Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)

Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies

Molecular phylogenetic analyses reveal a new southern hemisphere oniscidean family (Crustacea : Isopoda) with a unique water transport system

A significant diversity of terrestrial oniscidean isopods was recently discovered in the subterranean ‘calcrete islands’ of Western Australia, but the species and higher-level systematic status of much of the fauna are currently uncertain. Here we focus on one group of species that was initially assigned to the genus Trichorhina (Platyarthridae), based on several shared characters, and investigate the phylogenetic relationships of these species to 21 oniscidean genera, including 13 known families, using 18S rDNA sequence data. We then present phylogenetic analyses using 28S-only and combined 18S, 28S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) data for a more restricted sampling of taxa, and present results for a detailed morphological study of the antennae and other cephalic structures of exemplar taxa. Bayesian and maximum likelihood analyses of the extended 18S-only, the 28S-only and multi-gene datasets provide strong evidence for a distinct well-supported monophyletic group comprising the new Western Australian and one South American taxon. This clade is unrelated to all included members of Platyarthridae, which appears to be polyphyletic, and it forms a distinct group relative to other oniscidean families. Given these findings and the results of the morphological study, a new southern hemisphere oniscidean family, Paraplatyarthridae Javidkar & King, fam. nov. is erected based on Paraplatyarthrus subterraneus Javidkar & King, gen. & sp. nov. (type genus and species), and several undescribed taxa which occur in the arid (terrestrial and subterranean) regions of Western Australia and subtropical South America. Paraplatyarthridae is distinguishable from all other oniscidian families on a combination of character states including, among others, the presence of fan-like scale setae on the dorsal body, and the ventral second antenna with leaf-like scale setae and a furrow containing elongated hair-like capillary setae that form part of a water conducting system unique within Oniscidea. This study has important implications for the higher-level classification of oniscidean crustaceans and points to the need for a more detailed molecular phylogeny that includes a comprehensive sampling of southern hemisphere taxa.Mohammad Javidkar, Steven J. B. Cooper, Rachael A. King, William F. Humphreys and Andrew D. Austi

Biogeographic history of subterranean isopods from groundwater calcrete islands in Western Australia

Groundwater calcretes in arid central Western Australia contain a diverse invertebrate groundwater fauna (stygofauna). Surveys have uncovered a diverse oniscidean isopod subterranean fauna above the water table (troglofauna), including species of a recently described genus Paraplatyarthrus. The aim of this study was to investigate the biogeographic history of Paraplatyarthrus and the timing of transitions from surface to subterranean habitats. Phylogenetic relationships among the isopod troglofauna from 11 groundwater calcretes along three palaeodrainage systems were assessed using one mitochondrial gene, cytochrome c oxidase subunit 1 (COI), and two nuclear markers, lysyl-tRNA synthetase (LysRS) and 18S rRNA (18S) genes. Phylogenetic analyses revealed multiple sister lineage relationships between troglophile and troglobite lineages and evidence for divergent mtDNA lineages within species, providing a range of nodes for dating evolutionary transitions from surface to subterranean habitats. Relaxed molecular clock analyses provided evidence that evolutionary transitions from surface to subterranean environments took place between 13.3 and 1.75 million years ago, coinciding with the onset of aridification of Australia from the late Tertiary. In cases where groundwater calcretes contained multiple species, the taxa were not closely related phylogenetically, suggesting that these calcretes were independently colonised by multiple ancestral species. The study further confirmed the role of late/post-Miocene aridification as a key driver of the evolution of subterranean invertebrates in the calcrete islands of Western Australia, supporting the climatic relict hypothesis. Troglobites most likely evolved from the troglophile ancestors that were capable of dispersal among, and active colonisation of, calcretes.Mohammad Javidkar, Steven J.B. Cooper, William F. Humphreys, Rachael A. King, Simon Judd, Andrew D. Austi

Taxonomy of Paraplatyarthrus Javidkar and King (Isopoda: Oniscidea: Paraplatyarthridae) with description of five new species from Western Australia, and comments on Australian Trichorhina Budde-Lunde, 1908 (Platyarthridae)

The oniscidean fauna of Australia is generally poorly known but recent sampling has revealed a new family, Paraplatyarthridae, found in both terrestrial and groundwater calcretes of central Western Australia. The family was initially described based on a new genus and species, Paraplatyarthrus subterraneus Javidkar and King, 2015. Here we describe an additional five Paraplatyarthrus species from the Yilgarn region of Western Australia, based on both morphological and molecular evidence (COI divergences). Four species are subterranean: P. crebesconiscus Javidkar and King sp. nov., P. cunyuensis Javidkar and King sp. nov., P. occidentoniscus Javidkar and King sp. nov., and P. pallidus Javidkar and King sp. nov., and one is a surface species, P. nahidae Javidkar and King sp. nov. A key to their identification is provided along with information on their distribution. In addition, type material of the two described Australian species of Platyarthridae, Trichorhina australiensis Wahrberg, 1922 from Western Australia and T. tropicalis Lewis, 1998 from Queensland, are examined. Morphological reassessment of type material shows T. australiensis belongs to Paraplatyarthrus (comb. nov.) and that T. tropicalis is correctly placed in Trichorhina, confirming that the genus and family Platyarthridae occur in Australia.Mohammad Javidkar, Rachael A. King, Steven J. B. Cooper, William F. Humphreys, Andrew D. Austi