HKY+G models of nucleotide sequence evolution, respectively. Bayesian posterior probabilities (BPP) as indicated. Myuchelys including M. purvisi was monophyletic with strong support (BPP = 1.0) at all four loci. The outgroups were removed for clarity of presentation.FigureS7Majority rule consensus of the posterior distribution of trees from Bayesian analysis of the ZFHX1B locus generated under the HKY+I model of nucleotide sequence evolution. Bayesian posterior probabilities (BPP) as indicated. Myuchelys including M. purvisi was monophyletic with strong support (BPP ≥0.95). The outgroups were removed for clarity of presentation.Appendix S1List of taxa, GenBank numbers and modified primer sequences used in this analysis