Biology subjects

Beasley-Hall, P. G.

Publications and source records attributed to Beasley-Hall, P. G..

10 recordsLinked to original sources

bioRxiv2024

Environmental DNA reveals temporal and spatial variability of invertebrate communities in arid-lands ephemeral water bodies

ContextThroughout semi-arid and arid Australia surface freshwater is rare, and where it does occur, it is often ephemeral. This is the case for freshwater granite rock-holes that occur throughout much of southern Australia. Rock-holes support freshwater invertebrate communities, however, the ongoing threat of climate change means that this ecosystem is likely to experience hydrological disruptions. Rock-holes are also likely to be heavily impacted by invasive vertebrates. However, the ecology of this ecosystem is poorly understood despite its relative ecological significance and the extent of its associated threats. Aims and methodsTo provide a baseline ecological understanding of this ecosystem we documented species richness and variability at a series of rock-holes in the Gawler bioregion in South Australia using an environmental DNA approach. Key resultsMetabarcoding recorded invertebrates from 22 orders and 45 families. Community composition varied among rock-holes and throughout the year, with a peak in species richness in winter. Conclusions and implicationsThese findings demonstrate the importance of these ecosystems to a range of endemic taxa. We propose establishment of monitoring programs, development of custom barcode reference libraries for the rock-hole ecosystem and future research into the likely impacts of climate change on the communities associated with them.

ecology↗

bioRxiv2024

Environmental DNA and wildlife camera traps uncover complimentary vertebrate visitation patterns at freshwater granite rock-holes

Freshwater ecosystems are in decline globally. In Australia, threatening processes include invasive species, increasing drought frequency, climate change and changes to land use, all of which have been associated with declining vertebrate diversity, particularly in Australias arid interior. Efficient monitoring tools are required to effectively monitor and conserve freshwater ecosystems and their associated vertebrate communities. Environmental DNA (eDNA) metabarcoding is one tool that shows promise for monitoring these systems, but knowledge of how eDNA data compares to more established ecological assessment techniques is limited. To address this knowledge gap, we sampled vertebrate eDNA from seven freshwater water bodies of proposed conservation importance in the Australian arid-lands, at three timepoints to measure visitation and compare our findings to camera trapping data at the same locations. Using eDNA we detected 19 species of vertebrates, including native species (such as macropods, wombats and emus) and invasive species (such as feral goats, cats and foxes). In contrast, camera traps detected 32 species, and was much more successful at detecting bird visitation than eDNA. These communities varied both spatially between rock-holes, and temporally, with summer collection periods being distinct from winter-spring. Our results demonstrate the success of eDNA metabarcoding as a tool for monitoring vertebrate visitation to arid-lands freshwater ecosystems that is complementary to more traditional survey methods such as wildlife camera trapping. Finally, we provide conservation recommendations for these vertebrate communities and discuss the efficacy of eDNA for monitoring freshwater resources in arid-lands environments.

ecology↗

bioRxiv2024

Towards a global barcode reference library for subterranean fauna

Implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers a unique opportunity to gain new insights into subterranean communities around the world. However, for effective and meaningful identification of species from anonymous eDNA barcodes, a library of known reference sequences with associated correct taxonomic metadata -also called a barcode reference library (BRL) - is required. Here we propose an open, publicly accessible information resource for eDNA biomonitoring of subterranean fauna following findable, accessible, interoperable and reusable (FAIR) principles that can be expanded globally. While similar proposals have been made by other authors for individual taxon groups, here we have analysed a curated BRL of subterranean fauna compiled from existing GenBank and BOLD DNA sequence databases for a minimum of four genes (COI, 18S, 12S, and 16S rRNA). We demonstrate the value of such an initiative to eDNA metabarcoding where custom libraries are used to characterise entire ecosystems under examination. To examine the effectiveness of a custom BRL, we generated metabarcoding data for an exemplar system at Bungaroo Creek in the Pilbara (Australia), a globally significant location of stygofaunal diversity. We compared results of BLAST queries of eDNA Operational Taxonomic Units (OTUs) to our BRL and the GenBank nucleotide database, and observed that for all barcoding regions, the custom BRL identified subterranean ZOTUs that could not be identified using GenBank and worked better in tandem. We use the BRL presented here to propose a four-stage plan for developing data infrastructure for subterranean fauna, especially with respect to eDNA metabarcoding data. To our knowledge, this represents the first published instance of a subterranean BRL being tested against real eDNA metabarcoding data. These findings provide a step forward towards robust DNA-based bioassessments for subterranean biodiversity and further emphasise the need for the eDNA community to work together in facilitating a global BRL.

evolutionary biology↗

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗

bioRxiv2024

Molecular phylogenetics illuminates evolutionary history and hidden diversity of Australian cave crickets (Orthoptera: Rhaphidophoridae)

Cave crickets (Orthoptera: Rhaphidophoridae) are a globally distributed group of insects found in dark, humid microhabitats including natural caves, alpine scree, and forest litter. Ten extant subfamilies are currently recognised and Macropathinae, which comprises the entirety of the fauna in South America, South Africa, Australia, and New Zealand, is thought to be the most ancient of these. The New Zealand rhaphidophorid fauna comprises high phylogenetic diversity throughout its mesic zone, with most species occurring above-ground. In contrast, the Australian fauna is poorly known, with an apparently greater relative proportion of species utilising caves as refugia. A robust phylogenetic framework is needed to underpin future taxonomic work on the group and potentially contrasting patterns of taxonomic diversity within Macropathinae. Here, we performed fossil-calibrated phylogenetic analysis using whole mitochondrial genomes and nuclear markers to reconstruct the evolutionary history of Macropathinae, with a focus on the Australian fauna. By dramatically increasing taxon sampling relative to past studies, we recovered the Australian fauna as rampantly polyphyletic, with the remaining Macropathinae nested amongst six distinct Australian lineages. Deep divergences between major clades imply additional Australian lineages remain undetected, either due to extinction or sampling bias, and have likely confounded past biogeographic signal. We inferred the radiation of Macropathinae began during the Lower Cretaceous prior to the fragmentation of Gondwana with a potential Pangaean origin for Rhaphidophoridae. Finally, we found evidence for several undescribed taxa of Australian Rhaphidophoridae, all of which qualify as short-range endemics, and discuss the conservation implications of these restricted distributions.

evolutionary biology↗

bioRxiv2024

Sci-comm "behind the scenes": Gendered narratives of scientific outreach activities in the life sciences

Science communication (sci-comm) encompasses activities that promote scientific literacy, inform policy, and inspire future scientists. Despite its value, sci-comm is often considered less pretigious than research and other internal academic activities. In Australia, scientific organisations (e.g., learned societies) rely on members to perform a range of sci-comm activities, typically unpaid. In this pilot study, we surveyed 88 Australian life sciences organisations to examine who performs sci-comm and why. Most respondents were early-career women employed in university research positions. Participants largely agreed that organisational sci-comm brought limited career benefits and was often viewed as feminised or "care work" relative to their research roles. Yet, respondents also cited personal and professional gains and most wished to continue in such roles. Our findings suggest "invisible" sci-comm performed for scientific organisations is disproportionately undertaken by women at early career stages, with implications for career progression and gender equity in STEM.

scientific communication and education↗

bioRxiv2023

Diving into spring biodiversity: A natural heritage assessment of Australia's Great Artesian Basin discharge wetlands

ContextThe Great Artesian Basin (GAB) feeds thousands of springs in Australias arid centre, supporting relictual species not found elsewhere on Earth. Springs are considerably threatened by ongoing water abstraction by industry. Robust management plans are needed to prevent further extirpations of GAB taxa, but fundamental biodiversity knowledge is lacking. AimsWe aimed to characterise major organismal groups in South Australian GAB springs and surrounding wetlands, their conservation and taxonomic status, and potential biodiversity hotspots and connectivity of spring ecosystems. MethodsFocusing on South Australia as a case study, we conducted a comprehensive review of GAB spring biota based on the published scientific and grey literature. Key resultsAlmost 500 taxa have been recorded from GAB springs, the majority being invertebrates. Community composition is highly heterogeneous among spring clusters and the true extent of spring biodiversity is far greater than currently known. ConclusionsGAB springs have intrinsic value as refugia for both endemics and cosmopolitan taxa. GAB invertebrates are poorly conserved and largely lacking in taxonomic knowledge. We highlight several potential biodiversity hotspots that have been overlooked in the literature. ImplicationsFundamental biodiversity information on the GAB is crucial for decision-making in conservation management, for industry, and for Traditional Custodians. Lay summaryThe Great Artesian Basin (GAB) is Australias largest freshwater resource. Springs fed by the GAB support many species not found elsewhere on Earth, but conservation is hindered by a lack of fundamental knowledge about the plants, animals, and fungi reliant on these habitats. Using South Australia as a case study, we provide a comprehensive review of GAB biodiversity in that state.

ecology↗

bioRxiv2023

Shrinking in the dark: Parallel endosymbiont genome erosions are associated with repeated host transitions to an underground life

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabacterium at the genomic level, we sequenced and analysed 25 genomes from Australian soil-burrowing cockroaches (Blaberidae: Panesthiinae) which have undergone at least seven independent subterranean transitions from above-ground, wood-feeding ancestors. We find at least three independent instances of genome erosion have occurred in Blattabacterium strains exclusive to Australian soil-burrowing cockroaches. Such shrinkages have involved the repeated inactivation of genes involved in amino acid biosynthesis and nitrogen recycling, the core role of Blattabacterium in the host-symbiont relationship. The most drastic of these erosions have occurred in hosts thought to have transitioned underground the earliest relative to other lineages. As Blattabacterium is unable to fulfil its core function in such host groups, our findings suggest soil-burrowing cockroaches must acquire these nutrients from novel sources. Our study represents one of the first cases, to our knowledge, of parallel host adaptations leading to concomitant parallelism in their mutualistic symbionts, further underscoring the intimate relationship between these two partners.

genomics↗

bioRxiv2022

Highly dynamic evolution of the chemosensory gene repertoire driven by gene gain and expansion across subterranean beetles

Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground, through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. However, our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.

evolutionary biology↗

bioRxiv2021

Stressed out underground?: Transcriptomics illuminates the genome-wide response to heat stress in surface and subterranean diving beetles

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 (CTmax 38{degrees}C cf. 42-46 {degrees}C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35{degrees}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.

evolutionary biology↗