Steven John Baynard Cooper

South Australian Museum · Evolutionary Biology Unit

Understanding the profound influence of climatic and tectonic histories on adaptation and speciation is a crucial focus in biology research. While voyages like Humboldt’s expedition shaped our understanding of adaptation, the origin of current biodiversity remains unclear – whether it arose in situ or through dispersal from analogous habitats. Situ...

The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo‐XY sex chromosomes have independently evolved multip...

Numerous and diverse groundwater habitats suitable for sustaining aquatic invertebrate communities exist across Australia. These habitats include enclosed subterranean aquifer systems, fractured rock, alluvial aquifers, perched aquifers, artesian springs, and spring-fed seeps and marshes. Crustaceans are a dominant member of these groundwater-assoc...

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 corre...

Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as “old” and newly emerged sex chromosomes co-exist within the group....

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 described and Macropathinae, which comprises the entirety of the fauna in South America, South Africa, Australia, and New Zealand,...

Context: The Great Artesian Basin (GAB) feeds thousands of springs in Australia’s 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...

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Dis...

Over the last 5 million years, numerous species of Australian stygobiotic (subterranean and aquatic) beetles have evolved underground following independent colonization of aquifers by surface ancestors, providing a set of repeated evolutionary transitions from surface to subterranean life. We used this system as an ‘evolutionary experiment’ to inve...

Recent studies have identified a significant number of endogenous cellulase genes in various arthropods, including isopods, allowing them to process hydrocarbons efficiently as a food source. While this research has provided insight into underlying gene‐level processes in cellulose decomposition by arthropods, little is known about the existence an...

The largest diversity in the world of subterranean diving 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 ce...

Catastrophic wildfires impacted large areas of western Kangaroo Island (KI), South Aus-tralia in 2019-2020, burning habitat for many species, including large proportions of the distribu-tional range of the KI micro-trapdoor spider Moggridgea rainbowi, which led to it being listed as Endangered under Australia's Environment Protection and Biodiversi...

Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene...

The current taxonomic framework for describing new species of Psyllaephagus in Australia is largely intractable, mainly due to damaged or missing types and, as such, the genus has been neglected for almost 40 years. The repercussions of this include an absence of accurate host association records among Psyllaephagus and their hosts, several genera...

The Great Artesian Basin of Australia represents one of the largest and deepest basins of freshwater on Earth. Thousands of springs fed by the Basin are scattered across Australia’s arid zone, often representing the sole sources of freshwater for thousands of kilometers. As “islands” in the desert, the springs support endemic fauna and flora that h...

The Hexabathynella genus is the only genus of the family Parabathynellidae that has supposedly a worldwide distribution. Currently, there are 23 species described from five continents. In Australia, only two Hexabathynella species have been named from the eastern coast, however, a few taxa have been collected from Western Australia during stygofaun...

The Wet Tropics (WT) population of the yellow-bellied glider Petaurus australis Shaw, 1791 in North Queensland is listed as Endangered at the state and national level, but its taxonomic classification is currently uncertain. Here we expand on previous genetic and morphological analyses of the WT population with additional samples and genetic loci t...

The western half of the Australian arid zone harbours the richest diversity of obligate subterranean dytiscids in the world, which are found in isolated calcrete (carbonate) aquifers. Each calcrete usually supports from one to three beetle species that are locally endemic to a specific calcrete, and display the full array of adaptations to living i...

Dispersal, the movement of individuals across space, has important consequences at individual, population, species, community, and ecosystem levels. Dispersal depends on phenotypic traits influencing the propensity of an organism to disperse and extrinsic environmental features. Factors selecting for dispersal include environmental unpredictability...

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Dis...

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...

Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying the evolution of cave-related phenotypes are largely unexplored. We investigated genome-wide gene evolutionary dynamics in...

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,...

Amphipod crustaceans comprise a significant and enigmatic component of Australian groundwater ecosystems, particularly in the Pilbara region of Western Australia. Many amphipod species in the Pilbara, including species in the genus Nedsia Barnard & Williams, 1995 , are considered short range endemics, poorly or contentiously defined by taxonomic tr...

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,...

Subterranean specialization is often accompanied by dramatic phenotypic changes epitomized by regressive evolution (e.g. loss or reduction of eyes and pigmentation). Nevertheless, the genetic underpinnings underlying these changes have been largely unexplored. The beetle tribes Leptodirini (Leiodidae), Hydroporini and Bidessini (Dytiscidae) represe...

Subterranean realms possess high environmental stability with respect to light levels, temperature, and humidity. The transition to a subterranean lifestyle can therefore cause massive shifts in a species’ biology. How does the colonisation of these habitats affect the thermal tolerance of an organism? Past studies demonstrate species in extremely...

The Scirtidae Fleming, 1821 has been identified as one of the earliest diverging groups of Polyphagan beetles and is particularly speciose in Australia. However, very little is known about the origin of the Australian scirtids and there is a need for a robust, well-supported phylogeny to guide the genus and species descriptions and understand the r...

In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolu...

Amphipod crustaceans comprise a significant and enigmatic component of Australian groundwater ecosystems, particularly in the Pilbara region of Western Australia. Many amphipod species in the Pilbara, including species in the genus Nedsia Barnard & Williams, 1995, are considered short range endemics, poorly or contentiously defined by taxonomic tre...

Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The an...

Remnant natural populations of greater bilbies (Macrotis lagotis) are confined to the Australian arid zone where bilbies construct and shelter in multiple burrows within their home range. We investigated burrow use behaviour of bilbies in a translocated population in temperate southern Australia to determine if behaviour differed in this climatic z...

Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon str...

Thermal tolerance limits in animals are often thought to be related to temperature and thermal variation in their environment. Recently, there has been a focus on studying upper thermal limits due to the likelihood for climate change to expose more animals to higher temperatures and potentially extinction. Organisms living in underground environmen...

The Australian Scirtidae species previously identified as misplaced in the widespread genus Prionocyphon Redtenbacher are revisited as well as their possible relationship with the Australian genus Macrodascillus (Lea) using sequence data from the mitochondrial gene, cytochrome oxidase subunit 1 and two nuclear genes, elongation factor 1-alpha and T...

Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthrop...

The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus, and I. fusciventer, has been o...

Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progre...

Most subterranean animals are assumed to have evolved from surface ancestors following colonization of a cave system; however , very few studies have raised the possibility of "subterranean speciation" in underground habitats (i.e., obligate cave-dwelling organisms [troglobionts] descended from troglobiotic ancestors). Numerous endemic subterranean...

Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are...

Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwate...

Background The 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 ass...

The Australian Scirtidae genus Pseudomicrocara Armstrong, previously shown to be polyphyletic, is revised using both morphology and sequence data from the mitochondrial gene cytochrome oxidase subunit 1 and two nuclear genes, elongation factor 1-alpha and topoisomerase. Twenty-three genera, 16 of which are new, are recognised based on morphology, p...

Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi‐factor BMM) based on...

The Australian sugar glider, Petaurus breviceps s.l., is widely distributed across eastern and northern Australia. Examination of historical and contemporary collections of Petaurus specimens and phylogenetic analyses have revealed considerable taxonomic diversity within the genus. We aimed to utilize an integrative taxonomic approach, combining ge...

The Australian sugar glider, Petaurus breviceps s.l., is widely distributed across eastern and northern Australia. Examination of historical and contemporary collections of Petaurus specimens and phylogenetic analyses have revealed considerable taxonomic diversity within the genus. We aimed to utilize an integrative taxonomic approach, combining ge...

Publisher: Dryad https://doi.org/10.5061/dryad.2z34tmpj7 Citation Saccò, Mattia et al. (2021), Data from: Refining trophic dynamics through multi-factor Bayesian mixing models: a case study of subterranean beetles., v3, Dataset, https://doi.org/10.5061/dryad.2z34tmpj7 Abstract Food web dynamics are vital in shaping the functional ecology of ecosyst...

The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean–aquatic) species that are “trapped” evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial–subterranean invertebrates associated wi...

Context. Translocations have been widely used to re-establish populations of threatened Australian mammalian species. However, they are limited by the availability of sites where key threats can be effectively minimised or eliminated. Outside of 'safe havens', threats such as exotic predators, introduced herbivores and habitat degradation are often...

Southern brown (Isoodon obesulus) and golden (Isoodon auratus) bandicoots are iconic Australian marsupials that have experienced dramatic declines since European settlement. Conservation management programs seek to protect the remaining populations; however, these programs are impeded by major taxonomic uncertainties. We investigated the history of...

Like other crustacean families, the Parabathynellidae is a poorly studied subterranean and aquatic (stygobiontic) group in Australia, with many regions of available habitat having not yet been surveyed. Here we used a combined approach of molecular species delimitation methods, applied to mitochondrial and nuclear genetic data, to identify putative...

Groundwaters host highly adapted fauna, known as stygofauna, which play a key role in maintaining the functional integrity of subterranean ecosystems. Stygofaunal niche studies provide insights into the ecological dynamics shaping the delicate balance between the hydrological conditions and community diversity patterns. This work aims to unravel th...

Context: Many of Australia’s threatened mammals were once widespread across the continent and present in both arid, semiarid and temperate habitats. However, data on breeding biology can be lacking for some climatic regions due to local extinctions of populations. The breeding biology of the greater bilby (Macrotis lagotis) has previously only been...

Recent surveys of Australian arid-zone groundwater ecosystems have uncovered considerable species diversity and extreme endemism for the oniscidean isopod genus Haloniscus Chilton, 1920. Phylogenetic and species delimitation analyses have recognised several distinct species from the Great Artesian Basin springs in South Australia, inspiring a morph...

Insects have a gas-filled respiratory system, which provides a challenge for those that have become aquatic secondarily. Diving beetles (Dytiscidae) use bubbles on the surface of their bodies to supply O2 for their dives and passively gain O2 from the water. However, these bubbles usually require replenishment at the water’s surface. A highly diver...

Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al. (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al. (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use...

The braconid subfamily Microgastrinae are ecologically important parasitoids of larval lepidopterans, but are poorly studied in many regions of the world. In this study, we focus on describing new species of microgastrine wasps, in part from specimens collected on six different ‘Bush Blitz’ surveys of regional reserves in South Australia and Tasman...

A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intrageno...

The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major...

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...

Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Australian scincid lizard, Tiliqu...

Neutral evolution theory predicts that genes specific to the development/function of eyes in subterranean animals will evolve under relaxed selection, ultimately becoming pseudogenes. Independently evolved (3-8 million years ago) subterranean beetle (Dytiscidae) species of Western Australia have converged on eye loss, providing a powerful system to...

The parasitoid wasp family Ichneumonidae is among the most diverse groups of organisms, with conservative estimates suggesting that it contains more species than all vertebrates together. However, ichneumonids are also among the most severely understudied groups, and our understanding of their evolution is hampered by the lack of a robust higher-le...

Phylogeographic studies have provided evidence for speciation underground within the confines of a cave environment, questioning the assumption that cave animals evolved from surface ancestors (Juan et al. 2010). However, for many of these studies, it is difficult to rule out the possibility that phylogeographic patterns may have resulted from mult...

The aganippine spiny trapdoor spiders of the genus Bungulla Rix, Main, Raven & Harvey are revised, and 30 new species are described from Western Australia: B. ajana sp. nov., B. aplini sp. nov., B. banksia sp. nov., B. bella sp. nov., B. bidgemia sp. nov., B. biota sp. nov., B. bringo sp. nov., B. burbidgei sp. nov., B. dipsodes sp. nov., B. disrup...

The subfamily Microgastrinae contains an extraordinarily rich diversity of parasitoid wasps which parasitise larval lepidopterans. The Australian fauna has generally been poorly studied, particularly for the very speciose genera. One such genus is Dolichogenidea Vierek, which in Australia is known from only six described species. Here we describe t...

Synopsis: Two tribes of subterranean dytiscid diving beetles independently colonised groundwater systems of the Western Australian arid zone, a habitat transition that was most likely driven by the contraction of surface water bodies following late Neogene aridification of the Australian continent. These 'stygofauna' are now trapped within discret...

The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Norther...

The aganippine shield-backed trapdoor spiders of the monophyletic nigrum -group of Idiosoma Ausserer s. l. are revised, and 15 new species are described from Western Australia and the Eyre Peninsula of South Australia: I.arenaceum Rix & Harvey, sp. n. , I.corrugatum Rix & Harvey, sp. n. , I.clypeatum Rix & Harvey, sp. n. , I.dandaragan Rix & Harvey...