ORCID Profile
0000-0002-7360-7933
Current Organisation
South Australian Museum
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Publisher: Oxford University Press (OUP)
Date: 18-12-2019
Publisher: Elsevier BV
Date: 08-2022
DOI: 10.1016/J.YMPEV.2022.107522
Abstract: 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 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.
Publisher: Wiley
Date: 22-02-2021
DOI: 10.1111/AEN.12527
Abstract: 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 ided into two main morphs: in iduals 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 in iduals 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 in iduals 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 ergence 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 s ling 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.
Publisher: Wiley
Date: 26-06-2021
DOI: 10.1111/CSP2.483
Abstract: As the global bio ersity crisis deepens, with increasing habitat fragmentation and a changing climate, innovative options for conserving species are being explored. One such conservation action is genetic rescue: introduction of new alleles to promote population fitness. However, for critically endangered species where only one viable population remains, options for introducing new alleles are limited. Interspecies hybridization offers a potential solution but requires resolution of evolutionary relationships, a sound understanding of species biology, social license, and permissive legislative frameworks. Here, we show how phylogenetics and species biology can inform genetic rescue options for the orange‐bellied parrot (OBP Neophema chrysogaster ), a critically endangered Australian bird with one small remaining wild population. Our phylogenetic analysis of mitochondrial genomes and nuclear loci for all congeneric species provided strong support for OBPs being the sister species to a group comprising elegant, rock, and blue‐winged parrots. Accounting for species distribution, behavior, and ecology, a captive trial of interspecific hybridization with the blue‐winged parrot is recommended, including assessment of the fitness of hybrid in iduals. Introduction of new alleles into the OBP genome would achieve the conservation goal of improving genetic ersity in a critically endangered species. Concurrently, legislative issues will need to be resolved.
Publisher: Springer Science and Business Media LLC
Date: 28-09-2022
DOI: 10.1038/S41598-022-20229-0
Abstract: 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 (CT max 38 °C cf. 42–46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 in iduals 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 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.
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2021
DOI: 10.1101/2021.12.12.470823
Abstract: 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 (CT max 38°C cf . 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 in iduals 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 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.
Publisher: CSIRO Publishing
Date: 21-09-2022
DOI: 10.1071/IS21076
Abstract: Austrocarausius Brock, 2000 is a stick insect (Phasmatodea: Lonchodidae) genus containing two species restricted to the tropical rainforests of northern Queensland. Recent specimen collections between the two species’ type localities, Lizard Island and Rockh ton, have suggested that Austrocarausius might represent more than the two nominal species. Here, we apply morphological and molecular analyses to revise the taxonomy of this genus. Using both field-collected and historic museum s les, we developed morphological species hypotheses and descriptions. Genetic sequencing of mitochondrial COI and 16S were undertaken for species delimitation and phylogenetic analysis, including an estimate of the evolutionary timescale of the genus. Based on these results, we propose nine new Austrocarausius species, increasing the number of species in the genus to eleven: A. nigropunctatus (Kirby, 1896), A. mercurius (Stål, 1877), A. coronatus sp. nov., A. decorus sp. nov., A. eirmosus sp. nov., A. gasterbulla sp. nov., A. tuberosus sp. nov., A. macropunctatus sp. nov., A. truncatus sp. nov. A. waiben sp. nov. and A. walkeri sp. nov. Our results suggest Austrocarausius species ersified over the last c. 25–70 Ma, resulting in the now endemic distributions in the tropical rainforests of the central and northern Queensland coasts. This is the first integrative systematic study of an Australian phasmid genus, combining morphological, molecular and biogeographical methods. Additional species of Austrocarausius likely remain undescribed as can be inferred from methodical s ling of rainforest patches along the Queensland coast.
Publisher: Wiley
Date: 23-04-2018
DOI: 10.1111/JBI.13233
Publisher: Wiley
Date: 16-05-2021
DOI: 10.1111/SYEN.12487
Abstract: Soil‐burrowing cockroaches (Blaberidae: Geoscapheinae) are large insects endemic to Australia. Originally thought to represent a monophyletic group, these enigmatic species have in fact evolved burrowing behaviour, associated fossorial morphological modifications, and dietary transitions to dry leaf litter feeding multiple times from the wood‐feeding Panesthiinae in a striking ex le of parallel evolution. However, various relationships within these two subfamilies remain unresolved or poorly understood, notably the apparent paraphyly of Panesthiinae with respect to Geoscapheinae, the position and ersification of certain species within major clades, and several aspects of the overall group's biogeography and morphological evolution. Here, we investigate the phylogeny of Australian members of these two subfamilies using whole mitochondrial genomes paired with nuclear ribosomal markers and highly conserved genes from the bacterial endosymbiont Blattabacterium . Using the resulting robust, fossil‐calibrated phylogeny from these three sources we confirm the nonmonophyly of both subfamilies and recover Geoscapheinae as polyphyletic within a paraphyletic Panesthiinae. The nonmonophyly of natural groups, at all levels from subfamily to species, has been driven by repeated, independent acquisitions of burrowing forms in Geoscapheinae from panesthiine ancestors that colonized the continent on two separate occasions during the Miocene. We additionally find morphological variation within Geoscapheinae itself is correlated with species distributions. Older soil‐burrowing clades living in comparatively arid environments have additional morphological reductions beyond obvious fossorial adaptations compared to those in younger burrowing clades from more temperate habitats. Ultimately, the results presented here demonstrate connections among phylogeny, biogeography and morphology throughout Australian representatives of these two subfamilies, factors that could not be previously consolidated using existing phylogenetic frameworks. Given the discordance between molecular data implemented here and the existing taxonomic classification, we find no support for retaining Geoscapheinae as a discrete taxonomic grouping. In closing, we discuss the taxonomic implications of these results and present a roadmap for future research on Geoscapheinae and their panesthiine relatives.
Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2023
Publisher: No publisher found
Date: 2021
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2022
DOI: 10.1101/2022.12.08.519422
Abstract: 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. 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 deepen our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.YMPEV.2018.04.024
Abstract: Australian cave crickets are members of the subfamily Macropathinae (Orthoptera: Rhaphidophoridae). The subfamily is thought to have originated prior to the tectonic separation of the supercontinent Gondwana based on distributions of extant lineages and molecular phylogenetic evidence, although the Australian fauna have been underrepresented in previous studies. The current study augments existing multigene data (using 12S, 16S, and 28S rRNA genes) to investigate the placement of the Australian representatives within the Macropathinae and to assess ergence dates of select clades. Results suggest that the endemic Tasmanian genus Parvotettix is the sister lineage to the remaining members of the subfamily, an outcome that presents a paraphyletic Australian fauna in contrast to previous studies. All other Australian taxa represented in this study (Micropathus and Novotettix) emerged as a sister group to the New Zealand and South American macropathine lineages. Estimation of phylogenetic ergence ages among the aforementioned clades were calibrated using two methods, in absence of suitable fossil records: (i) tectonic events depicting the fragmentation of Gondwanan landmasses that invoke vicariant scenarios of present day geographic distributions and (ii) molecular evolutionary rates. Geological calibrations place the median age of the most recent common ancestor of extant macropathines at ∼125 to ∼165 Ma, whereas analyses derived from molecular substitution rates suggest a considerably younger origin of ∼32 Ma. This phylogenetic study represents the most rigorous taxonomic s ling of the Australian cave cricket fauna to date and stresses the influence of lineage representation on biogeographic inference.
No related grants have been discovered for Perry Beasley-Hall.