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.
Shortnecks_starBEAST
xml file for the *BEAST analyses of the nuclear DNA
shortnecks_nuDNA
Nexus file of the concatenated nuclear loci
Shortneck_COI
Nexus file of the COI mitochondrial DNA data.
FigureS4
Majority 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.
FigureS5
Majority 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.
FigureS6
Majority 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.
FigureS7
Majority 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 S1
List of taxa, GenBank numbers and modified primer sequences used in this analysis