Time capsules of biodiversity: Future research directions for groundwater-dependent ecosystems of the Great Artesian Basin

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 have undergone millions of years of evolution in almost total isolation. Here, we review the current body of knowledge surrounding Great Artesian Basin springs and their significance from ecological, evolutionary, and cultural perspectives using South Australian spring wetlands as a case study. We begin by identifying the status of these springs as critical sources of groundwater, the unique biodiversity they support, and their cultural significance to the Arabana people as Traditional Custodians of the land. We then summarize known threats to the springs and their biota, both exogenous and endogenous, and the potential impacts of such processes. Finally, considering the status of these at-risk habitats as time capsules of biodiversity, we discuss lessons that can be learnt from current conservation and management practices in South Australia. We propose key recommendations for improved biodiversity assessment and monitoring of Great Artesian Basin springs nationwide, including 1) enhanced legal protections for spring biota; 2) increased taxonomic funding and capacity; 3) improved biodiversity monitoring methods, and 4) opportunities for reciprocal knowledge-sharing with Aboriginal peoples when conducting biodiversity research.P. G. Beasley-Hall, N. P. Murphy, R. A. King, N. E. White, B. A. Hedges, S. J. B. Cooper, A. D. Austin, and M. T. Guzi

Differential transcriptomic responses 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 °C cf. 42–46 °C), but the genetic basis of this physiological diference 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 °C), as determined by comparative transcriptomics. However, genes involved in these responses difer between species and a far greater number were diferentially 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 diferentially 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 fndings 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.Perry G. Beasley-Hall, Terry Bertozzi, Tessa M. Bradford, Charles S. P. Foster, Karl Jones, Simon M.Tierney, William F. Humphreys, Andrew D.Austin, Steven J. B. Coope

Molecular systematics and biogeography of an Australian soil‐burrowing cockroach with polymorphic males, Geoscapheus dilatatus (Blattodea: Blaberidae)

An iconic group of arid‐adapted insects is the Australian soil‐burrowing cockroaches (Blaberidae: Geoscapheinae), large, wingless insects that evolved burrowing behaviour and associated forms in parallel from wood feeding ancestors in the subfamily Panesthiinae. A particularly problematic taxon within the Geoscapheinae is Geoscapheus dilatatus (Saussure, 1864), which might represent a species complex and whose delimitation has been complicated for decades by the species harbouring polymorphic males. Males can be divided into two main morphs: individuals possessing horn‐like protrusions on the anterior margin of the pronotum (‘tuberculate’) and those without these characters (‘non‐tuberculate’). A less common, third form consists of individuals that possess tubercles but are far larger than other tuberculate males and occur solely to the north of the species' distribution (‘atypical’ tuberculates). Here, we make use of whole mitochondrial genomes and nuclear ribosomal RNA data from individuals across the range of G. dilatatus to conduct the first phylogenetic analysis of this species to date. We recover all tuberculate males (including atypical forms) as monophyletic and the derived form of G. dilatatus, having evolved only once in this species, whereas non‐tuberculate forms are paraphyletic. Fossil‐calibrated molecular clock analysis revealed that the divergence between these two forms occurred during the late Miocene approximately 6.7 Mya, concurrent with an expansion of the continent's drier biomes. Environmental niche modelling suggests that tuberculate male forms are more climatically tolerant than their more restricted non‐tuberculate counterparts, and both forms' predicted fundamental niches are strongly limited by rainfall. Three species delimitation analyses implemented here failed to consistently delimit G. dilatatus beyond a single species. Ultimately, population genetic approaches paired with additional sampling will be necessary to determine these findings more concretely, but at present, we do not consider the results presented here sufficient to delimit G. dilatatus based on morphological differences found in the species' polymorphic males alone.Perry G Beasley-Hall, Harley A Rose, Thomas Bourguignon and Nathan L

Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

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 evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.Pau Balart-García, Leandro Aristide, Tessa M. Bradford, Perry G. Beasley-Hall, Slavko Polak, Steven J. B. Cooper, Rosa Fernánde

Parallel decay of vision genes in subterranean water beetles

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, ulti- mately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.Barbara L. Langille, Simon M. Tierney, Terry Bertozzi, Perry G. Beasley-Hall, Tessa M. Bradford, Erinn P. Fagan-Jeffries, Josephine Hyde, Remko Leijs, Matthew Richardson, Kathleen M. Saint, Danielle N. Stringer, Adrian Villastrigo, William F. Humphreys, Andrew D. Austin, Steven J.B. Coope