DOI: 10.5061/dryad.s1v34
title: Data from: Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae)

description: The formation and spread of the Australian arid zone during the Neogene
 was a profoundly transformative event in the biogeographic history of
 Australia, resulting in extinction or range contraction in lineages
 adapted to mesic habitats, as well as diversification and range expansion
 in arid-adapted taxa (most of which evolved from mesic ancestors).
 However, the geographic origins of the arid zone biota are still
 relatively poorly understood, especially among highly diverse invertebrate
 lineages, many of which are themselves poorly documented at the species
 level. Spiny trapdoor spiders (Idiopidae: Arbanitinae) are one such
 lineage, having mesic ‘on-the-continent’ Gondwanan origins, while also
 having experienced major arid zone radiations in select clades. In this
 study, we present new orthologous nuclear markers for the phylogenetic
 inference of mygalomorph spiders, and use them to infer the phylogeny of
 Australasian Idiopidae with a 12-gene parallel tagged amplicon
 next-generation sequencing approach. We use these data to test the mode
 and timing of diversification of arid-adapted idiopid lineages across
 mainland Australia, and employ a continent-wide sampling of the fauna’s
 phylogenetic and geographic diversity to facilitate ancestral area
 inference. We further explore the evolution of phenotypic and behavioural
 characters associated with both arid and mesic environments, and test an
 ‘out of south-western Australia’ hypothesis for the origin of arid zone
 clades. Three lineages of Idiopidae are shown to have diversified in the
 arid zone during the Miocene, one (genus Euoplos) exclusively in Western
 Australia. Arid zone Blakistonia likely had their origins in South
 Australia, whereas in the most widespread genus Aganippe, a more complex
 scenario is evident, with likely range expansion from southern Western
 Australia to southern South Australia, from where the bulk of the arid
 zone fauna then originated. In Aganippe, remarkable adaptations to
 phragmotic burrow-plugging in transitional arid zone taxa have evolved
 twice independently in Western Australia, while in Misgolas and Cataxia,
 burrow door-building behaviours have likely been independently lost at
 least three times in the eastern Australian mesic zone. We also show that
 the presence of idiopids in New Zealand (Cantuaria) is likely to be the
 result of recent dispersal from Australia, rather than ancient continental
 vicariance. By providing the first comprehensive, continental synopsis of
 arid zone biogeography in an Australian arachnid lineage, we show that the
 diversification of arbanitine Idiopidae was intimately associated with
 climate shifts during the Neogene, resulting in multiple Mio-Pliocene
 radiations.
description: Supplementary File 1 -
 DNA orthologs Initial Assessment SubsetSupplementary 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.Supplementary File 2 -
 AA orthologs Initial Assessment SubsetSupplementary 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.Supplementary File 3 -
 Comparison of phylogenetic informativeness measuresSupplementary 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).Supplementary File 4 -
 PhyDesign Informativeness Quantitation IA SubsetSupplementary 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.Supplementary File 5 -
 Specimen & laboratory dataSupplementary 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.Supplementary File 6 -
 LociSupplementary 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).Supplementary File 7 -
 FULL dataset MrBayesSupplementary 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.Supplementary File 8 -
 MAJORITY dataset MrBayesSupplementary 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.Supplementary File 9 -
 BEAST_9 analysisSupplementary File 9.
 BEAST .xml input file used for analysis of the ‘BEAST_9’
 dataset.Supplementary File 10 -
 BEAST_7 analysisSupplementary File 10.
 BEAST .xml input file used for analysis of the ‘BEAST_7’
 dataset.Supplementary File 11 -
 FULL analysis MrBayes topology detailSupplementary 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 &gt; 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 (*).Supplementary File 12 -
 Parsimony ancestral statesSupplementary 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.Supplementary File 13 -
 BEAST_7 tree for CantuariaSupplementary 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.