William Humphreys

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

Publisher: Elsevier BV

Date: 11-2016

DOI: 10.1016/J.YMPEV.2016.07.026

Abstract: Groundwater calcrete aquifers of central Western Australia have been shown to contain a high ersity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an in idual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, we utilised alternative s ling techniques above the water table and uncovered a significant fauna of subterranean terrestrial oniscidean isopods from the calcretes. We explored the ersity 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 ergent 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 in idual 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.

Phylogenetic placement and description of Ngaliadessus humphreysi gen. et sp. nov., Watts & Villastrigo (Coleoptera: Dytiscidae), a subterranean diving beetle from the Ngalia Basin in centr

Publisher: Wiley

Date: 08-2023

DOI: 10.1111/AEN.12649

Abstract: The largest ersity in the world of subterranean ing beetles (Dytiscidae) has been discovered in underground waters of the Australian arid zone. The majority of species are from the Dytiscidae genera Limbodessus Guignot, 1939 (Bidessini) and Paroster Sharp, 1882 (Hydroporini) and are distributed within two major regions: calcrete islands of central Western Australia and the Ngalia Basin of the Northern Territory. Here, we use an integrative approach based on morphological and molecular analyses to describe Ngaliadessus humphreysi gen. et sp. nov. Watts & Villastrigo representing a new genus and species of stygobiotic Bidessini collected from a single well in the Ngalia Basin. Phylogenetic analyses using whole mitochondrial genome, Histone 3 and 18S rRNA data, representing a comprehensive coverage of Bidessini genera, support the distinction of the genus and species as a separate evolutionary lineage sister to the Australasian genus Limbodessus and the widely distributed genus Allodessus Guignot, 1953. Our study further confirms that the Ngalia Basin, containing 13 subterranean dytiscid species from four distinct genera, is one of the most speciose areas within the world's most erse hotspot of subterranean ing beetles.

Divergent molecular lineages and not-so-cryptic species: The first descriptions of stygobitic chiltoniid amphipods (Talitroidea: Chiltoniidae) from Western Australia

Publisher: Oxford University Press (OUP)

Date: 2012

DOI: 10.1163/193724012X626566

Identification of trophic niches of subterranean diving beetles in a calcrete aquifer by DNA and stable isotope analyses

Publisher: CSIRO Publishing

Date: 2014

DOI: 10.1071/MF12356

Abstract: The Yilgarn calcrete aquifers in Western Australia are an interesting system for investigating the process of speciation within subterranean habitats, because of the limited opportunities for dispersal between isolated calcretes. The presence of different-sized ing beetles (Dytiscidae) in separate calcretes, including sympatric sister-species pairs, suggests that species may have evolved within calcretes by an adaptive shift as a result of ecological-niche differentiation. We have studied the potential for trophic niche partitioning in a sister triplet of ing beetles, of distinctly different sizes, from a single aquifer. Fragments of the mitochondrial COI gene, specific to known species of hipods and copepods, were polymerase chain reaction- lified from each of the three beetle species, indicating that there is an overlap in their prey items. Significant differences were found in the detected diets of the three species, and results showed a propensity for prey preferences of hipods by the large beetles and one species of copepod for the small beetles. A terrestrial source of carbon to the calcrete was suggested by stable isotope analyses. The combined approach of molecular, stable isotope and behavioural studies have provided insight into the trophic ecology of this difficult-to-access environment, providing a framework for more fine-scale analyses of the diet of different-sized species to examine speciation underground.

North Atlantic forcing of millennial-scale Indo-Australian monsoon dynamics during the Last Glacial period

Publisher: Elsevier BV

Date: 07-2013

DOI: 10.1016/J.QUASCIREV.2013.04.012

Decoupling of monsoon activity across the northern and southern Indo-Pacific during the Late Glacial

Publisher: Elsevier BV

Date: 11-2017

DOI: 10.1016/J.QUASCIREV.2017.09.014

Evolutionary transition from surface to subterranean living in Australian water beetles (Coleoptera: Dytiscidae) through adaptive and relaxed selection

Publisher: Oxford University Press (OUP)

Date: 19-10-2023

DOI: 10.1093/BIOLINNEAN/BLAD142

Diversity patterns in Australia

Publisher: Elsevier

Date: 2012

DOI: 10.1016/B978-0-12-383832-2.00029-3

Blind scolopendrid centipedes of the genus

Publisher: CSIRO Publishing

Date: 14-11-2019

DOI: 10.1071/IS19015

Abstract: Only a single blind species is known in the centipede family Scolopendridae, representing the monotypic genus Tonkinodentus Schileyko, 1992, from Vietnam. All of more than 400 other species have four ocelli on each side of the cephalic plate. A complex of three new blind species of the genus Cormocephalus Newport, 1844, is described from the subterranean fauna of the central Pilbara region of Western Australia. Phylogenies based on sequence data for the barcode region of COI and a concatenated matrix that also includes 12S rRNA, 28S rRNA and ITS2 unite the blind Pilbara species as a monophyletic group, albeit with moderate bootstrap support, informally named the C. sagmus species group. Cormocephalus sagmus, C. pyropygus and C. delta spp. nov. supplement 17 epigean congeners previously described from Australia. The new species are all morphologically similar, but can be distinguished using the shape and spinulation of the ultimate leg prefemur. Two additional genetically distinct lineages were recovered that are not described, owing to the specimens being immature or lacking diagnostic morphological characters. The subterranean radiation in the Pilbara is more closely related to species from forests in the south-west of Western Australia than to congeners from the arid zone. rn:lsid:zoobank.org:pub:6F67FD31-A373-4DC5-A5FD-374D32DEE02C

Protecting the innocent: studying short-range endemic taxa enhances conservation outcomes

Publisher: CSIRO Publishing

Date: 2011

DOI: 10.1071/IS11011

Abstract: A major challenge confronting many contemporary systematists is how to integrate standard taxonomic research with conservation outcomes. With a bio ersity crisis looming and ongoing impediments to taxonomy, how can systematic research continue to document species and infer the ‘Tree of Life’, and still maintain its significance to conservation science and to protecting the very species it strives to understand? Here we advocate a systematic research program dedicated to documenting short-range endemic taxa, which are species with naturally small distributions and, by their very nature, most likely to be threatened by habitat loss, habitat degradation and climate change. This research can dovetail with the needs of industry and government to obtain high-quality data to inform the assessment of impacts of major development projects that affect landscapes and their biological heritage. We highlight how these projects are assessed using criteria mandated by Western Australian legislation and informed by guidance statements issued by the Environmental Protection Authority (Western Australia). To illustrate slightly different biological scenarios, we also provide three case studies from the Pilbara region of Western Australia, which include ex les demonstrating a rapid rise in the collection and documentation of erse and previously unknown subterranean and surface faunas, as well as how biological surveys can clarify the status of species thought to be rare or potentially threatened. We argue that ‘whole of biota’ surveys (that include all invertebrates) are rarely fundable and are logistically impossible, and that concentrated research on some of the most vulnerable elements in the landscape – short-range endemics, including troglofauna and stygofauna – can help to enhance conservation and research outcomes.

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

Publisher: CSIRO Publishing

Date: 2015

DOI: 10.1071/IS15010

Abstract: A significant ersity 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 s ling 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 s ling of southern hemisphere taxa.

Flank margin cave development and tectonic uplift, Cape Range, Australia

Publisher: National Speleological Society

Date: 2017

DOI: 10.4311/2015ES0142

DNA barcoding of stygofauna uncovers cryptic amphipod diversity in a calcrete aquifer in Western Australia's arid zone

Publisher: Wiley

Date: 16-12-2010

DOI: 10.1111/J.1755-0998.2009.02706.X

Abstract: The arid Yilgarn region of Western Australia contains numerous subterranean calcrete aquifers with unique assemblages of obligate groundwater invertebrates (stygofauna). We aimed to establish a DNA barcoding framework for the macro-invertebrates present in a single calcrete, as a basis for future assessment of bio ersity of the Yilgarn calcretes and for investigating food webs. Intense s ling of a bore field grid in the Sturt Meadows calcrete was undertaken to obtain representatives of the entire macro-invertebrate ecosystem. A 623-bp fragment of the mitochondrial cytochrome c oxidase 1 (COI) gene was used to provide DNA barcodes for stygobiont macro-invertebrates plus terrestrial organisms that are found in the calcrete. Phylogenetic analyses revealed the existence of 12 ergent monophyletic groups of haplotypes. Subterranean hipods (Chiltoniidae) showed three groups of COI haplotypes with sequence ergences between them of >11%. Allozyme analyses found a large number of fixed allelic differences between these three hipod groups, indicating that there are three morphologically cryptic species within the Sturt Meadows calcrete. Unlike the sister triplet of dytiscid beetles present, the hipods are not sister clades and are more closely related to other Yilgarn and non-Yilgarn hipods than to each other. Our results show that the aquifer contains at least 12 macro-invertebrate species and DNA barcoding provides a useful means for discriminating species in this system.

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)

Publisher: Magnolia Press

Date: 16-03-2017

DOI: 10.11646/ZOOTAXA.4243.3.1

Abstract: The oniscidean fauna of Australia is generally poorly known but recent s ling 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 ergences). 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.

The ecology and distribution of groundwater fauna in a calcrete aquifer: does sampling alter the story?

Publisher: CSIRO Publishing

Date: 2008

DOI: 10.1071/IS07058

Abstract: There has been an increase in the number of studies examining the spatial and temporal patterns in species richness, community structure and population dynamics of groundwater organisms. These studies have raised the issue of uncertainty about the comparability of different s ling methods, and questions of whether s ling bias may exist. Recently, a erse subterranean fauna was discovered in calcrete (carbonate) aquifers of the Yilgarn Region of central Western Australia. Little is known about the community structure and population dynamics in these aquifers. One important issue is whether current s ling methods adequately s le the species richness and abundance of the fauna to allow for comparative studies. Here we investigate the effectiveness of three s ling methods: haul net s ling, pumping with a 12-V impeller pump, and a discrete interval s ler. The methods were trialled over 16 months with s les taken from 55 uncased bore holes. No significant taxonomic bias was detected across the s ling methods. However, s ling using a haul net was found to be the most efficient method for capturing the available taxa per unit time when s ling bores are less than 10 m deep, with pumping being the least efficient. These results are discussed in relation to the problems of studying stygofauna in Western Australian calcrete aquifers, and of groundwater faunas more generally.

The critical thermal maximum of diving beetles (Coleoptera: Dytiscidae): a comparison of subterranean and surface-dwelling species

Publisher: Elsevier BV

Date: 2021

DOI: 10.1016/J.CRIS.2021.100019

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

Publisher: Springer Science and Business Media LLC

Date: 03-04-2013

DOI: 10.1038/HDY.2013.22

Differential transcriptomic responses to heat stress in surface and subterranean diving beetles

Publisher: Cold Spring Harbor Laboratory

Date: 13-12-2021

DOI: 10.1101/2021.12.12.470823

Abstract: Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CT max 38°C cf . 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 in iduals to demonstrate that both species can mount a heat shock response at high temperatures (35°C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.

The evolution of epigean and stygobitic species of Koonunga Sayce, 1907 (Syncarida: Anaspidaceae) in Southern Australia, with the description of three new species.

Publisher: Public Library of Science (PLoS)

Date: 26-08-2015

DOI: 10.1371/JOURNAL.PONE.0134673

Ten new species of the genus Brevisomabathynella Cho, Park and Ranga Reddy, 2006 (Malacostraca, Bathynellacea, Parabathynellidae) from Western Australia

Publisher: Informa UK Limited

Date: 31-03-2010

DOI: 10.1080/00222930903537066

What lies beneath: Molecular phylogenetics and ancestral state reconstruction of the ancient subterranean Australian Parabathynellidae (Syncarida, Crustacea)

Publisher: Elsevier BV

Date: 07-2012

DOI: 10.1016/J.YMPEV.2012.03.010

Abstract: The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species ersity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated, suggesting that caution needs to be shown when using these characters for elucidating phylogenetic relationships, particularly when there are few morphological characters available for reconstructing relationships. The ancestral state analysis contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive.

Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm

Publisher: Wiley

Date: 10-09-2022

DOI: 10.1111/FWB.13987

Abstract: Coastal aquifers are vital water sources for humanity. Their quality and the ecosystem services they provide depend on the integrity of their subterranean biota. However, current anthropogenic impacts such as climate change effects and coastal population growth place enormous pressure on the sustainability of these environments. Despite the significance of subterranean biota to ecosystem function and the delivery of ecosystem services, stygofauna—groundwater‐dwelling aquatic animals—have until recently been largely ignored in aquifer monitoring and management. This issue is of importance in both coastal and inland zones. Common threats in inland and coastal areas are water extraction, reduced recharge caused by aridification, and pollution, while, in coastal zones, additional complications arise from sea‐level change and salt water ingress. This review examines stygofaunal ersity, impacts, and future conservation challenges in coastal aquifers. Focussing on Australia, we provide a summary of the available data on stygofaunal communities and distributions identify and describe potential threats to these communities across the erse coastal regions of the continent and propose future research priorities with the goal of facilitating the long‐term preservation of these ecosystems on the Australian continent. While we focus this review on Australia, the threats and management issues discussed are relevant globally. Recent subterranean studies in Australia have been primarily undertaken in inland areas, and while coastal data exist, ecological assessment of coastal subterranean ecosystems is incomplete, compromising the efficacy of conservation plans. This review indicates that the Australian continent hosts five major coastal stygofaunal bio ersity areas characterised by heterogeneous community assemblages, involving a total of 17 taxonomic groups spanning microscopic aquatic invertebrates to vertebrates. The most relevant impacts and threats identified were aquifer size reduction, intrusion of seawater, land clearing, contamination, and mining. Given the projections of increasing coastal development and subsequent loss or degradation of habitat during coming decades, it is important to improve our limited understanding of the ecology of coastal aquifers. Future research should include the refinement of biological assessment tools for coastal systems, functional and ecotoxicological studies, and faunal surveys of urban coastal aquifers. The recommendations and guidelines outlined in this review are applicable globally and provide a further step toward the sustainable use of coastal groundwater resources and the maintenance of healthy groundwater ecosystems.

‘Anchialine’ redefined as a subterranean estuary in a crevicular or cavernous geological setting

Publisher: Oxford University Press (OUP)

Date: 15-06-2015

DOI: 10.1163/1937240X-00002335

Phylogenetic analysis and systematic revision of Remipedia (Nectiopoda) from Bayesian analysis of molecular data

Publisher: Oxford University Press (OUP)

Date: 2013

DOI: 10.1163/1937240X-00002179

Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/ZO18008

Abstract: Australia was once thought to be a bio ersity desert when considering the subterranean world however, recent work has revealed a fascinating collection of cave creatures, many with surprising biogeographic histories. This has especially been so in the karstic regions of north-western Australia (Cape Range peninsula, Barrow Island, Pilbara), which is home not only to a erse collection of subterranean invertebrates, but also to the continent’s only known underworld-adapted vertebrates, which includes the cave fish in the genus Milyeringa. These cave gudgeons have recently been in a state of taxonomic flux, with species being both split and lumped, but this was done with limited data (incomplete geographic s ling and no nuclear DNA sequence data). Therefore, we have revisited the systematic status of Milyeringa in a total-evidence molecular approach by integrating all existing data (mitochondrial, allozymes) with new DNA sequences from nuclear and mitochondrial loci and new multilocus allozyme data. Our conclusion, that there are two species, matches the most recent taxonomic treatment, with Milyeringa veritas present on both the eastern and western sides of the Cape Range peninsula, and Milyeringa justitia on Barrow Island. This has implications for future research in the linked fields of biogeography and conservation.

Fine-scale comparative phylogeography of a sympatric sister species triplet of subterranean diving beetles from a single calcrete aquifer in Western Australia

Publisher: Wiley

Date: 20-08-2009

DOI: 10.1111/J.1365-294X.2009.04296.X

New populations of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout north-western Australia

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/MF18006

Abstract: The enigmatic blind cave eel Ophisternon candidum is one of Australia’s least known fishes and is one of only three vertebrates in Australia with an entirely subterranean existence. For more than half a century, O. candidum was thought to be restricted to some 100km of coastal cave systems in north-western Australia. Herein we report on two new populations, each separated by hundreds of kilometres, and provide the first complete list of all known records of subterranean Ophisternon in Western Australia. Using morphological and molecular data, we show that these populations are conspecific, with one population showing evidence of genetic differentiation. Geological and biogeographic explanations are explored, along with conservation considerations. All populations face actual and potential threats, especially from mining activities, and there is a need for management and conservation strategies specific to each population.

Too hot to handle: Cenozoic aridification drives multiple independent incursions of Schizomida (Hubbardiidae) into hypogean environments

Publisher: Elsevier BV

Date: 10-2019

DOI: 10.1016/J.YMPEV.2019.106532

Abstract: The formation of the Australian arid zone, Australia's largest and youngest major biome, has been recognized as a major driver of rapid evolutionary radiations in terrestrial plants and animals. Here, we investigate the phylogenetic ersity and evolutionary history of subterranean short-tailed whip scorpions (Schizomida: Hubbardiidae), which are a significant faunal component of Western Australian hypogean ecosystems. We sequenced two mitochondrial (12S, COI) and three nuclear DNA markers (18S, 28S, ITS2) from ∼600 specimens, largely from the genera Draculoides and Paradraculoides, including 20 previously named species and an additional 56 newly identified operational taxonomic units (OTUs). Phylogenetic analyses revealed a large and rapid species radiation congruent with Cenozoic aridification of the continent, in addition to the identification of a new genus in Western Australia and the first epigean schizomid from the Pilbara. Here, we also synonymise Paradraculoides with Draculoides (new synonymy), due to paraphyly and a lack of reliable characters to define the two genera. Our results are consistent with multiple colonisations of the subterranean realm from epigean ancestors as their forest habitat fragmented and retracted, with ongoing fragmentation and ersification of lineages underground. These findings illustrate the remarkable ersity and high incidence of short-range endemism of Western Australia's subterranean fauna, which has important implications for identifying and managing short-range endemic subterranean fauna. They also highlight the advantages of including molecular data in subterranean fauna surveys as all specimens can be utilized, regardless of sex and life stage. Additionally, we have provided the first multi-gene phylogenetic framework for Australian schizomids, which will enable researchers and environmental consultants to identify new taxa or align them to existing lineages.

Phylogeography of the ancient Parabathynellidae (Crustacea: Bathynellacea) from the Yilgarn region of Western Australia

Publisher: CSIRO Publishing

Date: 2008

DOI: 10.1071/IS07040

Abstract: The crustacean order Bathynellacea is a primitive group of subterranean aquatic (stygobitic) invertebrates that typically inhabits freshwater interstitial spaces in alluvia. A striking ersity of species from the bathynellacean family Parabathynellidae have been found in the calcretes of the Yilgarn palaeodrainage system in Western Australia. Taxonomic studies show that most species are restricted in their distribution to a single calcrete, which is consistent with the findings of other phylogeographic studies of stygofauna. In this, the first molecular phylogenetic and phylogeographic study of interspecific relationships among parabathynellids, we aimed to explore the hypothesis that species are short-range endemics and restricted to single calcretes, and to investigate whether there were previously unidentified cryptic species. Analyses of sequence data based on a region of the mitochondrial (mt) DNA cytochrome c oxidase 1 gene showed the existence of ergent mtDNA lineages and species restricted in their distribution to a single calcrete, in support of the broader hypothesis that these calcretes are equivalent to closed island habitats comprising endemic taxa. Divergent mtDNA lineages were also observed to comprise four new and 12 recognised morphospecies. These results reflect the findings of previous studies of stygobitic arthropods (beetles, hipods and isopods) from the Yilgarn region and reinforce the usefulness of using DNA-sequence data to investigate species boundaries and the presence of cryptic species.

Ontogeny of an anchialine ostracod from Western Australia and comments on the origin and distribution of Halocyprididae

Publisher: Brill

Date: 2010

DOI: 10.1163/001121610X498872

Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps

Publisher: Springer Science and Business Media LLC

Date: 06-06-2017

DOI: 10.1038/S41598-017-03107-Y

Abstract: Cave shrimps from the genera Typhlatya , Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and ergence (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp ergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.

Community extinction: the groundwater (stygo-)fauna of Curaçao, Netherlands Antilles

Publisher: Springer Science and Business Media LLC

Date: 05-10-2022

DOI: 10.1007/S10750-022-05032-2

Abstract: The research aimed to recollect specimens from Curaçao of the genus Halosbaena belonging to the rare crustacean order Thermosbaenacea, a genus with a relictual Tethyan distribution. It resulted in recording the apparent extinction of the entire, species-rich, subterranean fauna on the island that had occurred within a period of 43 years up to 2015. The composition of the groundwater fauna on Curaçao was s led in 2015 for comparison with s ling undertake 43 years previously. Despite using the same s ling methods previously used and comprehensive coverage of the available s ling sites, no stygofauna specimen was collected from s ling in 2015 in contrast to more than 50 species collected from the initial s ling in 1973. It is hypothesised that this faunal extinction was associated with the oil industry, but it is unclear whether it resulted from petroleum pollution of groundwater drawdown or recharge. This record of the extinction of an entire ecosystem, rather than merely some members of it, is perhaps unique, but is concerning amongst the more diffuse extinction events happening globally.

Evidence for population fragmentation within a subterranean aquatic habitat in the Western Australian desert

Publisher: Springer Science and Business Media LLC

Date: 23-02-2011

DOI: 10.1038/HDY.2011.6

Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches.

Publisher: The Royal Society

Date: 2015

DOI: 10.1098/RSOS.140386

Abstract: The regressive evolution of eyes has long intrigued biologists yet the genetic underpinnings remain opaque. A system of discrete aquifers in arid Australia provides a powerful comparative means to explore trait regression at the genomic level. Multiple surface ancestors from two tribes of ing beetles (Dytiscidae) repeatedly invaded these calcrete aquifers and convergently evolved eye-less phenotypes. We use this system to assess transcription of opsin photoreceptor genes among the transcriptomes of two surface and three subterranean dytiscid species and test whether these genes have evolved under neutral predictions. Transcripts for UV , long-wavelength and ciliary-type opsins were identified from the surface beetle transcriptomes. Two subterranean beetles showed parallel loss of all opsin transcription, as expected under ‘neutral’ regressive evolution. The third species Limbodessus palmulaoides retained transcription of a long-wavelength opsin ( lwop ) orthologue, albeit in an aphotic environment. Tests of selection on lwop indicated no significant differences between transcripts derived from surface and subterranean habitats, with strong evidence for purifying selection acting on L. palmulaoides lwop . Retention of sequence integrity and the lack of evidence for neutral evolution raise the question of whether we have identified a novel pleiotropic role for lwop , or an incipient phase of pseudogene development.

How blind are they? Phototactic responses in stygobiont diving beetles (Coleoptera: Dytiscidae) from calcrete aquifers of Western Australia

Publisher: Wiley

Date: 22-02-2018

DOI: 10.1111/AEN.12330

University Of Western Australia

Location: Australia

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Linkage Projects - Grant ID: LP0561563

Start Date: 07-2005

End Date: 11-2008

Amount: $342,977.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0776478

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End Date: 12-2010

Amount: $257,442.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0663675

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End Date: 12-2008

Amount: $195,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP120102132

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End Date: 02-2016

Amount: $240,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100508

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End Date: 06-2016

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Funder: Australian Research Council

Linkage Projects - Grant ID: LP0348753

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End Date: 12-2008

Amount: $228,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP140100555

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End Date: 12-2018

Amount: $340,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP180103851

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End Date: 12-2023

Amount: $316,745.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP100200494

Start Date: 10-2010

End Date: 12-2013

Amount: $320,000.00

Funder: Australian Research Council

Special Research Initiatives - Grant ID: SR0354817

Start Date: 2004

End Date: 12-2004

Amount: $10,000.00

Funder: Australian Research Council