Data from: Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae)

Rix MG, Cooper SJB, Meusemann K, Klopfstein S, Harrison SE, Harvey MS, Austin AD

Date Published: February 2, 2017

DOI: http://dx.doi.org/10.5061/dryad.s1v34

 

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Title Supplementary File 1 - DNA orthologs Initial Assessment Subset
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Description Supplementary File 1. Concatenated alignment of nucleotide sequence data for the ‘initial assessment subset’ of 151 orthologous loci. See character set partitions at end of matrix for the gene-specific breakdown of putative orthologs. See Supplementary File 4 for taxon abbreviations.
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Title Supplementary File 2 - AA orthologs Initial Assessment Subset
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Description Supplementary File 2. Concatenated alignment of amino acid sequence data for the ‘initial assessment subset’ of 151 orthologous loci. See character set partitions at end of matrix for the gene-specific breakdown of putative orthologs. See Supplementary File 4 for taxon abbreviations.
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Title Supplementary File 3 - Comparison of phylogenetic informativeness measures
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Description Supplementary File 3. Comparison of phylogenetic informativeness measures across three epochs (deep = Epoch 3; taxonomy = Epoch 2; species = Epoch 1; see Fig. 2, Supplementary File 4), using the 'initial assessment' subset of 151 orthologous loci (Supplementary Files 1-2).
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Title Supplementary File 4 - PhyDesign Informativeness Quantitation IA Subset
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Description Supplementary File 4. Phylogenetic informativeness quantitation outputs from PhyDesign (López-Giráldez and Townsend, 2011) for nucleotide (Tab 1) and amino acid (Tab 2) data, using the ‘initial assessment’ subset of 151 orthologous loci (Supplementary Files 1-2). Loci are listed and ranked according to their per-site informativeness over three epochs (0-25 Ma; 25-160 Ma; 160-294.965 Ma); the top-10 ranked loci for each epoch are highlighted in red.
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Title Supplementary File 5 - Specimen & laboratory data
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Description Supplementary File 5. Collection and repository data for every specimen sequenced as part of this study, along with conditions for polymerase chain reaction (PCR) amplification of amplicons and GenBank accession numbers. F = forward primer; R = reverse primer; Ta = annealing temperate.
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Title Supplementary File 6 - Loci
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Description Supplementary File 6. Locus summaries for genes used in the final optimised 12-gene ‘FULL’ dataset (see Tables 1-2). Genes are organised according to their phylogenetic informativeness over three epochs (see Table 2, Supplementary File 3), followed by additional unranked nuclear loci from previous studies. Test taxa listed are those sequenced as part of Phase 6 (see Materials and Methods).
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Title Supplementary File 7 - FULL dataset MrBayes
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Description Supplementary File 7. Concatenated alignment of nucleotide sequence data for the final 12-gene 129-taxon (FULL) dataset, including Bayesian command block. See character set partitions at end of matrix for the gene- and partition-specific breakdowns.
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Title Supplementary File 8 - MAJORITY dataset MrBayes
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Description Supplementary File 8. Concatenated alignment of nucleotide sequence data for the reduced representation 12-gene 120-taxon (MAJORITY) dataset, including Bayesian command block. See character set partitions at end of matrix for the gene- and partition-specific breakdowns.
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Title Supplementary File 9 - BEAST_9 analysis
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Description Supplementary File 9. BEAST .xml input file used for analysis of the ‘BEAST_9’ dataset.
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Title Supplementary File 10 - BEAST_7 analysis
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Description Supplementary File 10. BEAST .xml input file used for analysis of the ‘BEAST_7’ dataset.
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Title Supplementary File 11 - FULL analysis MrBayes topology detail
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Description Supplementary File 11. Bayesian majority-rule consensus tree (presented as two parts) resulting from a partitioned phylogenetic analysis of the ‘FULL’ (12-gene) dataset (129 taxa; 9,601 bp; 20 million generations). Non-idiopid outgroups have been omitted for ease of presentation, and posterior probability values are > 0.98 unless otherwise stated. The type species of valid genera are shown in red, and the type species of junior generic synonyms are shown in dark blue; specimens of named species from their respective type localities are highlighted (#). The schematic summary phylogeny of Figure 5 is shown at left for comparison, and clades not recovered as presented in the Bayesian and/or likelihood analyses of the ‘MAJORITY’ dataset are highlighted (*).
Download Supplementary File 11 - FULL analysis MrBa....docx (444.7 Kb)
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Title Supplementary File 12 - Parsimony ancestral states
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Description Supplementary File 12. Mesquite input file of characters and the tree resulting from Bayesian analysis of the ‘FULL’ dataset, used for parsimony ancestral state reconstruction. Character coding is as follows: CHARACTER 1 (distribution): 0 = south-western Western Australia; 1 = arid zone; 2 = temperate south-eastern Australia; 3 = eastern Australia. CHARACTER 2 (phragmosis): 0 = unmodified abdomen; 1 = phragmotic abdominal morphology. CHARACTER 3 (burrow morphology): 0 = closed, with a hinged trapdoor lid; 1 = open burrow; 2 = semi-closed burrow, with a sock-like entrance.
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Title Supplementary File 13 - BEAST_7 tree for Cantuaria
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Description Supplementary File 13. Chronogram resulting from a fossil-calibrated BEAST analysis of the reduced-representation ‘BEAST_7’ dataset, showing New Zealand taxa in the genus Cantuaria. The time-scale highlights 35 Ma and the beginning of the Miocene at 23 Ma. See Supplementary File 5 for the identification of numbered taxa.
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Download Supplementary File 13 - BEAST_7 tree for C....docx (236.5 Kb)
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When using this data, please cite the original publication:

Rix MG, Cooper SJB, Meusemann K, Klopfstein S, Harrison SE, Harvey MS, Austin AD (2017) Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Molecular Phylogenetics and Evolution 109: 302–320. http://dx.doi.org/10.1016/j.ympev.2017.01.008

Additionally, please cite the Dryad data package:

Rix MG, Cooper SJB, Meusemann K, Klopfstein S, Harrison SE, Harvey MS, Austin AD (2017) Data from: Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.s1v34
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