BEAST_CE_haps

BEAST analysis file used to estimate timing of molecular divergence between major haplogroups

Arlequin_CE_haps_by_catchment

The mitochondrial ND4, tRNA-Pro, and control region data of Chelodina expansa in Arlequin format. Data are grouped by major catchments

Network_CE_n164_variablesites_gapsexcluded

Mitochondrial data of Chelodina expansa in the Network format (version 4.610; Fluxus Technology Ltd), used to create the median-joining haplotype network in Figure 1

Shortneck_COI

Nexus file of the COI mitochondrial DNA data

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

shortnecks_nuDNA

Nexus file of the concatenated nuclear loc

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

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

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

Shortnecks_starBEAST

xml file for the *BEAST analyses of the nuclear DN