Steven Cooper

Phylogenetic placement and description of Ngaliadessus humphreysi gen. et sp. nov., Watts & Villastrigo (Coleoptera: Dytiscidae), a subterranean diving beetle from the Ngalia Basin in centr

Publisher: Wiley

Date: 08-2023

DOI: 10.1111/AEN.12649

Abstract: The largest ersity in the world of subterranean ing 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 central Western Australia and the Ngalia Basin of the Northern Territory. Here, we use an integrative approach based on morphological and molecular analyses to describe Ngaliadessus humphreysi gen. et sp. nov. Watts & Villastrigo representing a new genus and species of stygobiotic Bidessini collected from a single well in the Ngalia Basin. Phylogenetic analyses using whole mitochondrial genome, Histone 3 and 18S rRNA data, representing a comprehensive coverage of Bidessini genera, support the distinction of the genus and species as a separate evolutionary lineage sister to the Australasian genus Limbodessus and the widely distributed genus Allodessus Guignot, 1953. Our study further confirms that the Ngalia Basin, containing 13 subterranean dytiscid species from four distinct genera, is one of the most speciose areas within the world's most erse hotspot of subterranean ing beetles.

Evolutionary history of the Australasian Scirtinae (Scirtidae; Coleoptera) inferred from ultraconserved elements

Publisher: CSIRO Publishing

Date: 04-05-2022

DOI: 10.1071/IS21053

Abstract: The Scirtidae Fleming, 1821 has been identified as one of the earliest erging 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 relationships among taxa. In this study we carried out a phylogenetic analysis of the Australian Scirtinae Fleming, 1821, using DNA sequence data from ultraconserved elements (UCEs) and included representative taxa from New Zealand, New Caledonia, South America, South Africa and Eurasia in the analysis. Bayesian analyses of a concatenated dataset from 79 taxa recovered four major Southern Hemisphere groupings and two Australian–Eurasian groupings. The Veronatus group mainly consisted of genera from New Zealand, with the three Australian representatives only distantly related to each other. Relaxed molecular clock analyses, using the estimated age of the crown node of the Polyphaga for calibration, support a Gondwanan history for four of the groups of Australian Scirtinae and a northern origin for two groups. Our results highlight the value of commercially available UCEs for resolving the phylogenetic history of ancient groups of Coleoptera.

Differential transcriptomic responses to heat stress in surface and subterranean diving beetles

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.

Strong Population Genetic Structure for the Endangered Micro-Trapdoor Spider Moggridgea rainbowi (Mygalomorphae, Migidae) in Unburnt Habitat after Catastrophic Bushfires

Publisher: MDPI AG

Date: 30-06-2023

DOI: 10.3390/D15070827

Abstract: Catastrophic wildfires impacted large areas of western Kangaroo Island (KI), South Australia in 2019–2020, burning habitat for many species, including large proportions of the distributional range of the KI micro-trapdoor spider Moggridgea rainbowi, which led to it being listed as Endangered under Australia’s Environment Protection and Bio ersity Conservation Act (EPBC Act). In order to assess population genetic structure in M. rainbowi and detect diagnosable lineages and their distributional patterns across KI, 28 in iduals were genotyped for 2495 loci, s ling from all known populations of the species. Population genetic and phylogenetic analyses of nuclear and mitochondrial sequence data provided strong support for three Evolutionarily Significant Units (ESUs) within M. rainbowi two populations on eastern KI and a heavily fire-impacted western population. High levels of ergence and fixed allelic differences between 5 and 16% indicate a lack of gene flow between ESUs and long periods of isolation. Distributional patterns of these lineages match likely locations of isolation events caused by successive changes to sea level during the Quaternary (2.58 million years ago to present), which led to KI being intermittently connected to the mainland or separated into one or more islands. Our findings have strong conservation implications for M. rainbowi and highlight the importance of inclusion of population genetic structure to inform conservation strategies and to conserve lineage bio ersity at the species level and below.

Molecular evolution of ‘eye genes’ in blind beetles from the calcrete archipelago of Western Australia: evidence for neutral evolution of phototransduction genes

Publisher: Pensoft Publishers

Date: 02-10-2018

DOI: 10.3897/ACA.1.E30237

Abstract: 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 explore changes to the genome with respect to troglomorphic characters. Using next generation sequence data, we investigated the molecular evolution of ‘eye genes’ of subterranean beetle species to test if they are evolving neutrally. We used transcriptome data from five beetle species (three subterranean and two surface) to design baits for hybrid enrichment of 60 pigmentation and phototransduction genes from 31 subterranean and surface species. The current talk focuses on the results from the study of 8 photoreceptor genes that showed evidence for a lack of transcription or possible pseudogenisation in stygobitic species when compared to surface species. The mutations found in these genes included multiple insertions or deletions, resulting in frameshifts which led to the introduction of stop codons. Our study provides evidence for the parallel loss of key phototransduction genes, lending support to the neutral theory of regressive evolution.

Evolutionary transition from surface to subterranean living in Australian water beetles (Coleoptera: Dytiscidae) through adaptive and relaxed selection

Publisher: Oxford University Press (OUP)

Date: 19-10-2023

DOI: 10.1093/BIOLINNEAN/BLAD142

Evolution of endoglucanase genes in subterranean and surface isopod crustaceans from Central Western Australia

Publisher: Wiley

Date: 29-09-2023

DOI: 10.1002/ECE3.10552

Population genomic diversity and structure in the golden bandicoot: a history of isolation, extirpation, and conservation

Publisher: Springer Science and Business Media LLC

Date: 08-10-2023

DOI: 10.1038/S41437-023-00653-2

Phylogenomic insights into the evolution of subterranean Coleoptera

Publisher: Pensoft Publishers

Date: 14-07-2022

DOI: 10.3897/ACA.5.E87194

Abstract: 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) represent ideal systems for exploring the genomic basis of adaptation to life in subterranean habitats, as both are represented by epigean and hypogean species including numerous lineages that independently colonized terrestrial and freshwater underground habitats respectively (Cooper et al. 2002, Ribera et al. 2010). We investigated gene repertoire evolutionary dynamics in both surface-dwelling and subterranean Coleoptera in lineages that underwent six independent underground colonization events. We generated highly complete transcriptomes for eight aquatic and fourteen terrestrial beetles including epigean and hypogean species and explored the evolution of their gene repertoire through a phylogenomic approach. Our results indicated that gene loss was a major force facilitating adaptation to an underground lifestyle. In contrast, we also observed that gene gain and duplication were also remarkable drivers for subterranean adaptation. Gene families experiencing contractions were involved in carbohydrate metabolism, response to starvation, wing disk development, rhodopsin and ommochrome biosynthetic processes and response to hypoxia, among many other ex les. Conversely, gene families significantly expanded in subterranean lineages including those related to the regulation of apoptosis, alcohol metabolism, cell redox homeostasis, chitin-based cuticle development, larval instar development, oogenesis, and negative regulation of TORC1 signaling. Moreover we found that some gene families had experienced a more complex evolutionary dynamic encompassed by both expansion and contraction events, such as those involved in regulation of transcription, nervous system development, lipid metabolism, eye development, DNA repair and chemosensation, indicating that these gene families underwent an in-depth reshaping throughout the evolutionary time. At a lineage-specific level, we did not observe many differences between the gene repertoire of the hypogean and epigean Leptodirini species in terms of gene gain and loss. Nonetheless, Hydroporini and Bidessini stygobitic species showed more disparity in their gene repertoire compared to their surface-dwelling relatives. Our results thus indicate that genomic exaptation may have facilitated underground colonization in Leptodirini prior to the ersification of the tribe, while in Hydroporini and Bidessini recent gene family turnover (dominated by gene loss) may have been guiding the surface-to-groundwater transition. These findings shed light towards understanding how the genomic toolkit has been reshaped in hypogean fauna from a macroevolutionary perspective.

Phylogeography of southern brown and golden bandicoots: implications for the taxonomy and distribution of endangered subspecies and species

Publisher: CSIRO Publishing

Date: 2018

DOI: 10.1071/ZO19052

Abstract: 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 population connectivity to inform subspecies and species boundaries through a broad-scale phylogeographic and population genetic analysis of Isoodon taxa. Our analyses reveal a major east–west phylogeographic split within I. obesulus/I. auratus, supported by both mtDNA and nuclear gene analyses, which is not coincident with the current species or subspecies taxonomy. In the eastern lineage, all Tasmanian s les formed a distinct monophyletic haplotype group to the exclusion of all mainland s les, indicative of long-term isolation of this population from mainland Australia and providing support for retention of the subspecific status of the Tasmanian population (I. o. affinis). Analyses further suggest that I. o. obesulus is limited to south-eastern mainland Australia, representing a significant reduction in known range. However, the analyses provide no clear consensus on the taxonomic status of bandicoot populations within the western lineage, with further analyses required, ideally incorporating data from historical museum specimens to fill distributional gaps.

What’s the potential for environmental DNA (eDNA) to assess stygofauna and trogolofauna: pilot studies from Western Australia

Publisher: Pensoft Publishers

Date: 13-12-2018

DOI: 10.3897/ACA.1.E32377

Abstract: 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 detection. With metabarcoding, we confirm eDNA from both stygo- and troglofauna is detectable via molecules. In addition, our proof-of-concept and validation of using an eDNA approach was confirmed when both traditional morphological and metabarcoding assessments were compared. The metabarcoding results from the eDNA substrates are very encouraging when compared to the results of traditional morphological assessments, although highlighted the need for comprehensive DNA reference databases to be accessible for metabarcoding comparisons in order to obtain species identifications and community assemblage profiles. Furthermore, our results indicate a standardised field s ling collection method is warranted in order to maximise the success of subterranean eDNA detection from environmental substrates. eDNA data collected suggest metabarcoding approaches will become a powerful part of the toolkit to study subterranean fauna.

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

Publisher: Cold Spring Harbor Laboratory

Date: 22-08-2020

DOI: 10.1101/2020.08.22.247130

Abstract: 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 h ered 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. We 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 ersity of TEs and satDNAs constituting 66 to 75 % per genome assembly. A comparison of sequence ergence 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 ersification of the V. viatica species complex. In-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.

Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Publisher: Springer Science and Business Media LLC

Date: 29-06-2023

DOI: 10.1038/S41467-023-39603-1

Abstract: 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.

Integrative and accelerated taxonomy recognises a new species of Psyllaephagus (Hymenoptera: Encyrtidae), parasitic on Lasiopsylla striata (Hemiptera: Psyllidae) from Australia.

Publisher: Atlas of Living Australia

Date: 11-05-2023

DOI: 10.54102/AJT.SZJZ2

Abstract: 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 of which are lerp-forming psyllids that are ubiquitous on Eucalyptus spp. across Australia. In response, and to demonstrate the feasibility of robust and rapid species descriptions, here we describe a new species, Psyllaephagus iridis sp. nov. McClelland and the first record of a Eucalyptus host association for the psyllid Lasiopsylla striata Froggatt 1923, from a previously uns led location. It is the first instance where an Australian species of Psyllaephagus is described from accurately recorded reared material. Molecular data is associated with the species for future studies and this, combined with diagnostic morphology, and high-resolution images, provides a description of a new species which demonstrates a comprehensive yet robust method for an accelerated taxonomic treatment of the Australian Psyllaephagus fauna.

Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water

Publisher: American Chemical Society (ACS)

Date: 27-01-2020

DOI: 10.1021/JACS.9B12389

Abstract: Covalent organic frameworks (COFs) are commonly synthesized under harsh conditions yielding unprocessable powders. Control in their crystallization process and growth has been limited to studies conducted in hazardous organic solvents. Herein, we report a one-pot synthetic method that yields stable aqueous colloidal solutions of sub-20 nm crystalline imine-based COF particles at room temperature and ambient pressure. Additionally, through the combination of experimental and computational studies, we investigated the mechanisms and forces underlying the formation of such imine-based COF colloids in water. Further, we show that our method can be used to process the colloidal solution into 2D and 3D COF shapes as well as to generate a COF ink that can be directly printed onto surfaces. These findings should open new vistas in COF chemistry, enabling new application areas.

Systematics of Haloniscus Chilton, 1920 (Isopoda: Oniscidea: Philosciidae), with description of four new species from threatened Great Artesian Basin springs in South Australia

Publisher: Oxford University Press (OUP)

Date: 07-2019

DOI: 10.1093/JCBIOL/RUZ044

Abstract: Recent surveys of Australian arid-zone groundwater ecosystems have uncovered considerable species ersity 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 morphological reassessment of the genus and examination of specimens from the iconic Lake Eyre and Dalhousie Springs. We present a revised diagnosis of Haloniscus, transfer the genus from the family Scyphacidae to Philosciidae and describe four new species, H. fontanus Stringer, King & Taiti n. sp., H. microphthalmus Stringer, King & Taiti n. sp., H. rotundus Stringer, King & Taiti n. sp., and H. yardiyaensis Stringer, King & Taiti n. sp., based on combined morphological and molecular evidence. We compare the results of molecular-based species delimitation analyses with morphological data, provide distribution information, and present a key to the described species of Haloniscus. Two species presently included in Andricophiloscia Vandel, 1973, A. stepheni (Nicholls & Barnes, 1926) and A. pedisetosa Taiti & Humphreys, 2001, from Western Australia are also transferred to Haloniscus.

A new genus, Perplexacara, and new generic placements of species of Australian marsh beetles (Coleoptera: Scirtidae) based on morphology and molecular genetic data

Publisher: Magnolia Press

Date: 16-02-2021

DOI: 10.11646/ZOOTAXA.4927.4.4

Abstract: 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 Topoisomerase. The study confirmed the conclusion of Cooper et al. (2014) that the species did not belong in Prionocyphon. The study also included a species from each of three possibly related genera, Chameloscyphon Watts, Daploeuros Watts and Dasyscyphon Watts. Chameloscyphon huonensis Watts, Dasyscyphon victoriaensis Watts and Daploeuros lamingtonensis Watts were recovered as separate lineages with C. huonensis linking with Das. victoriaensis and Dap. lamingtonensis isolated. The species previously included in Prionocyphon were shown to belong in two genera, Macrodascillus and a new genus Perplexacara: Perplexacara caementum (Watts) new combination, P. latusmandibulara (Watts) new combination, P. macroflavida (Watts) new combination, Macrodascillus scalaris (Lea), M. insolitus (Watts) new combination and M. lamingtonensis (Watts) new combination.

Speciation underground in desert aquifers or just another case of hybridisation by blind beetles?

Publisher: Pensoft Publishers

Date: 18-09-2018

DOI: 10.3897/ACA.1.E29830

Abstract: 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 multiple colonisation events from the same ancestral surface species, introgressive hybridisation among related species, and/or the extinction of surface ancestral lineages. Such is the case for the subterranean ing beetle species (Dytiscidae) of the groundwater calcrete archipelago of central Western Australia, where more than 100 species have been described that appear to have evolved by a combination of ecological/allopatric speciation and in some cases possibly sympatric speciation. We have further explored these speciation theories by phylogeographic analyses of nuclear gene data (WG, TOPO, ARK, Cn) from 86 species in the genera Limbodessus and Paroster , including analyses of genes involved in photoreception for select Paroster taxa. Analyses provide further support for the presence of sympatric sister species, thus, rejecting the hypothesis that previous phylogeographic patterns, based on mitochondrial DNA, resulted from introgressive hybridisation. Our analyses also uncovered deleterious frameshift and stop mutations in a long wavelength opsin gene that mapped to the common ancestor of a sympatric sister triplet of stygobiont species, providing strong evidence that this ancestor was already adapted to living underground and that the species triplet evolved within the confines of a single groundwater calcrete. Our analyses show that while the majority (~75%) of these stygobiont beetle species evolved from surface ancestors, a significant number ersified underground through a process of either sympatric or parapatric speciation.

Stressed out underground?: Illuminating the genomic response to heat stress in surface and subterranean predaceous diving beetles

Publisher: Pensoft Publishers

Date: 14-07-2022

DOI: 10.3897/ACA.5.E90170

Abstract: 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 stable environments might lose the ability to mount a heat shock response, which involves the expression of heat shock proteins to remediate misfolded or denaturing proteins as a result of heat stress. Such organisms might therefore be at particular risk of decline in the face of climate change. However, similarly robust data are limited for subterranean organisms. To help address this knowledge gap, here we compared the heat-shock response of a surface-dwelling and subterranean species of predaceous ing beetle (Dytiscidae, Hydroporinae), Paroster nigroadumbratus and P. macrosturtensis, the latter of which is restricted to a single groundwater aquifer in the Yilgarn region of Western Australia. Though P. macrosturtensis is able to survive warmer conditions than it encounters in nature based on past survival experiments, it is nonetheless less robust in the face of temperature extremes compared to surface-dwelling relatives the genomic basis of this difference is unknown. By sequencing transcriptomes of experimentally heat-shocked in iduals we demonstrate both species can indeed mount a heat shock response at high temperatures (35ºC). However, the genes involved in these responses differ and a far greater number are differentially expressed in the surface species, including those involved in remediating oxidative stress, which might explain its more robust response to heat stress. In contrast, the subterranean species significantly upregulated a heat shock protein gene under conditions it encounters in nature, suggesting it is far more sensitive to ambient stressors. These findings have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.

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

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.

University Of Adelaide

Location: Australia

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