ORCID Profile
0000-0002-5257-0019
Current Organisation
CSIRO National Research Collections Australia
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Developmental Genetics (incl. Sex Determination) | Genetics | Evolution of Developmental Systems | Epigenetics (incl. Genome Methylation and Epigenomics) | Evolutionary Impacts of Climate Change | Host-Parasite Interactions | Ecology | Ecosystem Function | Behavioural Ecology |
Expanding Knowledge in the Biological Sciences | Ecosystem Adaptation to Climate Change | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Expanding Knowledge in the Environmental Sciences | Forest and Woodlands Flora, Fauna and Biodiversity
Publisher: The Royal Society
Date: 15-06-2016
Abstract: Sex differences in morphology, physiology, and behaviour are caused by sex-linked genes, as well as by circulating sex-steroid levels. Thus, a shift from genotypic to environmental sex determination may create an organism that exhibits a mixture of male-like and female-like traits. We studied a lizard species (Central Bearded Dragon, Pogona vitticeps ), in which the high-temperature incubation of eggs transforms genetically male in iduals into functional females. Although they are reproductively female, sex-reversed dragons (in iduals with ZZ genotype reversed to female phenotype) resemble genetic males rather than females in morphology (relative tail length), general behaviour (boldness and activity level), and thermoregulatory tactics. Indeed, sex-reversed ‘females’ are more male-like in some behavioural traits than are genetic males. This novel phenotype may impose strong selection on the frequency of sex reversal within natural populations, facilitating rapid shifts in sex-determining systems. A single period of high incubation temperatures (generating thermally induced sex reversal) can produce functionally female in iduals with male-like (or novel) traits that enhance in idual fitness, allowing the new temperature-dependent sex-determining system to rapidly replace the previous genetically based one.
Publisher: Springer Science and Business Media LLC
Date: 12-2017
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Wiley
Date: 27-11-2021
DOI: 10.1111/DDI.13203
Abstract: Species with temperature‐dependent sex determination (TSD) are particularly vulnerable to climate change because a resultant skew in population sex ratio can have severe demographic consequences and increase vulnerability to local extinction. The Australian central bearded dragon ( Pogona vitticep s) has a thermosensitive ZZ male/ZW female system of genetic sex determination (GSD). High incubation temperatures cause reversal of the ZZ genotype to a viable female phenotype. Nest temperatures in the wild are predicted to vary on a scale likely to produce heterogeneity in the occurrence of sex reversal, and so we predict that sex reversal will correlate positively with inferred incubation conditions. Mainland Australia. Wild‐caught specimens of P. vitticeps vouchered in museum collections and collected during targeted field trips were genotypically and phenotypically sexed to determine the distribution of sex reversal across the species range. To determine whether environmental conditions or genetic structure can explain this distribution, we infer the incubation conditions experienced by each in idual and apply a multi‐model inference approach to determine which conditions associate with sex reversal. Further, we conduct reduced representation sequencing on a subset of specimens to characterize the population structure of this broadly distributed species. Here we show that sex reversal in this widespread Australian dragon lizard is spatially restricted to the eastern part of the species range. Neither climatic variables during the inferred incubation period nor geographic population genetic structure explain this disjunct distribution of sex reversal. The main source of genetic variation arose from isolation by distance across the species range. We propose that local genetic adaptation in the temperature threshold for sex reversal can counteract the sex‐reversing influence of high incubation temperatures in P. vitticeps . Our study demonstrates that complex evolutionary processes need to be incorporated into modelling biological responses to future climate scenarios.
Publisher: S. Karger AG
Date: 2016
DOI: 10.1159/000450972
Abstract: Is sex a product of genes, the environment, or both? In this review, we describe the ersity of sex-determining mechanisms in reptiles, with a focus on systems that display gene-environment interactions. We summarise the field and laboratory-based evidence for the occurrence of environmental sex reversal in reptiles and ask whether this is a widespread evolutionary mechanism affecting the evolution of sex chromosomes and speciation in vertebrates. Sex determination systems exist across a continuum of genetic and environmental influences, blurring the lines between what was once considered a strict dichotomy between genetic sex determination and temperature-dependent sex determination. Across this spectrum, we identify the potential for sex reversal in species with clearly differentiated heteromorphic sex chromosomes i (Pogona vitticeps /i , i Bassiana duperreyi /i , i Eremias multiocellata, Gekko japonicus) /i , weakly differentiated homomorphic sex chromosomes i (Niveoscincus ocellatus) /i , and species with only a weak heritable predisposition for sex i (Emys orbicularis, Trachemys scripta) /i . We argue that sex reversal is widespread in reptiles (Testudines, Lacertidae, Agamidae, Scincidae, Gekkonidae) and has the potential to have an impact on in idual fitness, resulting in reproductively, morphologically, and behaviourally unique phenotypes. Sex reversal is likely to be a powerful evolutionary force responsible for generating and maintaining lability and ersity in reptile sex-determining modes.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-06-2017
Abstract: Alternative splicing in chromatin-modifying genes is associated with temperature-dependent sex in ergent reptile lineages.
Publisher: Springer Science and Business Media LLC
Date: 15-04-2022
DOI: 10.1038/S41598-022-09872-9
Abstract: Defences of hosts against brood parasitic cuckoos include detection and ejection of cuckoo eggs from the nest. Ejection behaviour often involves puncturing the cuckoo egg, which is predicted to drive the evolution of thicker eggshells in cuckoos that parasitise such hosts. Here we test this prediction in four Australian cuckoo species and their hosts, using Hall-effect magnetic-inference to directly estimate eggshell thickness in parasitised clutches. In Australia, hosts that build cup-shaped nests are generally adept at ejecting cuckoo eggs, whereas hosts that build dome-shaped nests mostly accept foreign eggs. We analysed two datasets: a small s le of hosts with known egg ejection rates and a broader s le of hosts where egg ejection behaviour was inferred based on nest type (dome or cup). Contrary to predictions, cuckoos that exploit dome-nesting hosts (acceptor hosts) had significantly thicker eggshells relative to their hosts than cuckoos that exploit cup-nesting hosts (ejector hosts). No difference in eggshell thicknesses was observed in the smaller s le of hosts with known egg ejection rates, probably due to lack of power. Overall cuckoo eggshell thickness did not deviate from the expected avian relationship between eggshell thickness and egg length estimated from 74 bird species. Our results do not support the hypothesis that thicker eggshells have evolved in response to host ejection behaviour in Australian cuckoos, but are consistent with the hypothesis that thicker eggshells have evolved to reduce the risk of breakage when eggs are dropped into dome nests.
Publisher: Springer Science and Business Media LLC
Date: 05-10-2018
DOI: 10.1038/S41598-018-33170-Y
Abstract: Vertebrate sex differentiation follows a conserved suite of developmental events: the bipotential gonads differentiate and shortly thereafter sex specific traits become dimorphic. However, this may not apply to squamates, a erse vertebrate lineage comprising of many species with thermosensitive sexual development. Of the three species with data on the relative timing of gonad differentiation and genital dimorphism, the females of two ( Niveoscincus ocellatus and Barisia imbricata ) exhibit a phase of temporary pseudohermaphroditism or TPH (gonads have differentiated well before genital dimorphism). We report a third ex le of TPH in Pogona vitticeps , an agamid with temperature-induced male to female sex reversal. These findings suggest that for female squamates, genital and gonad development may not be closely synchronised, so that TPH may be common. We further observed a high frequency of ovotestes, a usually rare gonadal phenotype characterised by a mix of male and female structures, exclusively associated with temperature-induced sex reversal. We propose that ovotestes are evidence of a period of antagonism between male and female sex-determining pathways during sex reversal. Female sexual development in squamates is considerably more complex than has been appreciated, providing numerous avenues for future exploration of the genetic and hormonal cues that govern sexual development.
Publisher: Wiley
Date: 02-2018
DOI: 10.1111/DDI.12717
Publisher: American Association for the Advancement of Science (AAAS)
Date: 11-05-2018
Abstract: Temperature-responsive epigenetic regulation clarifies a 50-year-old mystery in reptiles
Publisher: Cold Spring Harbor Laboratory
Date: 11-10-2021
DOI: 10.1101/2021.10.11.463868
Abstract: Australia is remarkable for its lizard ersity, with very high endemicity because of continental-scale ersification and adaptive radiation. We employed 10X Genomics Chromium linked-reads technology to generate male and female draft genomes of the jacky dragon ( Amphibolurus muricatus ), an Australian dragon lizard (family Agamidae). The assemblies are 1.8 Gb in size and have a repeat content (38%) and GC content (42%) similar to other dragon lizards. The contig N50 values for the assemblies were 37.2 kb (female) and 28.8 kb (male), with corresponding scaffold N50 values of 720.5 kb and 369 kb. The longest scaffold was 6.5 Mb in each assembly. The BUSCO completeness percentages were 92.2% and 90.8% respectively. These statistics are comparable to other lizard genomes assembled using similar technology. Phylogenetic comparisons show that Australian dragon lizard species split from a common ancestor around 33.4 million years ago. The draft A. muricatus assemblies will be a valuable resource for understanding lizard sex determination and the evolution and conservation of Australian dragon lizards.
Publisher: Wiley
Date: 03-2022
DOI: 10.1002/ECE3.8627
Abstract: Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific isions to be factored into conservation planning—subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic ersity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 in iduals) covering the distribution of the Australian eastern three‐lined skink, Bassiana duperreyi , to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well‐supported diagnosable operational taxonomic units (OTUs) existed within B . duperreyi . Low levels of ergence of B . duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait ( ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re‐evaluation of this species complex and the need for bio ersity assessment to include an examination of cryptic species and/or cryptic ersity below the level of species. Such information on lineage ersity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.
Publisher: Wiley
Date: 06-02-2020
DOI: 10.1111/BRV.12582
Publisher: Springer Science and Business Media LLC
Date: 02-07-2018
Publisher: PeerJ
Date: 05-01-2016
DOI: 10.7717/PEERJ.1550
Abstract: Although the majority of passerine birds are socially monogamous, true genetic monogamy is rare, with extra-pair paternity (EPP) occurring in almost 90% of surveyed socially monogamous species. We present the first molecular data on the genetic breeding system of the long-tailed finch, Poephila acuticauda , a grass finch endemic to the tropical northern savannah of Australia. Although the species forms socially monogamous pair bonds during the breeding season, we found that extra-pair males sired 12.8% of 391 offspring, in 25.7% of 101 broods. Our findings provide only the second estimate of extra-pair paternity in the estrildid finch family.
Publisher: Elsevier BV
Date: 02-2010
Publisher: S. Karger AG
Date: 2021
DOI: 10.1159/000515687
Abstract: Sex reversal is the process by which an in idual develops a phenotypic sex that is discordant with its chromosomal or genotypic sex. It occurs in many lineages of ectothermic vertebrates, such as fish, hibians, and at least one agamid and one scincid reptile species. Sex reversal is usually triggered by an environmental cue that alters the genetically determined process of sexual differentiation, but it can also be caused by exposure to exogenous chemicals, hormones, or pollutants. Despite the occurrence of both temperature-dependent sex determination (TSD) and genetic sex determination (GSD) broadly among reptiles, only 2 species of squamates have thus far been demonstrated to possess sex reversal in nature (GSD with overriding thermal influence). The lack of species with unambiguously identified sex reversal is not necessarily a reflection of a low incidence of this trait among reptiles. Indeed, sex reversal may be relatively common in reptiles, but little is known of its prevalence, the mechanisms by which it occurs, or the consequences of sex reversal for species in the wild under a changing climate. In this review, we present a roadmap to the discovery of sex reversal in reptiles, outlining the various techniques that allow new occurrences of sex reversal to be identified, the molecular mechanisms that may be involved in sex reversal and how to identify them, and approaches for assessing the impacts of sex reversal in wild populations. We discuss the evolutionary implications of sex reversal and use the central bearded dragon ( i Pogona vitticeps /i ) and the eastern three-lined skink ( i Bassiana duperreyi /i ) as ex les of how species with opposing patterns of sex reversal may be impacted differently by our rapidly changing climate. Ultimately, this review serves to highlight the importance of understanding sex reversal both in the laboratory and in wild populations and proposes practical solutions to foster future research.
Publisher: Oxford University Press (OUP)
Date: 28-09-2015
Publisher: Wiley
Date: 09-05-2019
Abstract: Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths members of their more- erse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60-year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow-hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near-complete mitochondrial genomes at a coverage of 40-83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world-wide, genetic data from eggshell could provide a rapid and cost-effective approach to examining temporal changes in avian ersity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome-wide evolutionary processes.
Publisher: Springer Science and Business Media LLC
Date: 02-2021
Publisher: Wiley
Date: 08-07-2011
Publisher: Springer Science and Business Media LLC
Date: 07-08-2014
Publisher: Cold Spring Harbor Laboratory
Date: 24-09-2021
DOI: 10.1101/2021.09.23.461594
Abstract: In some vertebrate species, gene-environment interactions can determine sex, driving bipotential gonads to differentiate into either ovaries or testes. In the central bearded dragon ( Pogona vitticeps ), the genetic influence of sex chromosomes (ZZ/ZW) can be overridden by high incubation temperatures, causing ZZ male to female sex reversal. Previous research showed ovotestes, a rare gonadal phenotype with traits of both sexes, develop during sex reversal, leading to the hypothesis that sex reversal relies on high temperature feminisation to outcompete the male genetic cue. To test this, we conducted temperature switching experiments at key developmental stages, and analysed the effect on gonadal phenotypes using histology and transcriptomics. We found sexual fate is more strongly influenced by the ZZ genotype than temperature. Any exposure to low temperatures (28°C) caused testes differentiation, whereas sex reversal required longer exposure to high temperatures. We revealed ovotestes exist along a spectrum of female-ness to male-ness at the transcriptional level. We found inter-in idual variation in gene expression changes following temperature switches, suggesting both genetic sensitivity to, and the timing and duration of the temperature cue influences sex reversal. These findings bring new insights to the mechanisms underlying sex reversal, improving our understanding of thermosensitive sex systems in vertebrates.
Publisher: Future Science Ltd
Date: 06-2009
DOI: 10.2144/000113156
Abstract: Multiplex Manager 1.0 is a user-friendly cross-platform program that designs efficient combinations of existing genetic marker loci into multiplex polymerase chain reactions and optimizes using prior marker information. The program has the flexibility to solve two design problems: combining all markers into the smallest number of reactions, or alternatively, selecting a subset from many available markers to design an efficient and robust multiplex. Our program minimizes the number of reactions, the genetic linkage, and the difference in annealing temperature. At the same time it maximizes the spacing between markers, the heterozygosity, and the number of alleles. The final output provides easily interpreted and informative graphical representations of reactions, as well as the option of manually editing final reactions. Multiplex Manager 1.0 is freely available at www.multiplexmanager.com .
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-04-2022
Abstract: Sex determination and differentiation in reptiles are complex. In the model species, Pogona vitticeps , high incubation temperature can cause male to female sex reversal. To elucidate the epigenetic mechanisms of thermolabile sex, we used an unbiased genome-wide assessment of intron retention during sex reversal. The previously implicated chromatin modifiers ( jarid2 and kdm6b ) were two of three genes to display sex reversal–specific intron retention. In these species, embryonic intron retention resulting in C-terminally truncated jarid2 and kdm6b isoforms consistently occurs at low temperatures. High-temperature sex reversal is uniquely characterized by a high prevalence of N-terminally truncated isoforms of jarid2 and kdm6b , which are not present at low temperatures, or in two other reptiles with temperature-dependent sex determination. This work verifies that chromatin-modifying genes are involved in highly conserved temperature responses and can also be transcribed into isoforms with new sex-determining roles.
Publisher: Springer Science and Business Media LLC
Date: 10-12-2012
Publisher: Wiley
Date: 07-01-2021
DOI: 10.1002/JEZ.2441
Publisher: Cold Spring Harbor Laboratory
Date: 20-04-2021
DOI: 10.1101/2021.04.18.440380
Abstract: Museum specimens represent an unparalleled record of historical genomic data. However, the wide-spread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine s le processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically erse specimens collected between 1936 and 2015 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3X nuclear genome coverage from formalin-fixed tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out- performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. We demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and non-destructive assessment criteria. Sequencing of formalin-fixed specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
Publisher: Wiley
Date: 20-04-2009
DOI: 10.1111/J.1755-0998.2009.02528.X
Abstract: We describe 18 microsatellite markers isolated in the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps). The number of alleles ranged from seven to 16 per locus (mean N(a) = 10.4 ± 0.54 SE) and the expected heterozygosity ranged from 0.732 to 0.889 (mean H(E) = 0.836 ± 0.01 SE). Three of the 18 loci exhibited significant heterozygote deficiency, but the remaining 15 will be used to analyse population genetic structure and the mating system of this highly social species.
Publisher: MDPI AG
Date: 05-11-2020
DOI: 10.3390/SYM12111835
Abstract: The Cosmic-Ray Extremely Distributed Observatory (CREDO) is a newly formed, global collaboration dedicated to observing and studying cosmic rays (CR) and cosmic-ray ensembles (CRE): groups of at least two CR with a common primary interaction vertex or the same parent particle. The CREDO program embraces testing known CR and CRE scenarios, and preparing to observe unexpected physics, it is also suitable for multi-messenger and multi-mission applications. Perfectly matched to CREDO capabilities, CRE could be formed both within classical models (e.g., as products of photon–photon interactions), and exotic scenarios (e.g., as results of decay of Super-Heavy Dark Matter particles). Their fronts might be significantly extended in space and time, and they might include cosmic rays of energies spanning the whole cosmic-ray energy spectrum, with a footprint composed of at least two extensive air showers with correlated arrival directions and arrival times. As the CRE are predominantly expected to be spread over large areas and, due to the expected wide energy range of the contributing particles, such a CRE detection might only be feasible when using all available cosmic-ray infrastructure collectively, i.e., as a globally extended network of detectors. Thus, with this review article, the CREDO Collaboration invites the astroparticle physics community to actively join or to contribute to the research dedicated to CRE and, in particular, to pool together cosmic-ray data to support specific CRE detection strategies.
Publisher: Wiley
Date: 15-02-2012
Publisher: JMIR Publications Inc.
Date: 20-11-2021
Abstract: chwartz Rounds are a unique, organization-wide interdisciplinary intervention aimed at enhancing staff well-being, compassionate care, teamwork, and organizational culture in health care settings. They provide a safe space wherein both clinical and nonclinical health staff can connect and share their experiences about the social and emotional aspects of health care. lthough Schwartz Rounds have been assessed and widely implemented in the United States and United Kingdom, they are yet to be formally evaluated in Australian health care settings. The purpose of this study is to evaluate the feasibility and impact of Schwartz Rounds on staff well-being, compassionate care, and organizational culture, in a tertiary metropolitan hospital in Brisbane, Australia. his mixed methods repeated measures pilot study will recruit 24 participants in 2 groups from 2 departments, the intensive care unit and the gastroenterology department. Participants from each group will take part in 3 unit-based Schwartz Rounds. Primary outcomes will include the study and intervention feasibility measures, while secondary outcomes will include scores on the Maslach Burnout Inventory–Human Services Survey, the Schwartz Centre Compassionate Care Scale, and the Culture of Care Barometer. Primary and secondary outcomes will be collected at baseline, after the Rounds, and 3-month follow-up. Two focus groups will be held approximately 2 months after completion of the Schwartz Rounds. Descriptive statistics, paired t tests, chi-square tests, and analysis of variance will be used to compare quantitative data across time points and groups. Qualitative data from focus groups and free-text survey questions will be analyzed using an inductive thematic analysis approach. he study was approved by the Mater Hospital Human Research Ethics Committee (reference number: HREC/MML/71868) and recruitment commenced in July 2021 study completion is anticipated by May 2022. he study will contribute to the assessment of feasibility and preliminary efficacy of the Schwartz Rounds in a tertiary Australian hospital during the COVID-19 pandemic. ustralian New Zealand Clinical Trials Registry ACTRN12621001473853 www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=382769& isReview=true ERR1-10.2196/35083
Publisher: Springer Science and Business Media LLC
Date: 11-08-2021
DOI: 10.1007/S10530-021-02609-1
Abstract: The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become one of New Zealand’s most significant pests. Although derived from two subspecies, possums in New Zealand are generally considered to be a single entity. In a previous analysis, we showed that possums in the Hawkes Bay region of New Zealand appeared to consist of at least two overlapping populations. Here, we extend that analysis using a genotype-by-sequencing approach to examine the origins and population structure of those possums and compare their genetic ersity to animals s led from Australia. We identify two populations of each subspecies in Hawkes Bay and provide clear evidence of a contact zone between them in which a hybrid form is evident. Our analysis of private alleles shows higher rates of dispersal into the contact zone than away from it, suggesting that the contact zone functions as a sink (and hence as a barrier) between the two subspecies. Given the widespread and overlapping distribution of the two subspecies across both large islands in New Zealand, it is possible that many such contact zones exist. These results suggest an opportunity for a more targeted approach to controlling this pest by recognising sub-specific differences and identifying the contact zones that may form between them.
Publisher: Springer Science and Business Media LLC
Date: 15-01-2021
DOI: 10.1038/S41598-020-79852-4
Abstract: Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three s ling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird’s egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen’s appearance or integrity. This method proved superior to swabbing the external surface or s ling the interior however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species’ accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.
Publisher: Wiley
Date: 14-08-2006
Publisher: Springer Science and Business Media LLC
Date: 11-10-2021
DOI: 10.1038/S41598-021-99702-1
Abstract: Altered climate regimes have the capacity to affect the physiology, development, ecology and behaviour of organisms dramatically, with consequential changes in in idual fitness and so the ability of populations to persist under climatic change. More directly, extreme temperatures can directly skew the population sex ratio in some species, with substantial demographic consequences that influence the rate of population decline and recovery rates. In contrast, this is particularly true for species whose sex is determined entirely by temperature (TSD). The recent discovery of sex reversal in species with genotypic sex determination (GSD) due to extreme environmental temperatures in the wild broadens the range of species vulnerable to changing environmental temperatures through an influence on primary sex ratio. Here we document the levels of sex reversal in nests of the Australian alpine three-lined skink ( Bassiana duperreyi ), a species with sex chromosomes and sex reversal at temperatures below 20 °C and variation in rates of sex reversal with elevation. The frequency of sex reversal in nests of B. duperreyi ranged from 28.6% at the highest, coolest locations to zero at the lowest, warmest locations. Sex reversal in this alpine skink makes it a sensitive indicator of climate change, both in terms of changes in average temperatures and in terms of climatic variability.
Publisher: Wiley
Date: 05-2008
Publisher: Wiley
Date: 03-02-2020
DOI: 10.1111/JEB.13587
Abstract: Sex reversal at high temperatures during embryonic development (e.g., ZZ females) provides the opportunity for new genotypic crosses (e.g., ZZ male × ZZ female). This raises the alarming possibility that climatic warming could lead to the loss of an entire chromosome-one member of the sex chromosome pair (the Y or W)-and the transition of populations to environmental sex determination (ESD). Here we examine the evolutionary dynamics of sex-determining systems exposed to climatic warming using theoretical models. We found that the loss of sex chromosomes is not an inevitable consequence of sex reversal. A large frequency of ZZ sex reversal (50% reversal from male to female) typically ides the outcome between loss of the ZW genotype and the stable persistence of ZZ males, ZW females and ZZ females. The amount of warming associated with sex chromosome loss depended on several features of wild populations-environmental fluctuation, immigration, heritable variation in temperature sensitivity and differential fecundity of sex-reversed in iduals. Chromosome loss was partially or completely buffered when sex-reversed in iduals suffered a reproductive fitness cost, when immigration occurred or when heritable variation for temperature sensitivity existed. Thus, under certain circumstances, sex chromosomes may persist cryptically in systems where the environment is the predominant influence on sex.
Publisher: Springer Science and Business Media LLC
Date: 29-09-2020
DOI: 10.1186/S12864-020-07071-2
Abstract: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence ergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. We generated 96.7 × 10 9 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 10 9 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi . Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
Publisher: The Royal Society
Date: 20-01-2021
Abstract: Sex determination and differentiation in reptiles is complex. Temperature-dependent sex determination (TSD), genetic sex determination (GSD) and the interaction of both environmental and genetic cues (sex reversal) can drive the development of sexual phenotypes. The jacky dragon ( Amphibolurus muricatus ) is an attractive model species for the study of gene–environment interactions because it displays a form of Type II TSD, where female-biased sex ratios are observed at extreme incubation temperatures and approximately 50 : 50 sex ratios occur at intermediate temperatures. This response to temperature has been proposed to occur due to underlying sex determining loci, the influence of which is overridden at extreme temperatures. Thus, sex reversal at extreme temperatures is predicted to produce the female-biased sex ratios observed in A. muricatus . The occurrence of ovotestes during development is a cellular marker of temperature sex reversal in a closely related species Pogona vitticeps . Here, we present the first developmental data for A. muricatus , and show that ovotestes occur at frequencies consistent with a mode of sex determination that is intermediate between GSD and TSD. This is the first evidence suggestive of underlying unidentified sex determining loci in a species that has long been used as a model for TSD.
Publisher: Springer Science and Business Media LLC
Date: 27-11-2010
Publisher: Springer Science and Business Media LLC
Date: 16-09-2011
Publisher: Wiley
Date: 14-02-2020
DOI: 10.1002/JEZ.2353
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2021
DOI: 10.1101/2021.02.03.429474
Abstract: How temperature determines sex remains unknown. A recent hypothesis proposes that conserved cellular mechanisms (calcium and redox ‘CaRe’ status) sense temperature and identify genes and regulatory pathways likely to be involved in driving sexual development. We take advantage of the unique sex determining system of the model organism, Pogona vitticeps , to assess predictions of this hypothesis. P. vitticeps has ZZ male: ZW female sex chromosomes whose influence can be overridden in genetic males by high temperatures, causing male-to-female sex reversal. We compare a developmental transcriptome series of ZWf females and temperature sex reversed ZZf females. We demonstrate that early developmental cascades differ dramatically between genetically driven and thermally driven females, later converging to produce a common outcome (ovaries). We show that genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. Our study greatly advances the search for the mechanisms by which temperature determines sex. In many reptiles and fish, environment can determine, or influence, the sex of developing embryos. How this happens at a molecular level that has eluded resolution for half a century of intensive research. We studied the bearded dragon, a lizard that has sex chromosomes (ZZ male and ZW female), but in which that temperature can override ZZ sex chromosomes to cause male to female sex reversal. This provides an unparalleled opportunity to disentangle, in the same species, the biochemical pathways required to make a female by these two different routes. We sequenced the transcriptomes of gonads from developing ZZ reversed and normal ZW dragon embryos and discovered that different sets of genes are active in ovary development driven by genotype or temperature. Females whose sex was initiated by temperature showed a transcriptional profile consistent with the recently-proposed Calcium-Redox hypotheses of cellular temperature sensing. These findings are an important for understanding how the environment influences the development of sex, and more generally how the environment can epigenetically modify the action of genes.
Publisher: Cold Spring Harbor Laboratory
Date: 28-07-2023
DOI: 10.1101/2023.07.26.550239
Abstract: Co-ordinated regulation or dysregulation of chromatin architecture underpins fundamental biological processes, such as embryonic development, disease, cellular programming and response to environmental stress. The dynamic and plastic nature of chromatin accessibility is a major driver of phenotypic ersity, but we know shockingly little about the temporal dynamics of chromatin reorganisation and almost nothing prior to the existence of flash-frozen specimens. Linking two disparate fields by their common use and application of the preservative formaldehyde, we present an approach to characterise chromatin architecture in formaldehyde-preserved specimens up to 117 years old. We characterise how over-fixation modulates but does not eliminate genome-wide patterns of differential chromatin accessibility. Our novel analytical approach identifies promoter regions enriched for gene ontology terms matching the tissue of origin, resulting in sex-specific and environment-dependent genome-wide profiles. Contrary to prevailing dogma, we show that over-fixation is essential for the successful recovery of historical chromatin architecture. Our methodological and analytical advances open the door to the first detailed and comprehensive view of the epigenetic past and reveal a new role for museum collections in understanding chromatin architecture dynamics over the last century.
Publisher: MDPI AG
Date: 30-10-2020
DOI: 10.3390/SYM12111802
Abstract: We present the purpose, long-term development vision, basic design, detection algorithm and preliminary results obtained with the Cosmic Ray Extremely Distributed Observatory (CREDO) Detector mobile application. The CREDO Detector app and related infrastructure are unique in terms of their scale, targeting many form-factors and open-access philosophy. This philosophy translates to the open-source code of the app, open-access in terms of both data inflow as well as data consumption and above all, the citizen science philosophy that means that the infrastructure is open to all who wish to participate in the project. The CREDO infrastructure and CREDO Detector app are designed for the large-scale study of various radiation forms that continuously reach the Earth from space, but with the sensitivity to local radioactivity as well. Such study has great significance both scientifically and educationally as cosmic radiation has an impact on erse research areas from life on Earth to the functioning of modern electronic devices. The CREDO Detector app is now working worldwide across phones, tablets, laptops, PCs and cheap dedicated registration stations. These erse measurements contribute to the broader search for large-scale cosmic ray correlations, as well as the CREDO-specific proposed extensive air showers and incoherent secondary cosmic rays.
Publisher: MDPI AG
Date: 03-2022
DOI: 10.3390/SYM14030501
Abstract: The Cosmic Ray Extremely Distributed Observatory (CREDO) pursues a global research strategy dedicated to the search for correlated cosmic rays, so-called Cosmic Ray Ensembles (CRE). Its general approach to CRE detection does not involve any a priori considerations, and its search strategy encompasses both spatial and temporal correlations, on different scales. Here we search for time clustering of the cosmic ray events collected with a small sea-level extensive air shower array at the University of Adelaide. The array consists of seven one-square-metre scintillators enclosing an area of 10 m × 19 m. It has a threshold energy ~0.1 PeV, and records cosmic ray showers at a rate of ~6 mHz. We have examined event arrival times over a period of over 2.5 years in two equipment configurations (without and with GPS timing), recording ~300 k events and ~100 k events. We determined the event time spacing distributions between in idual events and the distributions of time periods which contained specific numbers of multiple events. We find that the overall time distributions are as expected for random events. The distribution which was chosen a priori for particular study was for time periods covering five events (four spacings). Overall, these distributions fit closely with expectation, but there are two outliers of short burst periods in data for each configuration. One of these outliers contains eight events within 48 s. The physical characteristics of the array will be discussed together with the analysis procedure, including a comparison between the observed time distributions and expectation based on randomly arriving events.
Publisher: CSIRO Publishing
Date: 28-09-2020
DOI: 10.1071/ZO21017
Abstract: Australian lizards are a erse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable ersity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship mechanisms involved in mating, egg production, and sperm competition nesting and gestation sex determination and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.
Publisher: Elsevier BV
Date: 04-2020
DOI: 10.1016/J.TREE.2019.12.005
Abstract: Epigenomic state preserved in museum specimens could be leveraged to provide unique insights into gene regulation trends associated with accelerating environmental change during the Anthropocene. We address the challenges facing museum epigenomics and propose a collaborative framework for researchers and curators to explore this new field.
Publisher: Springer Science and Business Media LLC
Date: 10-06-2016
Publisher: Elsevier BV
Date: 24-06-2021
DOI: 10.1186/S40657-021-00266-5
Abstract: Bird nests are an important part of avian ecology. They are a powerful tool for studying not only the birds that built them, but a wide array of topics ranging from parasitology, urbanisation and climate change to evolution. Despite this, bird nests tend to be underrepresented in natural history collections, a problem that should be redressed through renewed focus by collecting institutions. Here we outline the history and current best practice collection and curatorial methods for the nest collection of the Australian National Wildlife Collection (ANWC). We also describe an experiment conducted on nests in the ANWC using ultrasonic humidification to restore the shape of nests damaged by inappropriate storage. The experiment showed that damaged nests can be successfully reshaped to close to their original dimensions. Indeed, restored nests were significantly closer to their original shape than they were prior to restoration. Thus, even nests damaged by years of neglect may be fully incorporated into active research collections. Best practice techniques include extensive note taking and photography in the field, subs ling of nests that cannot or should not be collected, appropriate field storage, metadata management, and prompt treatment upon arrival at the collection facility. Renewed focus on nest collections should include appropriate care and restoration of current collections, as well as expansion to redress past underrepresentation. This could include collaboration with researchers studying or monitoring avian nesting ecology, and nest collection after use in bird species that rebuild anew each nesting attempt. Modern expansion of museum nest collections will allow researchers and natural history collections to fully realise the scientific potential of these complex and beautiful specimens.
Publisher: PeerJ
Date: 08-01-2019
DOI: 10.7717/PEERJ.6180
Abstract: The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider ( Petaurus breviceps ), endemic to Australia and New Guinea is a popular domestic pet due to its small size and “cute” demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with s les collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the s les tested within this study.
Publisher: Springer Science and Business Media LLC
Date: 07-2015
DOI: 10.1038/NATURE14574
Abstract: Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for ex le, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in hibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.
Publisher: S. Karger AG
Date: 2021
DOI: 10.1159/000518374
Publisher: Wiley
Date: 10-2022
Abstract: Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine s le processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically erse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.
Start Date: 2017
End Date: 2020
Funder: Australian Research Council
View Funded ActivityStart Date: 2018
End Date: 2020
Funder: Australian Research Council
View Funded ActivityStart Date: 2022
End Date: 12-2025
Amount: $1,257,021.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2017
End Date: 12-2021
Amount: $1,006,500.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2018
End Date: 05-2023
Amount: $424,192.00
Funder: Australian Research Council
View Funded Activity