Bayesian tree files - 6-intron+mtDNA partitioned topology

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio

Bayesian tree files - 6-intron partitioned tree

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio

Bayesian tree files - 5-intron partitioned topologies

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio

Fasta alignment files for all genetic loci used

FASTA alignment files of the sequences for each molecular marker used in the current study. The number of individuals is indicated in the file name (e.g. N=122). Information concerning choice of loci, primers used and alignment optimisation is described in section 2.2 of the paper (2.2 DNA extraction & PCR), in Table S2 and section 2.3 Sequencing & alignments. The alignment files provided (and used in the paper) are the optimised alignments (i.e. sites in the alignment which consisted of one or a few individuals having a 1bp insertion were typically highlighted a bad following T-COFFEE analysis and were removed). The original sequences are available on GenBank (see Table S1)

Bayesian tree files - Subsets of the mtDNA locus topologies

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio

Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format).

Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format). This analysis is described in section 2.5 of the paper, Species delimitation & divergence time estimation, and was conducted in BEAST v. 1.8. The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.5. The LogCombiner files contain all trees generated from 5 independent runs with burn-in removed for each analysis (i.e. 180,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 180,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files

Maximum likelihood tree files

Maximum likelihood tree files generated using RAXML for each nuclear intron and mtDNA and 6-nuclear intron partition. Please see the ReadME file for the full data package for further information

Bayesian tree files - Combinations-of-mtDNA+each intron in turn

Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more informatio