Biology subjects

Cooper, S. J. B.

Publications and source records attributed to Cooper, S. J. B..

5 recordsLinked to original sources

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↗

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↗

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↗

bioRxiv2020

Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BackgroundThe repeatome, the collection of repetitive DNA sequences represented by transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), is found in high proportion in organisms across the tree of life. Grasshoppers have large genomes (average 9 Gb), containing large amounts of repetitive DNA which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of the repeatome and its contribution to genome evolution, in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex. ResultsWe obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far (the largest being two locust grasshoppers). Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs constituting 66 to 75 % per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome size is likely due to similar rates of TE accumulation across the four races. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a repertoire of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. ConclusionIn-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Although the TE and satDNA repertoires were rather similar between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

genomics↗