Academic literature on the topic 'Troglofauna'

The Yilgarn and Pilbara regions of Western Australia are considered biodiversity hotspots for subterranean invertebrates. While the relatively well studied (aquatic) stygofauna are typically constrained to geographically isolated habitats (‘subterranean islands’) and have likely originated from multiple independent epigean ancestors, the troglofauna found in cavernicolous calcretes and fractured rock remains largely unstudied. Here we focus on the pseudoscorpion genera Tyrannochthonius Chamberlin, 1929 and Lagynochthonius Beier, 1951, as common components of the troglofauna, to determine whether they also display highly restricted distributional patterns, and have independent origins. Bayesian and maximum likelihood analyses of sequence data from the mtDNA cytochrome c oxidase I (COI) and the small subunit 18S nuclear genes for subterranean and epigean species from both genera reveal divergent mtDNA lineages that are restricted to single aquifers and/or geographic locations. This strong geographic structuring of troglobitic pseudoscorpions is indicative of short-range endemism and supports the ‘subterranean island’ hypothesis. Further, independent sister relationships between subterranean and epigean taxa indicate multiple invasions into subterranean habitats, likely driven by post-Miocene aridification, consistent with that predicted for the stygofauna. The phylogeny also reveals that Tyrannochthonius + Lagynochthonius is monophyletic but that Lagynochthonius is polyphyletic and nested inside Tyrannochthonius. The results of this study point to common processes that have shaped the diversity and uniqueness of both stygofaunal and troglofaunal communities in Western Australia.

This study is the first attempt to document troglofaunal diversity of crepuscular cave ecosystem from the state of Goa. Twelve faunal species (seven invertebrates and five vertebrates) have been documented from an insular crepuscular cave which measures 18.62m in floor length and shows a transition of light and hygrothermal profile between its entrance and dead end. Absence of primary producers, thermal constancy, high humidity, poor ventilation, and competitive exclusion due to limited food resources restricts the faunal diversity of this cave; though trophic linkages are interesting yet speculative, as is typical of subterranean ecosystem. Among the macro-invertebrates, cavernicolous Whip Spider is a significant species here; whereas the important vertebrates encountered are the Fungoid frog and the Indian Cricket frog, besides roosts of the Rufous Horseshoe bat. Eco-energetic subsidy, possibly offered by crickets and bats that regularly feed outside this oligotrophic cave ecosystem is discussed. The need to document the unique and vulnerable troglofauna of this sensitive ecosystem from the conservation perspective is highlighted.

Knowledge of subterranean fauna has mostly been derived from caves and streambeds, which are relatively easily accessed. In contrast, subterranean fauna inhabiting regional groundwater aquifers or the vadose zone (between surface soil layers and the watertable) is difficult to sample. Here we provide species lists for a globally significant subterranean fauna hotspot in the Robe Valley of the Pilbara region, Western Australia. This fauna was collected from up to 50 m below ground level using mining exploration drill holes and monitoring wells. Altogether, 123 subterranean species were collected over a distance of 17 km, comprising 65 troglofauna and 58 stygofauna species. Of these, 61 species were troglobionts and 48 stygobionts. The troglofauna occurs in small voids and fissures in mesas comprised mostly of an iron ore formation, while the stygofauna occurs in the alluvium of a river floodplain. The richness of the Robe Valley is not a localized aberration, but rather reflects the richness of the arid Pilbara region. While legislation in Western Australia has recognized the importance of subterranean fauna, mining is occurring in the Robe Valley hotspot with conditions of environmental approval that are designed to ensure species persistence.

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.

A major challenge confronting many contemporary systematists is how to integrate standard taxonomic research with conservation outcomes. With a biodiversity 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 examples demonstrating a rapid rise in the collection and documentation of diverse 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.

Little is known about the ecology of the troglofauna species occurring outside caves – which we term landscape troglofauna – because of the difficulties associated with viewing and sampling the habitats of these species. Some of the important information missing for most landscape species is as basic as the depth and substrate in which they occur. For example, does a particular species occur relatively close to the surface, over a range of depths or is it always found quite deep? Does the species use detritals, bedrock habitats or both? In addition to being important for understanding the structure and resilience of subterranean communities, this information is very useful for determining the likely impact of development projects on troglofauna species and their habitat. Because animals are difficult to collect, species ranges within a development site, and beyond it, are often inferred from the extent of their known habitat. In this talk, we address four issues relevant to the ecology and sampling of troglofauna. First, we examine whether troglofaunal capture rates can be related to season, antecedent rainfall or other factors. Second, we examine the effect on sampling yield of setting multiple troglofauna traps. Third, we examine the depths at which various groups of troglofauna mostly occur and check whether there is a match between depth of occurrence and assignment to troglophile or troglobiont categories. Finally we use results of troglofauna sampling in holes for which we have drill logs to we illustrate how knowledge about species’ substrate types is used in environmental impact assessment. This work is a first step to improving our understanding of habitat preferences of troglofauna in Western Australia and some of the responses of troglofauna to environmental variables. It is hoped the work will lead to the framing of more detailed studies.

Environmental DNA (eDNA) and metabarcoding have recently been combined with the aim of detecting species through the small amounts of DNA animals shed into the environment. The technique has successfully been applied in the biomonitoring of vertebrates and decapods and, in a collaborative project with the Trace and Environmental DNA laboratory, Curtin University, we tested its utility in troglofauna sampling. Traditional troglofauna surveys have low yields and consequently, provide limited information about species’ ranges. The ability to detect more occurrences of a species and better define the species’ range by combining traditional troglofauna sampling and eDNA is very exciting. The study area we used is in the central Pilbara and prior survey of the area had documented a moderate troglofauna community. We collected 147 samples from 74 drill holes that comprised 58 scrapes samples, 75 litter trap samples and 14 water samples. Pairs of scrape and water samples were collected from each drill hole, with one set sent for morphological identification and the second set frozen for metabarcoding. A pair of water samples comprised lowering a bailer down the drill hole, retrieving 1 L of water from the top of the water column (for eDNA) after which stygofauna net haul sampling was undertaken. Trap samples collected 124 troglofauna specimens, scrapes 37 troglofauna and net hauls two species of stygofauna and no troglofauna; troglofaunal groups collected include cockroaches, diptera, bugs, schizomids, millipedes, pseudoscorpions, palpigrads, isopods, beetles, silverfish, pauropods and symphylans. Surface species were abundant in the traps (7,760 specimens) and present in most scrapes (81 specimens); they mostly comprised mites and collembola, with lower numbers of flies and ants. The high diversity of animals collected and inevitable human contamination could be expected to pose significant hurdles to use of eDNA. The preliminary eDNA results are compared with the results of traditional sampling.

Biological organisms living in any environment can expel DNA into their surroundings through fecal matter, mucus, shed skin, gametes, etc. Here we examine the utility of metabarcoding from a variety of environmental DNA (eDNA) substrates collected from the Pilbara region, Western Australia, to assess the feasibility for both stygo- and troglofauna detection. With metabarcoding, we confirm eDNA from both stygo- and troglofauna is detectable via molecules. In addition, our proof-of-concept and validation of using an eDNA approach was confirmed when both traditional morphological and metabarcoding assessments were compared. The metabarcoding results from the eDNA substrates are very encouraging when compared to the results of traditional morphological assessments, although highlighted the need for comprehensive DNA reference databases to be accessible for metabarcoding comparisons in order to obtain species identifications and community assemblage profiles. Furthermore, our results indicate a standardised field sampling collection method is warranted in order to maximise the success of subterranean eDNA detection from environmental substrates. eDNA data collected suggest metabarcoding approaches will become a powerful part of the toolkit to study subterranean fauna.

Groundwater calcretes of central Western Australia have revealed an extraordinary diversity of short-range endemic invertebrate subterranean fauna. Although considerable attention has been given to the aquatic dwellers of the calcretes (stygofauna), the subterranean terrestrial fauna of the calcretes (troglofauna), particularly the oniscidean isopods, have been poorly studied. This thesis, including four data chapters, presents the results of multiple-gene and morphological analyses to establish a phylogenetic framework for elucidation of species diversity, systematics, and the biogeographic history of oniscidean isopod troglofauna in arid central Western Australia. The first data chapter focuses on higher level systematic relationships of the isopod fauna. In order to examine the monophyly of the family Platyarthridae, representatives of the main oniscidean families and genera from Australia, South America, Africa and Europe were analysed using molecular and morphological approaches, including data from a Scanning Electron Microscopy study. The phylogenetic analyses of mitochondrial and nuclear genes (COI, 18S, and 28S) showed that Platyarthridae is polyphyletic, and also revealed a very distinct Australian lineage with a unique water conducting system on antenna 2. Based on both morphological and molecular data, a new southern hemisphere oniscidean family, Paraplatyarthridae, occurring from subtropical/temperate to arid regions of Australia and South America, is proposed and described. The second data chapter focuses on the molecular systematics, species diversification and distributional patterns of the oniscidean troglofauna in calcrete aquifers of central Western Australia. The results, based on morphological and multiple-gene molecular approaches, reveal a significant diversity of oniscidean DNA lineages. The application of different species delineation methods, suggests the existence of 28 putative species belonging to four oniscidean families, which most likely represent distinct undescribed species. The phylogenetic analyses show (with some exceptions) that the majority of oniscidean DNA lineages were restricted in their distribution to individual calcrete bodies, lending support to the hypothesis that individual calcretes are equivalent to “Subterranean Islands”. In addition, the occurrence of subtropical, littoral and benthic oniscidean groups in the calcretes suggests complex historical events, including the marine inundation of the Eucla basin during the late Eocene, have shaped the taxonomic representation of the current oniscidean troglofauna. The third data chapter investigates the biogeographic history of the widespread genus Paraplatyarthrus, which showed noticeable morphological diversity, from troglophilic to troglobitic forms. The phylogenetic and molecular clock dating analyses provided evidence that evolutionary transitions from surface to subterranean habitats took place from the late Miocene, and further indicated that troglophile ancestral species independently colonised the calcrete aquifers. These findings support both the climatic relict and adaptive shift hypotheses to explain the evolution of the oniscidean isopod troglofanua with aridity being a significant driver of diversification underground. The final data chapter comprises the morphological description of five new species of the genus Paraplatyarthrus (Paraplatyarthridae fam. nov.) and provides a key to their identification.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2014