Evolution of endoglucanase genes in subterranean and surface isopod crustaceans from Central Western Australia.

Recent studies have identified a significant number of endogenous cellulase genes in various arthropods, including isopods, allowing them to process hydrocarbons efficiently as a food source. While this research has provided insight into underlying gene-level processes in cellulose decomposition by arthropods, little is known about the existence and expression of cellulase genes in species from cave environments where carbohydrates are sparse. To investigate whether endogenous cellulase genes are maintained in subterranean species, we sequenced the transcriptomes of two subterranean paraplatyarthrid isopod species from calcrete (carbonate) aquifers of central Western Australia and a related surface isopod species. Seven protein-coding open-reading frames associated with endoglucanase genes were identified in all species. Orthology inference analyses, using a wide range of cellulase sequences from available databases, supported the endogenous origin of the putative endoglucanase genes. Selection analyses revealed that these genes are primarily subject to purifying selection in most of the sites for both surface and subterranean isopod species, indicating that they are likely to encode functional peptides. Furthermore, evolutionary branch models supported the hypothesis of an adaptive shift in selective pressure acting on the subterranean lineages compared with the ancestral lineage and surface species. Branch-site models also revealed a few amino acid sites on the subterranean branches to be under positive selection, suggesting the acquisition of novel adaptations to the subterranean environments. These findings also imply that hydrocarbons exist in subsurface aquifers, albeit at reduced levels, and have been utilized by subterranean isopods as a source of energy for millions of years.

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 (<100 bp) and longer (>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.

Pleistocene climate fluctuations as the major driver of genetic diversity and distribution patterns of the Caspian green lizard, Lacerta strigata Eichwald, 1831.

Green lizards of the genus Lacerta have served as excellent models for studying the impact of Pleistocene climatic oscillations on genetic structures. The Caspian green lizard, Lacerta strigata, occupies various habitats across the Caucasus and the South Caspian Sea, with the Hyrcanian Forests and north of the Alborz Mountains forming the core of the range. This study aimed to re-examine the phylogenetic relationships of L. strigata with other congeneric members and to assess the genetic structure and historical demography of the species. Furthermore, Species Distribution Models (SDMs) were performed to infer the species' potential habitat suitability and were then projected on climate scenarios reflecting current and past (6 ky and 21 ky before present) conditions. A total of 39 individuals collected from most of the distribution range, together with additional lacertid species sequences from the GenBank database, were examined using mtDNA (Cyt b and 12S ribosomal RNA) and nuclear (C-mos and ß-fibrinogen) sequence data. Based on the phylogenetic analyses, L. strigata was found to be a sister taxon to all other members of the genus. The species included two main clades (regional western and eastern) that diverged in a period between the Early and Middle Pleistocene. Based on the BBM and S-Diva analyses, both dispersal and vicariance events explained the phylogeographic structure of the species in the Hyrcanian Forests. The historical demographic analyses using Bayesian skyline plots showed a mild increase in the effective population size from about 120 Kya for the western regional clade. According to phylogeographic structures and SDMs evidence, as in other species within the region, it appears that the south of the Caspian Sea (Hyrcanian Forests), and the Alborz Mountains acted as multiple refugia during cold periods and promoted expansion outwards amid the warm periods. Overall, the results provided evidence that the genetic structure of the species has been influenced by the Pleistocene climatic fluctuations.

Dispersal beyond geographic barriers: a contribution to the phylogeny and demographic history of Pristurus rupestris Blanford, 1874 (Squamata: Sphaerodactylidae) from southern Iran.

Pristurus rupestris is a member of Semaphore geckos with a wide distribution range. Recently, 14 candidate species of P. rupestris rupestris have been identified in the Hajar Mountains (Arabia), yet the knowledge on the Iranian counterparts is limited. The present study elucidates the phylogenetic position of the Iranian P. rupestris and investigates the hypothesis on its historical colonization from Oman to Iran and the associated islands. Therefore, 20 Iranian specimens along with 115 individuals from Oman were examined using two mitochondrial genes including the Cytochrome b and the 12S ribosomal RNA. The molecular phylogenetic analyses revealed that the individuals collected from Iran are well nested within the candidate Species 3 of P. r. rupestris, demonstrating a single population with high gene flow. Additionally, the molecular analyses showed that the genetic diversity within the Iranian Blanford's Semaphore geckos is low and that the candidate Species 3 experienced a recent expansion approximately 17 thousand years ago (Kya). The historical demographic analyses (BSP) showed a mild increase in the effective population size between 15-20 Kya. These time estimations coincide with the Last Glacial Maximum, when the Persian Gulf was almost dry, reinforcing the hypothesis that the species might have colonized southern Iran from Oman through the Persian Gulf. In addition, we propose P. r. iranicus to be synonymized with P. r. rupestris.

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.

Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia.

Groundwater calcrete aquifers of central Western Australia have been shown to contain a high diversity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an individual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, we utilised alternative sampling techniques above the water table and uncovered a significant fauna of subterranean terrestrial oniscidean isopods from the calcretes. We explored the diversity and evolution of this fauna using molecular analyses based on one mitochondrial gene, Cytochrome C Oxidase Subunit I (COI), two Ribosomal RNA genes (28S and 18S), and one protein coding nuclear gene, Lysyl-tRNA Synthetase (LysRS). The results from 12 calcretes showed the existence of 36 divergent DNA lineages belonging to four oniscidean families (Paraplatyarthridae, Armadillidae, Stenoniscidae and Philosciidae). Using a combination of phylogenetic and species delimitation methods, we hypothesized the occurrence of at least 27 putative new species of subterranean oniscideans, of which 24 taxa appeared to be restricted to an individual calcrete, lending further support to the "subterranean island hypothesis". Three paraplatyarthrid species were present on adjacent calcretes and these exceptions possessed more ommatidia and body pigments compared with the calcrete-restricted taxa, and are likely to represent troglophiles. The occurrence of stenoniscid isopods in the calcretes of central Western Australia, a group previously only known from the marine littoral zone, suggests a link to the marine inundation of the Eucla basin during the Late Eocene. The current oniscidean subterranean fauna consists of groups known to be subtropical, littoral and benthic, reflecting different historical events that have shaped the evolution of the fauna in the calcretes.