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Bradford T.M.,CSIRO | Bradford T.M.,University of Adelaide | Adams M.,University of Adelaide | Adams M.,South Australian Museum | And 7 more authors.
Heredity | Year: 2013

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km 2 region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete. © 2013 Macmillan Publishers Limited All rights reserved.


Guzik M.T.,University of Adelaide | Austin A.D.,South Australian Museum | Cooper S.J.B.,University of Adelaide | Cooper S.J.B.,South Australian Museum | And 10 more authors.
Invertebrate Systematics | Year: 2010

Australia was historically considered a poor prospect for subterranean fauna but, in reality, the continent holds a great variety of subterranean habitats, with associated faunas, found both in karst and non-karst environments. This paper critically examines the diversity of subterranean fauna in several key regions for the mostly arid western half of Australia. We aimed to document levels of species richness for major taxon groups and examine the degree of uniqueness of the fauna. We also wanted to compare the composition of these ecosystems, and their origins, with other regions of subterranean diversity world-wide. Using information on the number of 'described' and 'known' invertebrate species (recognised based on morphological and/or molecular data), we predict that the total subterranean fauna for the western half of the continent is 4140 species, of which ∼10% is described and 9% is 'known' but not yet described. The stygofauna, water beetles, ostracods and copepods have the largest number of described species, while arachnids dominate the described troglofauna. Conversely, copepods, water beetles and isopods are the poorest known groups with less than 20% described species, while hexapods (comprising mostly Collembola, Coleoptera, Blattodea and Hemiptera) are the least known of the troglofauna. Compared with other regions of the world, we consider the Australian subterranean fauna to be unique in its diversity compared with the northern hemisphere for three key reasons: the range and diversity of subterranean habitats is both extensive and novel; direct faunal links to ancient Pangaea and Gondwana are evident, emphasising their early biogeographic history; and Miocene aridification, rather than Pleistocene post-ice age driven diversification events (as is predicted in the northern hemisphere), are likely to have dominated Australia's subterranean speciation explosion. Finally, we predict that the geologically younger, although more poorly studied, eastern half of the Australian continent is unlikely to be as diverse as the western half, except for stygofauna in porous media. Furthermore, based on similar geology, palaeogeography and tectonic history to that seen in the western parts of Australia, southern Africa, parts of South America and India may also yield similar subterranean biodiversity to that described here. © CSIRO.


Bradford T.,University of Adelaide | Adams M.,South Australian Museum | Humphreys W.F.,Collections and Research Center | Austin A.D.,University of Adelaide | And 2 more authors.
Molecular Ecology Resources | Year: 2010

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 biodiversity of the Yilgarn calcretes and for investigating food webs. Intense sampling 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 divergent monophyletic groups of haplotypes. Subterranean amphipods (Chiltoniidae) showed three groups of COI haplotypes with sequence divergences between them of >11%. Allozyme analyses found a large number of fixed allelic differences between these three amphipod groups, indicating that there are three morphologically cryptic species within the Sturt Meadows calcrete. Unlike the sister triplet of dytiscid beetles present, the amphipods are not sister clades and are more closely related to other Yilgarn and non-Yilgarn amphipods 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. © 2009 Blackwell Publishing Ltd.


Bradford T.M.,CSIRO | Bradford T.M.,University of Adelaide | Humphreys W.F.,University of Adelaide | Humphreys W.F.,South Australian Museum | And 4 more authors.
Marine and Freshwater Research | Year: 2014

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 diving 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 diving beetles, of distinctly different sizes, from a single aquifer. Fragments of the mitochondrial COI gene, specific to known species of amphipods and copepods, were polymerase chain reaction-amplified 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 amphipods 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. © 2014 CSIRO .


Humphreys W.F.,Collections and Research Center | Humphreys W.F.,University of Adelaide | Humphreys W.F.,University of Western Australia | Bishop R.E.,Pennsylvania State University | And 9 more authors.
Journal of Crustacean Biology | Year: 2015

An improved understanding of the anchialine ecosystem and geology warrants a redefinition of the term 'anchialine. Originating from subareal biological observations, the term anchialine now encompasses chemical, physical, geological and biological elements within the subterranean realm. We propose a more accurate definition of the term anchialine as a tidally-influenced subterranean estuary located within crevicular and cavernous karst and volcanic terrains that extends inland to the limit of seawater penetration. This subterranean estuary is characterized by sharp physical and chemical stratification and merges with a marine system at the coast and a groundwater system inland. The anchialine ecosystem supports a relatively diverse biotic assemblage of stygobiotic species of marine origin dominated by members of Crustacea, both numerically and by species richness. © 2015 by The Crustacean Society.


Kornicker L.S.,Smithsonian Institution | Humphreys W.F.,Collections and Research Center | Humphreys W.F.,University of Western Australia | Humphreys W.F.,University of Adelaide | And 2 more authors.
Crustaceana | Year: 2010

Juvenile instars II, IV, and V of the anchialine halocyprid ostracod Danielopolina kornickeri Danielopol, Baltanas & Humphreys, 2000 (Thaumatocyprididae) are described and illustrated. In addition, a supplementary description of the adult male is presented. Specimens had been collected in Bundera Sinkhole, the type locality of the species in Western Australia. Also, juvenile instars I and II of the deep-sea species Thaumatoconcha radiata Kornicker & Sohn, 1976, which is in the same family as members of the genus Danielopolina, are described and illustrated. It is tentatively concluded that during its ontogeny, D. kornickeri has 6 growth stages; morphological characters useful in identifying the stage and sex of juveniles of D. kornickeri are presented. Finally, the hypothesis is proposed for an anchialine cave ancestor to the present-day planktonic Halocyprididae, now widely spread in the oceans. © 2010 BRILL.


Humphreys W.,Collections and Research Center | Humphreys W.,University of Adelaide | Humphreys W.,University of Western Australia | Tetu S.,Macquarie University | And 5 more authors.
Natura Croatica | Year: 2012

The anchialine system at Bundera sinkhole, Australia, exhibits pronounced hydrogeochemical structure through depth that is reflected in the composition and distribution of the fauna. It is a strongly structured microbial ecosystem the components of which also change with depth and which is dominated by sulfur bacteria and chemolithotrophic microbial classes.


King R.A.,South Australian Museum | King R.A.,University of Adelaide | Bradford T.,University of Adelaide | Bradford T.,CSIRO | And 4 more authors.
Journal of Crustacean Biology | Year: 2012

The Australian stygofauna comprises a unique and diverse assemblage of invertebrates, of which the amphipod crustaceans are a dominant but poorly described element. Recent exploration of the Western Australian stygofauna, in particular the Yilgarn region of central Western Australia, has shown evidence of great species diversity, with numerous individual calcrete aquifers found to contain unique assemblages of invertebrate species. A recent fine-scale biodiversity initiative, using COI barcoding, of a single calcrete aquifer (Sturt Meadows) in the Yilgarn region reported the presence of three divergent and morphologically cryptic stygobitic lineages of amphipods from Chiltoniidae, which represent undescribed taxa. This paper details the subsequent systematic analysis of these COI lineages and presents a broader phylogeny and detailed morphological analyses of the lineages. The report of cryptic species was not supported upon morphological examination and three new species from three new genera (Scutachiltonia n. gen., Stygochiltonia n. gen., and Yilgarniella n. gen.) are described from the Sturt Meadows calcrete aquifer. The three genera do not form a monophyletic group and are instead believed to have evolved from separate colonisation events from distinct ancestors rather than from speciation events within the aquifer. This work contributes to a broader research initiative, documenting the presence of a rich subterranean invertebrate fauna in the Yilgarn region. © 2012 The Crustacean Society. Published by Koninklijke Brill NV, Leiden.


Bishop R.E.,Pennsylvania State University | Humphreys W.F.,Collections and Research Center | Humphreys W.F.,University of Adelaide | Humphreys W.F.,University of Western Australia | Longley G.,San Marcos University of Costa Rica
Subterranean Biology | Year: 2014

This study addresses the causes of the metabolic depression observed when examining the metabolism of hypogean versus epigean organisms. We examined the two current hypotheses regarding the cause of metabolic cave adaptation, a paucity of food and low oxygen availability, both necessary for ATP production, by first determining if the hypogean environment examined, Edwards Aquifer, was resource limited. Stable isotope analyses indicate that there is extensive microbial chemolithoautotrophic production providing resources for the hypogean organisms. δ13C values ( ≤30% ) were well below that of terrestrial biome indicating that C in the aquifer originates from chemolithoautotrophic inorganic carbon fixation, not photosynthetically derived material resulting from terrigenous sources. Data suggest the artesian system is a complex geochemical ecosystem providing inorganic energy sources from both methane and sulfates. Metabolism, examined via key aerobic and anaerobic proxies, and organismal proximate composition indicated there was no difference between metabolic rates and energy storage of Palaemonetes antrorum (stygobitic) and Palaemonetes kadiakensis (epigean). This indicates that resources within the oxic aquifer are not limited. We demonstrate that it is necessary for one, or both, of these selective pressures to be present for metabolic cave adaptation to occur. © Renée E. Bishop et al.


Bishop R.E.,Pennsylvania State University | Humphreys W.,Collections and Research Center | Humphreys W.,University of Western Australia | Cooper S.,South Australian Museum
Natura Croatica | Year: 2012

Subterranean estuaries formed within carbonate deposits in the paleodrainage systems of Western Australia are habitats for an great diversity of stygiobitic beetles, some of which are sympatric sister species. This study examines the metabolism of stygiobiont beetles using respiration and key metabolic enzymes to determine whether sympatric sister species differ in energy allocation and respiration.

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