ORCID Profile
0000-0002-6328-398X
Current Organisations
Foshan University
,
University of Sydney
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Research Topics
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.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Genetic Immunology | Population, Ecological and Evolutionary Genetics | Zoology not elsewhere classified | Animal Immunology | Wildlife and Habitat Management | Environmental Science and Management | Genetics | Conservation and Biodiversity | Zoology |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity of environments not elsewhere classified | Effects of Climate Change and Variability on Australia (excl. Social Impacts) | Ecosystem Assessment and Management of Forest and Woodlands Environments | Expanding Knowledge in the Agricultural and Veterinary Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales | Forest and Woodlands Flora, Fauna and Biodiversity
Related Links
Publications
Best genome sequencing strategies for annotation of complex immune gene families in wildlife
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/GIGASCIENCE/GIAC100
Abstract: The bio ersity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic ersity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation. Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
Author Correction: Universal DNA methylation age across mammalian tissues
Publisher: Springer Science and Business Media LLC
Date: 06-09-2023
Immunization strategies producing a humoral IgG immune response against devil facial tumor disease in the majority of Tasmanian devils destined for wild release
Publisher: Frontiers Media SA
Date: 19-02-2018
Toneburst-evoked auditory brainstem response in a leopard seal, Hydrurga leptonyx
Publisher: Acoustical Society of America (ASA)
Date: 2011
DOI: 10.1121/1.3514370
Abstract: Toneburst-evoked auditory brainstem responses (ABRs) were recorded in a captive subadult male leopard seal. Three frequencies from 1 to 4 kHz were tested at sound levels from 68 to 122 dB peak equivalent sound pressure level (peSPL). Results illustrate brainstem activity within the 1–4 kHz range, with better hearing sensitivity at 4 kHz. As is seen in human ABR, only wave V is reliably identified at the lower stimulus intensities. Wave V is present down to levels of 82 dB peSPL in the right ear and 92 dB peSPL in the left ear at 4 kHz. Further investigations testing a wider frequency range on seals of various sex and age classes are required to conclusively report on the hearing range and sensitivity in this species.
MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils
Publisher: Oxford University Press (OUP)
Date: 13-06-2019
Abstract: Mate choice contributes to driving evolutionary processes when animals choose breeding partners that confer genetic advantages to offspring, such as increased immunocompetence. The major histocompatibility complex (MHC) is an important group of immunological molecules, as MHC antigens bind and present foreign peptides to T-cells. Recent studies suggest that mates may be selected based on their MHC profile, leading to an association between an in idual’s MHC ersity and their breeding success. In conservation, it may be important to consider mate choice in captive breeding programs, as this mechanism may improve reproductive rates. We investigated the reproductive success of Tasmanian devils in a group housing facility to determine whether increased MHC-based heterozygosity led in iduals to secure more mating partners and produce more offspring. We also compared the breeding success of captive females to a wild devil population. MHC ersity was quantified using 12 MHC-linked microsatellite markers, including 11 previously characterized markers and one newly identified marker. Our analyses revealed that there was no relationship between MHC-linked heterozygosity and reproductive success either in captivity or the wild. The results of this study suggest that, for Tasmanian devils, MHC-based heterozygosity does not produce greater breeding success and that no specific changes to current captive management strategies are required with respect to preserving MHC ersity.
MHC diversity and female age underpin reproductive success in an Australian icon; the Tasmanian Devil
Publisher: Springer Science and Business Media LLC
Date: 08-03-2018
DOI: 10.1038/S41598-018-20934-9
Abstract: Devil Facial Tumour Disease (DFTD), a highly contagious cancer, has decimated Tasmanian devil ( Sarcophilus harrisii ) numbers in the wild. To ensure its long-term survival, a captive breeding program was implemented but has not been as successful as envisaged at its launch in 2005. We therefore investigated the reproductive success of 65 captive devil pair combinations, of which 35 produced offspring (successful pairs) whereas the remaining 30 pairs, despite being observed mating, produced no offspring (unsuccessful pairs). The devils were screened at six MHC Class I-linked microsatellite loci. Our analyses revealed that younger females had a higher probability of being successful than older females. In the successful pairs we also observed a higher difference in total number of heterozygous loci, i.e. when one devil had a high total number of heterozygous loci, its partner had low numbers. Our results therefore suggest that devil reproductive success is subject to disruptive MHC selection, which to our knowledge has never been recorded in any vertebrate. In order to enhance the success of the captive breeding program the results from the present study show the importance of using young (2-year old) females as well as subjecting the devils to MHC genotyping.
Reproductive success is predicted by social dynamics and kinship in managed animal populations
Publisher: F1000 Research Ltd
Date: 11-05-2016
DOI: 10.12688/F1000RESEARCH.8713.1
Abstract: Kin and group interactions are important determinants of reproductive success in many species. Their optimization could, therefore, potentially improve the productivity and breeding success of managed populations used for agricultural and conservation purposes. Here we demonstrate this potential using a novel approach to measure and predict the effect of kin and group dynamics on reproductive output in a well-known species, the meerkat Suricata suricatta . Variation in social dynamics predicts 30% of the in idual variation in reproductive success of this species in managed populations, and accurately forecasts reproductive output at least two years into the future. Optimization of social dynamics in captive meerkat populations doubles their projected reproductive output. These results demonstrate the utility of a quantitative approach to breeding programs informed by social and kinship dynamics. They suggest that this approach has great potential for improvements in the management of social endangered and agricultural species.
Characterization of reproductive gene diversity in the endangered Tasmanian devil
Publisher: Wiley
Date: 26-11-2021
A case for genetic parentage assignment in captive group housing
Publisher: Springer Science and Business Media LLC
Date: 04-06-2019
Determination of steroid hormones in whale blow: It is possible
Publisher: Wiley
Date: 07-2009
A demonstration of conservation genomics for threatened species management
Publisher: Wiley
Date: 24-07-2020
Effects of deslorelin implants on reproduction and feeding behavior in Tasmanian devils (Sarcophilus harrisii) housed in free-range enclosures
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.THERIOGENOLOGY.2017.10.047
Abstract: In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic ersity by managing the reproductive contribution of each in idual, which can be facilitated through the use of selective contraception. This becomes critical when captive populations are held for several generations, and managers must prevent the confines of housing space and financial support from compromising genetic integrity. For ex le, the Tasmanian devil insurance population, established in 2006, is strategically managed to equalize founder representation. This becomes difficult when devils are housed in large groups in free-range enclosures (FREs). This study examined the efficacy, duration and potential side effects of Suprelorin
Stopping the spin cycle: genetics and bio-banking as a tool for addressing the laundering of illegally caught wildlife as ‘captive-bred’
Publisher: Springer Science and Business Media LLC
Date: 14-06-2018
Devil women
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/PC18021
Abstract: The Tasmanian devil, an iconic carnivorous marsupial, is at risk of extinction due to a contagious cancer called devil facial tumour disease. Saving any species from extinction requires strong partnerships between government agencies, zoo bodies and academia. The Devil Tools & Tech project brought these groups together under a single banner to achieve a common goal. The project has strong leadership from women. Here we tell our personal stories as to how we came to be involved in saving the devil and emphasise the importance of strong networks for women to reach their full potential.
Adaptation and conservation insights from the koala genome
Publisher: Springer Science and Business Media LLC
Date: 02-07-2018
Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial
Publisher: Cold Spring Harbor Laboratory
Date: 14-02-2022
DOI: 10.1101/2022.02.13.480287
Abstract: The numbat ( Myrmecobius fasciatus ) is a critically endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10× Genomics chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 Kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation with Fgenesh++, identifying 21,465 protein-coding genes and 78.7% complete mammalian BUSCOs. To investigate adaptation to the numbat’s termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, as expected. Similarly, umami taste receptors were also expressed in the tongue, however sweet taste receptors were not expressed in this tissue. This pattern of taste receptor expression, combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialized termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials and have not undergone expansion or contraction. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.
Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern
Publisher: Wiley
Date: 12-09-2021
DOI: 10.1111/MEC.16141
Abstract: Structural variants (SVs) are large rearrangements ( bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on in idual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future‐focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP‐based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and ecoevolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
Tasmanian Devil Facial Tumor Disease
Publisher: Elsevier
Date: 2019
A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi
Publisher: GigaScience Press
Date: 10-12-2021
DOI: 10.46471/GIGABYTE.35
Abstract: Bio ersity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie (Bettongia penicillata ogilbyi), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.
Increasing generations in captivity is associated with increased vulnerability of Tasmanian devils to vehicle strike following release to the wild
Publisher: Springer Science and Business Media LLC
Date: 19-05-2017
DOI: 10.1038/S41598-017-02273-3
Abstract: Captive breeding of threatened species, for release to the wild, is critical for conservation. This strategy, however, risks producing captive-raised animals with traits poorly suited to the wild. We describe the first study to characterise accumulated consequences of long-term captive breeding on behaviour, by following the release of Tasmanian devils to the wild. We test the impact of prolonged captive breeding on the probability that captive-raised animals are fatally struck by vehicles. Multiple generations of captive breeding increased the probability that in iduals were fatally struck, a pattern that could not be explained by other confounding factors (e.g. age or release site). Our results imply that long-term captive breeding programs may produce animals that are naïve to the risks of the post-release environment. Our analyses have already induced changes in management policy of this endangered species, and serve as model of productive synergy between ecological monitoring and conservation strategy.
Koala Genome Survey: An Open Data Resource to Improve Conservation Planning
Publisher: MDPI AG
Date: 22-02-2023
Abstract: Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic ersity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
Measuring Stress in Antarctic Seals
Publisher: Springer Berlin Heidelberg
Date: 2009
Too much of a good thing? Finding the most informative genetic data set to answer conservation questions
Publisher: Wiley
Date: 20-04-2019
Abstract: Molecular markers are a useful tool allowing conservation and population managers to shed light on genetic processes affecting threatened populations. However, as technological advancements in molecular techniques continue to evolve, conservationists are frequently faced with new genetic markers, each with nuanced variation in their characteristics as well as advantages and disadvantages for informing various questions. We used a well-studied population of Tasmanian devils (Sarcophilus harrisii) from Maria Island, Tasmania, to illustrate the issues associated with combining multiple genetic data sets and to help answer a question posed by many population managers: which data set will provide the most precise and accurate estimates of the population processes we are trying to measure? We analysed in idual heterozygosity (as internal relatedness, IR) of 96 in iduals, calculated using four genetic marker types (putatively neutral microsatellites, major histocompatibility complex-linked microsatellites, reduced representation sequencing, and candidate region resequencing). We found no correlation in IR values across marker types, suggesting that various genetic markers reflect different aspects of genomic ersity. In addition, some marker types were more informative than others for conservation decision-making. Reduced representation sequencing provided the highest precision (lowest error) for estimating population-level genetic ersity, and most closely reflected genome-wide heterozygosity both theoretically and empirically. Within the conservation context, our results highlight important considerations when choosing a molecular technique for wildlife genetics.
Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils
Publisher: PeerJ
Date: 16-06-2020
DOI: 10.7717/PEERJ.9220
Abstract: Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. We used 32 microsatellite loci to examine changes in genetic ersity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. We found that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program”, which is currently augmenting small, isolated populations.
How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population
Publisher: Wiley
Date: 04-11-2021
DOI: 10.1002/EAP.2462
Abstract: Conservation introductions to islands and fenced enclosures are increasing as in situ mitigations fail to keep pace with population declines. Few studies consider the potential loss of genetic ersity and increased inbreeding if released in iduals breed disproportionately. As funding is limited and post‐release monitoring expensive for conservation programs, understanding how s ling effort influences estimates of reproductive variance is useful. To investigate this relationship, we used a well‐studied population of Tasmanian devils ( Sarcophilus harrisii ) introduced to Maria Island, Tasmania, Australia. Pedigree reconstruction based on molecular data revealed high variance in number of offspring per breeder and high proportions of unsuccessful in iduals. Computational subs ling of 20%, 40%, 60%, and 80% of observed offspring resulted in inaccurate estimates of reproductive variance compared to the pedigree reconstructed with all s led in iduals. With decreased s ling effort, the proportion of inferred unsuccessful in iduals was overestimated and the variance in number of offspring per breeder was underestimated. To accurately estimate reproductive variance, we recommend s ling as many in iduals as logistically possible during the early stages of population establishment. Further, we recommend careful selection of colonizing in iduals as they may be disproportionately represented in subsequent generations. Within the conservation management context, our results highlight important considerations for s le collection and post‐release monitoring during population establishment.
Differences in wing shape of captive, critically endangered, migratory Orange-bellied Parrot Neophema chrysogaster relative to wild conspecifics
Publisher: Informa UK Limited
Date: 21-01-2021
Protect the Antarctic Peninsula — before it’s too late
Publisher: Springer Science and Business Media LLC
Date: 18-10-2020
Significant decline in anticancer immune capacity during puberty in the Tasmanian devil
Publisher: Springer Science and Business Media LLC
Date: 16-03-2017
DOI: 10.1038/SREP44716
Abstract: Tasmanian devils ( Sarcophilus harrisii ) are at risk of extinction in the wild due to Devil Facial Tumour Disease (DFTD), a rare contagious cancer. The prevalence of DFTD differs by age class: higher disease prevalence is seen in adults (2–3 years) versus younger devils ( years). Here we propose that immunological changes during puberty may play a role in susceptibility to DFTD. We show that the second year of life is a key developmental period for Tasmanian devils, during which they undergo puberty and pronounced changes in the immune system. Puberty coincides with a significant decrease in lymphocyte abundance resulting in a much higher neutrophil:lymphocyte ratio in adults than subadults. Quantitative PCR analysis of gene expression of transcription factors T-bet and GATA-3 and cytokines interferon gamma (IFN-γ) and interleukin 4 (IL-4) revealed a drastic increase in GATA-3 and IL-4 expression during puberty. These changes led to a significantly lower IFN-γ:IL-4 ratio in 2-year-olds than year olds (on average 1.3-fold difference in males and 4.0-fold in females), which reflects a major shift of the immune system towards Th2 responses. These results all indicate that adult devils are expected to have a lower anticancer immune capacity than subadults, which may explain the observed pattern of disease prevalence of DFTD in the wild.
Genetic analysis of scat samples to inform conservation of the Tasmanian devil
Publisher: Royal Zoological Society of New South Wales
Date: 2020
DOI: 10.7882/AZ.2020.005
Abstract: Recent advances in molecular genetics have enabled a great deal of information about species to be obtained from analysis of non-invasively collected s les such as scat. Scat provides genetic information via residual host DNA on the outside of the scat, via characterising the genetic makeup of intestinal microbes that are present in the scat, or by examining the DNA remnants of prey items that have passed through the animal’s digestive tract. In this review, we provide a case study to demonstrate how these approaches are being used to better understand the threatened Tasmanian devil in the landscape, and to support the species’ conservation. Scat analysis enables us to quantify the genetic ersity of remote populations, where trapping is logistically challenging. We are beginning to learn how conservation management impacts the microbiome of threatened species, and investigate how various management strategies may be impacting the erse array of bacteria and viruses that devils, like all animal species, are host to. We are using scat s les to better understand the interaction between devils and other animals in their environment by learning more about what they eat. We explore the strengths and challenges of these approaches by comparing our work to that conducted in other species. Finally, we provide specific ex les of how our results are being integrated into conservation strategy for the devil.
Metapopulation management of an Endangered species with limited genetic diversity in the presence of disease: the Tasmanian devil Sarcophilus harrisii
Publisher: Wiley
Date: 25-10-2016
DOI: 10.1111/IZY.12144
A targeted approach to investigating immune genes of an iconic Australian marsupial
Publisher: Wiley
Date: 17-05-2022
DOI: 10.1111/MEC.16493
Abstract: Disease is a contributing factor to the decline of wildlife populations across the globe. Koalas, iconic yet declining Australian marsupials, are predominantly impacted by two pathogens, Chlamydia and koala retrovirus. Chlamydia is an obligate intracellular bacterium and one of the most widespread sexually transmitted infections in humans worldwide. In koalas, Chlamydia infections can present as asymptomatic or can cause a range of ocular and urogenital disease signs, such as conjunctivitis, cystitis and infertility. In this study, we looked at differences in response to Chlamydia in two northern populations of koalas using a targeted gene sequencing of 1209 immune genes in addition to genome‐wide reduced representation data. We identified two MHC Class I genes associated with Chlamydia disease progression as well as 25 single nucleotide polymorphisms across 17 genes that were associated with resolution of Chlamydia infection. These genes are involved in the innate immune response (TLR5) and defence (TLR5, IFNγ, SERPINE1, STAT2 and STX4). This study deepens our understanding of the role that genetics plays in disease progression in koalas and leads into future work that will use whole genome resequencing of a larger s le set to investigate in greater detail regions identified in this study. Elucidation of the role of host genetics in disease progression and resolution in koalas will directly contribute to better design of Chlamydia vaccines and management of koala populations which have recently been listed as “endangered.”
Spatial movement of adult leopard seals (Hydrurga leptonyx) in Prydz Bay, Eastern Antarctica
Publisher: Springer Science and Business Media LLC
Date: 14-01-2005
Investigating inbreeding in a free-ranging, captive population of an Australian marsupial
Publisher: Springer Science and Business Media LLC
Date: 12-05-2020
Impacts of early viability selection on management of inbreeding and genetic diversity in conservation
Publisher: Wiley
Date: 04-2015
DOI: 10.1111/MEC.13141
Abstract: Maintaining genetic ersity is a crucial goal of intensive management of threatened species, particularly for those populations that act as sources for translocation or re-introduction programmes. Most captive genetic management is based on pedigrees and a neutral theory of inheritance, an assumption that may be violated by selective forces operating in captivity. Here, we explore the conservation consequences of early viability selection: differential offspring survival that occurs prior to management or research observations, such as embryo deaths in utero. If early viability selection produces genotypic deviations from Mendelian predictions, it may undermine management strategies intended to minimize inbreeding and maintain genetic ersity. We use empirical ex les to demonstrate that straightforward approaches, such as comparing litter sizes of inbred vs. noninbred breeding pairs, can be used to test whether early viability selection likely impacts estimates of inbreeding depression. We also show that comparing multilocus genotype data to pedigree predictions can reveal whether early viability selection drives systematic biases in genetic ersity, patterns that would not be detected using pedigree-based statistics alone. More sophisticated analysis combining genomewide molecular data with pedigree information will enable conservation scientists to test whether early viability selection drives deviations from neutrality across wide stretches of the genome, revealing whether this form of selection biases the pedigree-based statistics and inference upon which intensive management is based.
Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial
Publisher: Springer Science and Business Media LLC
Date: 09-07-2019
DOI: 10.1007/S11033-019-04966-6
Abstract: Reduced-representation sequencing methods have wide utility in conservation genetics of non-model species. Several methods are now available that reduce genome complexity to examine a wide range of markers in a large number of in iduals. We produced two datasets collected using different laboratory techniques, comprising a common set of s les from the greater bilby (Macrotis lagotis). We examined the impact of differing data filtering thresholds on downstream population inferences. We found that choice of restriction enzyme and data filtering thresholds, especially the rate of allowable missing data, impacted our ability to detect population structure. Estimates of F
The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione) [version 1; peer review: 2 approved]
Publisher: F1000 Research Ltd
Date: 18-07-2023
DOI: 10.12688/F1000RESEARCH.138571.1
Abstract: The Kroombit tinkerfrog ( Taudactylus pleione ) is a stream-dwelling hibian of the Myobatrachidae family. It is listed as Critically Endangered and is at high risk of extinction due to chytridiomycosis. Here, we provide the first genome assembly of the evolutionarily distinct Taudactylus genus. We sequenced PacBio HiFi reads to assemble a high-quality long-read genome and identified the mitochondrial genome. We also generated a global transcriptome from a tadpole to improve gene annotation. The genome was 5.52 Gb in length and consisted of 4,196 contigs with a contig N50 of 8.853 Mb and an L50 of 153. This study provides the first genomic resources for the Kroombit tinkerfrog to assist in future phylogenetic, environmental DNA, conservation breeding, and disease susceptibility studies.
Long-range transverse Ising model built with dipolar condensates in two-well arrays
Publisher: IOP Publishing
Date: 25-01-2017
No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding
Publisher: Springer Science and Business Media LLC
Date: 12-05-2017
DOI: 10.1038/S41598-017-02000-Y
Abstract: Inbreeding depression occurs when inbred in iduals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 in iduals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six erse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in in idual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.
Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild
Publisher: Wiley
Date: 26-12-2019
DOI: 10.1111/EVA.12715
Health Assessments of Koalas after Wildfire: A Temporal Comparison of Rehabilitated and Non-Rescued Resident Individuals
Publisher: MDPI AG
Date: 09-09-2023
DOI: 10.3390/ANI13182863
Determination of testosterone in saliva and blow of bottlenose dolphins (Tursiops truncatus) using liquid chromatography–mass spectrometry
Publisher: Elsevier BV
Date: 25-01-2005
DOI: 10.1016/J.JCHROMB.2004.10.058
Abstract: A rapid, accurate and reproducible assay utilising high performance liquid chromatography-mass spectrometry (LC-MS) has been developed and validated for determining testosterone concentrations in saliva and blow of bottlenose dolphins. S le preparation used solid phase extraction with specific preconditioning of cartridges. Analytes were eluted with 100% acetonitrile, dried under nitrogen and stored at -80 degrees C. S les were reconstituted in 60% acetonitrile for LC-MS analysis. Chromatographic separation was achieved with an Alltech Macrosphere C8 stainless steel analytical column (2.1 mm x 150 mm i.d., 5 microm particle size, 300 angstroms pore size) using a 55% mobile phase B isocratic method (mobile phase A = 0.5% acetic acid mobile phase B = 0.5% acetic acid, 90% acetonitrile). S les were analysed in SIM at m/z 289.20 (testosterone mw 288.40) and a positive ion ESI. The limit of quantification was 0.5 ng/ml with a limit of detection of 0.2 ng/ml. The concentration curve was linear from 0.5 to 50 ng/ml (y = 0.01x + 0.0045, r(2) = 0.959, r = 0.979, p < 0.001). The R.S.D.s of intra- and inter-batch precision were less than 15% for saliva and 11% blow. Recovery of the assay for saliva was 93.0 +/- 7.9% (50 ng/ml) and 91.5 +/- 3.72% (1 ng/ml), and for blow was 83.3 +/- 6.8% (50 ng/ml) and 85.8 +/- 4.6% (1 ng/ml). Recovery of the internal standard in saliva was 73.0 +/- 14.2% and in blow was 78.63 +/- 4.29. The described assay was used to determine the presence of endogenous testosterone in saliva (9.73-23 ng/ml, n = 10) and blow (14.71-86.20 ng/ml, n = 11) s les of captive bottlenose dolphins.
Genomics for conservation: a case study of behavioral genes in the Tasmanian devil
Publisher: Springer Science and Business Media LLC
Date: 26-03-2021
Are any populations 'safe'? Unexpected reproductive decline in a population of Tasmanian devils free of devil facial tumour disease
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/WR16234
Abstract: Context Conservation management relies on baseline demographic data of natural populations. For Tasmanian devils (Sarcophilus harrisii), threatened in the wild by two fatal and transmissible cancers (devil facial tumour disease DFTD: DFT1 and DFT2), understanding the characteristics of healthy populations is crucial for developing adaptive management strategies to bolster populations in the wild. Aims Our analysis aims to evaluate contemporary reproductive rates for wild, DFTD-free Tasmanian devil populations, and to provide a baseline with which to compare the outcome of current translocation activities. Methods We analysed 8 years of field-trapping data, including demographics and reproductive rates, across 2004–16, from the largest known DFTD-free remnant population at Woolnorth, Tasmania. Key results Surprisingly, we found a dramatic and statistically significant decline in female breeding rate when comparing data collected from 2004–2009 with data from 2014–2016. Unfortunately we do not have any data from the intermediate years. This decline in breeding rate was accompanied by a subtle but statistically significant decline in litter sizes. These changes were not associated with a change in body condition over the same period. Furthermore, we could not attribute the decline in breeding to a change in population size or sex ratio. Preliminary analysis suggested a possible association between annual breeding rate and coarse measures of environmental variation (Southern Oscillation Index), but any mechanistic associations are yet to be determined. Conclusions The decline in breeding rates was unexpected, so further monitoring and investigation into potential environmental and/or biological reasons for the decline in breeding rate are recommended before the arrival of DFTD at Woolnorth. Implications Our results provide valuable data to support the conservation management of Tasmanian devils in their native range. They also highlight the importance of continued monitoring of ‘safe’ populations, in the face of significant threats elsewhere.
A Tasmanian devil breeding program to support wild recovery
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/RD18152
Abstract: Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an ‘insurance population’ to enable the preservation of genetic ersity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic ersity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful ex le of how genetic research can be used to understand and improve reproductive success in a threatened species.
A role for selective contraception of individuals in conservation
Publisher: Wiley
Date: 10-03-2018
DOI: 10.1111/COBI.13042
Abstract: Contraception has an established role in managing overabundant populations and preventing undesirable breeding in zoos. We propose that it can also be used strategically and selectively in conservation to increase the genetic and behavioral quality of the animals. In captive breeding programs, it is becoming increasingly important to maximize the retention of genetic ersity by managing the reproductive contribution of each in idual and preventing genetically suboptimal breeding through the use of selective contraception. Reproductive suppression of selected in iduals in conservation programs has further benefits of allowing animals to be housed as a group in extensive enclosures without interfering with breeding recommendations, which reduces adaptation to captivity and facilitates the expression of wild behaviors and social structures. Before selective contraception can be incorporated into a breeding program, the most suitable method of fertility control must be selected, and this can be influenced by factors such as species life history, age, ease of treatment, potential for reversibility, and desired management outcome for the in idual or population. Contraception should then be implemented in the population following a step-by-step process. In this way, it can provide crucial, flexible control over breeding to promote the physical and genetic health and sustainability of a conservation dependent species held in captivity. For Tasmanian devils (Sarcophilus harrisii), black-flanked rock wallabies (Petrogale lateralis), and burrowing bettongs (Bettongia lesueur), contraception can benefit their conservation by maximizing genetic ersity and behavioral integrity in the captive breeding program, or, in the case of the wallabies and bettongs, by reducing populations to a sustainable size when they become locally overabundant. In these ex les, contraceptive duration relative to reproductive life, reversibility, and predictability of the contraceptive agent being used are important to ensure the potential for in iduals to reproduce following cessation of contraception, as exemplified by the wallabies when their population crashed and needed females to resume breeding.
Genetic Management of Captive and Reintroduced Bilby Populations
Publisher: Wiley
Date: 06-11-2020
DOI: 10.1002/JWMG.21777
Genomes of two Extinct‐in‐the‐Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights
Publisher: Wiley
Date: 21-03-2023
Abstract: Genomics can play important roles in bio ersity conservation, especially for Extinct‐in‐the‐Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue‐tailed skink ( Cryptoblepharus egeriae ) and Lister's gecko ( Lepidodactylus listeri ) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand in iduals however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long‐read and Hi‐C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic ersity to infer ancient demography and more recent histories of inbreeding. We observe high genome‐wide heterozygosity in the skink (0.007 heterozygous sites per base‐pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue‐tailed skink reference genome falls within long ( Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population‐level and comparative genomic studies in reptiles.
Identifying cost‐effective recovery actions for a critically endangered species
Publisher: Wiley
Date: 18-11-2021
DOI: 10.1111/CSP2.546
Abstract: Threatened species managers are often required to make swift decisions in the face of considerable uncertainty. We tested a structured approach for evaluating conservation options for the critically endangered orange‐bellied parrot. The Orange‐bellied Parrot Recovery Team provides advice to government agencies to inform the allocation of a limited number of captive‐bred birds to different release scenarios. Using a structured expert elicitation approach, we determined that scenarios where more fledglings were released were more cost‐effective compared to other options. Following this finding in 2019, the recovery team adjusted plans and allocated additional birds to fledgling release, a response that contributed to an increase in wild birds migrating in 2020 and 2021. The challenges facing orange‐bellied parrot conservation, including limitations in animals, time and resources, and high uncertainty, are common for threatened species recovery programs. Here we show that a structured process can help managers grapple with these complex trade‐offs to make timely decisions.
First evidence of deviation from Mendelian proportions in a conservation programme
Publisher: Wiley
Date: 19-06-2021
DOI: 10.1111/MEC.16004
Abstract: Classic Mendelian inheritance is the bedrock of population genetics and underpins pedigree‐based management of animal populations. However, assumptions of Mendelian inheritance might not be upheld in conservation breeding programmes if early viability selection occurs, even when efforts are made to equalise genetic contributions of breeders. To test this possibility, we investigated deviations from Mendelian proportions in a captive metapopulation of the endangered Tasmanian devil. This marsupial population is ideal for addressing evolutionary questions in conservation due to its large size, range of enclosure types (varying in environmental conditions), good genomic resources (which aid interpretation), and the species’ biology. Devil mothers give birth to more offspring than they can nurse in the pouch, providing the potential for intense viability selection amongst embryos. We used data from 140 known sire‐dam‐offspring triads to isolate within‐family selection from population‐level mechanisms (such as mate choice or inbreeding), and compared observed offspring genotypes at 123 targeted SNPs to neutral (i.e., Mendelian) expectations. We found lower offspring heterozygosity than expected, and subtle patterns that varied across a gradient of management intensity from zoo‐like enclosures to semi‐wild environments for some loci. Meiotic drive or maternal‐foetal incompatibilities are consistent with our results, although we cannot statistically confirm these mechanisms. We found some evidence that maternal genotype affects annual litter size, suggesting that family‐level patterns are driven by differential offspring mortality before birth or during early development. Our results show that deviations from Mendelian inheritance can occur in conservation programmes, despite best‐practice management to prevent selection.
Preserving the demographic and genetic integrity of a single source population during multiple translocations
Publisher: Elsevier BV
Date: 2020
Assessing evolutionary processes over time in a conservation breeding program: a combined approach using molecular data, simulations and pedigree analysis
Publisher: Springer Science and Business Media LLC
Date: 02-02-2021
Genetic impacts of conservation management actions in a critically endangered parrot species
Publisher: Springer Science and Business Media LLC
Date: 15-07-2020
Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils
Publisher: PeerJ
Date: 26-09-2019
DOI: 10.7287/PEERJ.PREPRINTS.27985V1
Abstract: Background. Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. Methods. We used 32 microsatellite loci to examine changes in genetic ersity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. Results. We found that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population has entered an extinction vortex and that to protect the population, genetic rescue may be required. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program” which is currently augmenting small, isolated populations.
Congenital vestibular disease in captive Sumatran tigers (Panthera tigris ssp. sumatrae) in Australasia
Publisher: Elsevier BV
Date: 11-2015
DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem
Publisher: Wiley
Date: 05-2022
DOI: 10.1002/ECE3.8936
Abstract: Top carnivores are essential for maintaining ecosystem stability and bio ersity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species’ native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species’ native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short‐tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.
Pedigree reconstruction using molecular data reveals an early warning sign of gene diversity loss in an island population of Tasmanian devils (Sarcophilus harrisii)
Publisher: Springer Science and Business Media LLC
Date: 27-09-2017
DNA methylation networks underlying mammalian traits
Publisher: American Association for the Advancement of Science (AAAS)
Date: 11-08-2023
Abstract: Using DNA methylation profiles ( n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all s les, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.
Low innate immune-gene diversity in the critically endangered orange-bellied parrot (Neophema chrysogaster)
Publisher: Informa UK Limited
Date: 20-11-2020
The relevance of pedigrees in the conservation genomics era
Publisher: Wiley
Date: 22-10-2021
DOI: 10.1111/MEC.16192
Abstract: Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize ersity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional ersity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed s ling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
Pedigree analysis reveals a generational decline in reproductive success of captive Tasmanian devil (Sarcophilus harrisii): implications for captive management of threatened species
Publisher: Oxford University Press (OUP)
Date: 04-04-2017
Abstract: Captive breeding programs are an increasingly popular tool to augment the conservation of threatened wild populations. Many programs keep detailed pedigrees, which are used to prescribe breeding targets to meet demographic and genetic goals. Annual breeding targets are based on previous productivity, but do not account for changes in reproductive success that may occur over generations in captivity and which may impair the ability of a program to meet its goals. We utilize a large studbook from the Tasmanian devil (Sarcophilus harrisii) captive breeding program to investigate biological, genetic, and environmental factors that affect variation in reproductive success among in iduals and over generations of captive breeding. Reproductive success declined with increasing generations in captivity: wild-born females had a 56.5% chance of producing a litter compared to a 2.8% chance for generation 5 captive-born females (N = 182) and when they did, wild-born females produced more offspring (3.1 joeys, 95% CI: 2.76-3.38, compared to 2.7 joeys, 95% CI: 2.55-2.90, in captive-born females [N = 105]). Reproductive success also declined as dam age at first breeding increased. Our results reveal a conflict with the widely cited conservation strategy to limit opportunity for selection by extending generation length through delaying reproduction, as captive breeding programs that delay female breeding with this goal in mind risk reduced productivity. Our data demonstrate the benefit of pedigree analysis to identify biological processes that reveal crucial trade-offs with conservation best-practice.
The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies
Publisher: GigaScience Press
Date: 05-11-2020
DOI: 10.46471/GIGABYTE.7
Abstract: Antechinus are a genus of mouse-like marsupials that exhibit a rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for the brown antechinus (Antechinus stuartii). The reference genome is 3.3 Gb in size with a scaffold N50 of 73Mb and 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds to chromosomes and identify 0.78 Mb of Y-chromosome scaffolds. Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively. Transcriptome data displayed expression of common Alzheimer’s related genes in the antechinus brain and highlight the potential of utilising the antechinus as a future disease model. The valuable genomic resources provided herein will enable future research to explore the genetic basis of semelparity and age-related processes in the antechinus.
Landscape-level field data reveal broad-scale effects of a fatal, transmissible cancer on population ecology of the Tasmanian devil
Publisher: Springer Science and Business Media LLC
Date: 07-2018
Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics
Publisher: American Society for Microbiology
Date: 06-2019
DOI: 10.1128/JVI.00205-19
Abstract: The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral ersity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.
Contraceptive efficacy and dose-response effects of the gonadotrophin-releasing hormone (GnRH) agonist deslorelin in Tasmanian devils (Sarcophilus harrisii)
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/RD18407
Abstract: Contraception is increasingly used to manage breeding opportunities in conservation-dependent species. This study aimed to determine the efficacy, duration of effect, optimal dose and potential side effects of Suprelorin contraceptive implants in Tasmanian devils, for use in the conservation breeding program. In our pilot study, Suprelorin was found to effectively suppress oestrous cycles in female devils, yet caused a paradoxical increase in testosterone in males. Therefore, we focussed on females in further trials. Females received one (n=5), two (n=5) or no (n=5) Suprelorin implants, with quarterly gonadotrophin-releasing hormone (GnRH) challenges used to test pituitary responsiveness over two breeding seasons. Both Suprelorin doses suppressed pituitary responsiveness for at least one breeding season, with a reduced effect in the second. There was a dose-response effect on duration rather than magnitude of effect, with high-dose devils remaining suppressed for longer than low-dose animals. There were no apparent negative effects on general health, yet captivity and contraception together may cause weight gain. Suprelorin contraceptive implants are now routinely used in the Save the Tasmanian Devil Program insurance metapopulation to meet the aims of maintaining genetic and behavioural integrity by controlling in idual reproductive contributions in group housing situations.
Development of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population
Publisher: Springer Science and Business Media LLC
Date: 14-10-2015
Disentangling the mechanisms of mate choice in a captive koala population
Publisher: PeerJ
Date: 21-08-2018
DOI: 10.7717/PEERJ.5438
Abstract: Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair’s age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides
Publisher: Cold Spring Harbor Laboratory
Date: 22-09-2023
The effects of group versus intensive housing on the retention of genetic diversity in insurance populations
Publisher: Springer Science and Business Media LLC
Date: 02-2018
From reference genomes to population genomics: Comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species
Publisher: Springer Science and Business Media LLC
Date: 03-06-2019
Using phylogenetics to explore interspecies genetic rescue options for a critically endangered parrot
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.
Escaping captivity: The biological invasion risk from vertebrate species in zoos
Publisher: Elsevier BV
Date: 2015
Disentangling the mechanisms of mate choice in a captive koala population
Publisher: PeerJ
Date: 27-12-2017
DOI: 10.7287/PEERJ.PREPRINTS.3487V1
Abstract: Successful captive breeding programs are crucial to the long-term survival of threatened species. However, pair incompatibility limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioural or genetic, or a combination of both, is crucial to improving breeding programs. We used twenty-eight years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both MHC-linked and non-MHC-linked microsatellite markers, to show that both behavioural and genetic determinants can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a pair copulating. Familiarity was also reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at class II MHC loci influenced both pre- and post-copulatory female choice. Genome-wide similarity and similarity at the MHCII DAB locus were also found to influence female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with increased or decreased mating success. We predict that utilising a variety of behavioural and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms within a species and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.
The Earth BioGenome Project 2020: Starting the clock
Publisher: Proceedings of the National Academy of Sciences
Date: 18-01-2022
Preserving Australian native fauna: zoo-based breeding programs as part of a more unified strategic approach
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/ZO13014
Abstract: High extinction rates and loss of bio ersity is a critical conservation matter. Twenty-two Australian mammal species have become extinct in the last 200 years. Of the 95 mammal species under the EPBC Act, 51 have recovery plans and 15 of these have captive components. Zoo-based programs as part of a recovery plan can ‘buy’ time for critically endangered species. In Australia, programs are established as a result of government recovery plans, though more consultation with the zoo industry in initial development phase is needed. Often by the time the decision is taken to remove in iduals from the wild for captive breeding, the source populations are fragmented and small. As zoo-based programs become more successful, issues with space limitations arise. This may be rectified with regular release of in iduals or avoidance of maintaining post-reproductive and/or non-reproductive animals long-term. Those involved in recovery efforts should make few assumptions on the captive productivity of species, unless the species has been held before. Success of the captive component of a recovery program can be measured by the number of animals bred for release and the level of genetic ersity retained by the program. Although recovery teams are responsible for strategy development, good communication between parties from an early stage is essential. Where a captive component is needed, a more unified strategy, developed early, should provide our native fauna with a realistic chance of recovery. Zoo-based breeding programs are useful in assisting with the preservation of some Australian fauna, whilst for others they will have limited relevance.
Extinct in the wild: The precarious state of Earth’s most threatened group of species
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-02-2023
Abstract: Extinct in the Wild (EW) species are placed at the highest risk of extinction under the International Union for Conservation of Nature Red List, but the extent and variation in this risk have never been evaluated. Harnessing global databases of ex situ animal and plant holdings, we report on the perilous state of EW species. Most EW animal species—already compromised by their small number of founders—are maintained at population sizes far below the thresholds necessary to ensure demographic security. Most EW plant species depend on live propagation by a small number of botanic gardens, with a minority secured at seed bank institutions. Both extinctions and recoveries are possible fates for EW species. We urgently call for international effort to enable the latter.
The Tasmanian devil microbiome-implications for conservation and management
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities
Publisher: Wiley
Date: 30-01-2023
DOI: 10.1111/ACV.12855
Abstract: Reproductive skew occurs when a few in iduals monopolize breeding output, which can act as a mechanism of natural selection. However, when population sizes become small, reproductive skew can depress effective population size and worsen inbreeding. Identifying the cause of reproductive skew is important for mitigating its effect on conservation of small populations. We hypothesized that superb parrots Polytelis swainsonii , which strongly select for the morphology of tree cavity nests, may be reproductively skewed toward pairs that monopolize access to nests. We use SNP genotyping to reconstruct a pedigree, estimate molecular relatedness and genetic ersity of wild superb parrot in the Australian Capital Territory. We successfully genotyped 181 nestlings (a census between 2015–2019) and showed they were the progeny of 34 monogamous breeding pairs. There was a strong reproductive skew – 21 pairs bred only once producing 40% of the nestlings, whereas 13 pairs bred two to four times, producing 60% of the total nestlings. Five of these repeat‐breeders produced 28% of all nestlings, which was nearly triple the productivity of one‐time breeders. Repeat breeders usually monopolized access to their nest cavities, but the few pairs that switched nests did not differ in fecundity from those that stayed. The cause of nest switching was unknown, but uninterrupted access to a suitable nest (not minor variations in morphology between nests) better predicted fitness of breeding superb parrots. Pedigrees offer powerful insights into demographic processes, and identifying reproductive skew early provides opportunities to proactively avoid irreversible loss of genetic ersity via conservation management. We identify new research questions based on our results to clarify the relationship between access to resources and breeding success.
Reply to DeWoody et al.: Inequitable access to affordable sequencing limits the benefits from population genomic insights
Publisher: Proceedings of the National Academy of Sciences
Date: 26-09-2022
Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program
Publisher: Elsevier BV
Date: 07-2022
A rapid multiplex PCR assay for presumptive species identification of rhinoceros horns and its implementation in Vietnam
Publisher: Public Library of Science (PLoS)
Date: 14-06-2018
Universal DNA methylation age across mammalian tissues
Publisher: Springer Science and Business Media LLC
Date: 10-08-2023
DOI: 10.1038/S43587-023-00462-6
Abstract: Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy ( r 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
Characterisation of 16 microsatellite markers via 454 sequencing, to aid ex-situ conservation of the scimitar-horned oryx, Oryx dammah
Publisher: Springer Science and Business Media LLC
Date: 24-04-2023
Marsupial Gut Microbiome
Publisher: Frontiers Media SA
Date: 29-05-2020
Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial
Publisher: GigaScience Press
Date: 17-03-2022
DOI: 10.46471/GIGABYTE.47
Abstract: The numbat (Myrmecobius fasciatus) is an endangered Australian marsupial, and the last surviving member of the Myrmecobiidae family. The numbat regularly undergoes torpor and is unique amongst marsupials as it is the only diurnal and termitivorous species. Here we sequenced the first draft genome of the numbat using 10× Genomics Chromium linked-read technology, resulting in a 3.42 Gbp genome with a scaffold N50 of 223 kbp. A global transcriptome from liver, lung and tongue was also generated to aid genome annotation, identifying 21,465 protein-coding genes. To investigate adaptation to the numbat’s termitivorous diet and arid/semi-arid range, we interrogated the most highly expressed transcripts within the tongue and manually annotated taste, vomeronasal and aquaporin gene families. Antimicrobial proteins and proteins involved in digestion were highly expressed in the tongue, alongside umami taste receptors. However, sweet taste receptors were not expressed in this tissue, which combined with the putative contraction of the bitter taste receptor gene repertoire in the numbat genome, may indicate a potential evolutionary adaptation to their specialised termitivorous diet. Vomeronasal and aquaporin gene repertoires were similar to other marsupials. The draft numbat genome is a valuable tool for conservation and can be applied to population genetics/genomics studies and to investigate the unique biology of this interesting species.
Urinary cortisol sampling: a non-invasive technique for examining cortisol concentrations in the Weddell seal,Leptonychotes weddellii
Publisher: Wiley
Date: 2006
DOI: 10.1002/ZOO.20088
Influence of genetic provenance and birth origin on productivity of the Tasmanian devil insurance population
Publisher: Springer Science and Business Media LLC
Date: 10-07-2015
Body mass is not a useful measure of adaptation to captivity in the Orange-bellied Parrot Neophema chrysogaster
Publisher: Informa UK Limited
Date: 12-12-2020
Saving the Tasmanian Devil
Publisher: CSIRO Publishing
Date: 2019
Abstract: The Tasmanian devil is threatened by Devil Facial Tumour Disease (DFTD), a transmissible form of cancer that has reduced the population by over 80%. Persecution, extreme climate events, vehicle collision and habitat destruction also put pressure on this endangered species. The recovery effort to save the Tasmanian devil commenced over 15 years ago as a collaborative initiative between the Tasmanian government, the Australian government, the Zoo and Aquarium Association Australasia, and many research institutions. Saving the Tasmanian Devil documents the journey taken by partner organisations in discovering what DFTD is, the effect it has on wild devil populations, and the outcomes achieved through research and management actions. Chapters describe all aspects of devil conservation, including the captive devil populations, applied pathology, immunology and genetic research findings, adaptive management, and the importance of advocacy and partnerships. This book will provide management practitioners and conservation scientists with insight into the complexities of undertaking a program of this scale, and will also be of value to researchers, students and others interested in conservation.
Founder relationships and conservation management: empirical kinships reveal the effect on breeding programmes when founders are assumed to be unrelated
Publisher: Wiley
Date: 30-11-2019
DOI: 10.1111/ACV.12463
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing
Publisher: Wiley
Date: 06-10-2021
Abstract: The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host‐pathogen co‐evolution. However, due to the high degree of gene duplication and ersification of MHC genes, it is often technically challenging to accurately characterise MHC genetic ersity in non‐model species. Here we conducted a systematic review to identify common issues associated with current widely used MHC typing approaches. Then to overcome these challenges, we developed a long‐read based MHC typing method along with a new analysis pipeline. Our approach enables the sequencing of fully phased MHC alleles spanning all key functional domains and the separation of highly similar alleles as well as the removal of technical artefacts such as PCR heteroduplexes and chimeras. Using this approach, we performed population‐scale MHC typing in the Tasmanian devil ( Sarcophilus harrisii ), revealing previously undiscovered MHC functional ersity in this endangered species. Our new method provides a better solution for addressing research questions that require high MHC typing accuracy. Since the method is not limited by species or the number of genes analysed, it will be applicable for studying not only the MHC but also other complex gene families.
Post release immune responses of Tasmanian devils vaccinated with an experimental devil facial tumour disease vaccine
Publisher: Cold Spring Harbor Laboratory
Date: 07-12-2020
DOI: 10.1101/2020.12.06.408963
Abstract: Disease is increasingly becoming a driver of wildlife population declines and extinction risk. Vaccines have been one of the most successful health interventions in human history, but few have been tested for mitigating wildlife disease. The transmissible cancer, devil facial tumour disease (DFTD), triggered the Tasmanian devil’s ( Sarcophilus harrisii ) inclusion on the international endangered species list. Development of a protective DFTD vaccine would provide a valuable management approach for conservation of the species. In 2016, 33 devils from a DFTD-free insurance population were given an experimental DFTD vaccination prior to their release on the north coast of Tasmania. The release site was already home to an incumbent population of devils, including some in iduals with DFTD. To determine the efficacy of the vaccination protocol and the longevity of the response it induced, six trapping trips took place at the site over the 2.5 years following release. Eight of the 33 vaccinated devils were re-trapped, and six of those developed DFTD within the monitoring period. Despite the apparent lack of protection provided by the vaccine for the re-trapped devils, we observed several signs of immune activation not usually found in unvaccinated devils. Firstly, sera collected from the eight devils showed that anti-DFTD antibodies persisted for up to two years post vaccination. Secondly, tumour infiltrating lymphocytes were found in three out of four biopsies collected from vaccinated devils which contrasts with the “immune deserts” typical of DFT’s only one out of twenty incumbent devils with DFTD trapped during the same period had a tumour biopsy exhibiting immune cell infiltrate. Thirdly, immunohistochemical analysis of tumour biopsies from the vaccinated devils identified the functional immune molecules associated with antigen presenting cells (MHC-II) and T cells (CD3), and the immune checkpoint molecule PD-1, all associated with anti-tumour immunity in other species. These results correlate with our previous study on captive devils in which a prophylactic vaccine primed the devil immune system and, following DFTD challenge and tumour growth, immunotherapy induced complete tumour regressions. The field trial results presented here provide further evidence that the devil immune system can be primed to recognise DFTD cells, but additional immune manipulation could be needed for complete protection or induction of tumour regressions.
“Devil Tools & Tech”: A Synergy of Conservation Research and Management Practice
Publisher: Wiley
Date: 04-01-2017
DOI: 10.1111/CONL.12221
Response to Britt et al. 2018 “The importance of non-academic co-authors in bridging the conservation genetics gap” Biological Conservation 218, 118–123
Publisher: Elsevier BV
Date: 06-2018
MHC Genes and Mate Choice
Publisher: Elsevier
Date: 2019
Size Fractionation of Two‐Dimensional Sub‐Nanometer Thin Manganese Dioxide Crystals towards Superior Urea Electrocatalytic Conversion
Publisher: Wiley
Date: 16-02-2016
Abstract: A universal technique has been proposed to sort two-dimensional (2D) sub-nanometer thin crystals (manganese dioxide MnO2 and molybdenum disulfide MoS2 ) according to their lateral dimensions. This technique is based on tuning the zeta potential of their aqueous dispersions which induces the selective sedimentation of large-sized 2D crystals and leaves the small-sized counterparts in suspension. The electrocatalytic properties of as-obtained 2D ultrathin crystals are strongly dependent on their lateral size. As a proof-of-concept study, the small-sized MnO2 nanocrystals were tested as the electrocatalysts for the urea-oxidation reaction (UOR), which showed outstanding performance in both half reaction and full electrolytic cell. A mechanism study reveals the enhanced performance is associated with the remarkable structural properties of MnO2 including ultrathin (ca. 0.95 nm), laterally small-sized (50-200 nm), and highly exposed active centers.
Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore
Publisher: Wiley
Date: 17-04-2020
DOI: 10.1111/ACV.12589
Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)
Publisher: Wiley
Date: 17-07-2015
DOI: 10.1111/MEC.13291
Abstract: The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in ersity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC) however, these genes only account for a fraction of immune gene ersity. Devils lack ersity at functionally important immunity loci, including MHC and Toll-like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long licon assays to target nine genes. These licons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic ersity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining ersity may hold adaptive potential. The low functional ersity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining ersity will be critical for the long-term management of this species. Examining genetic variation in erse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic ersity analysis in threatened species.
Adaptive Genetic Management of a Reintroduction Program from Captive Breeding to Metapopulation Management of an Arboreal Marsupial
Publisher: MDPI AG
Date: 12-07-2023
DOI: 10.3390/D15070848
Abstract: The application of genetic data to conservation management programs can be hindered by the mismatch in timelines for management decisions and the acquisition of genetic data, particularly genomic sequence data that may require outsourcing. While applying genetic principles where data are absent can provide general guidelines for actions, genetic data can often fine-tune actions through adaptive management. We describe the adaptive genetic management of the establishment of a metapopulation of a small arboreal marsupial, the red-tailed phascogale (Phascogale calura). Two captive breeding programs were established as source populations, with genetic principles applied to the establishment of the first program and empirical genetic data used to guide the establishment of the second program. Genetic data from both programs were then used to allocate founders to three new populations to create a metapopulation with ersity both within and among the sites. Building and maintaining the ersity of metapopulations when recovering threatened species will reduce pressure on the original source populations and increase the resilience of the species.
Threatened Species Initiative: Empowering conservation action using genomic resources
Publisher: Proceedings of the National Academy of Sciences
Date: 18-01-2022
Abstract: Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional ersity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.
Multiple paternity and precocial breeding in wild Tasmanian devils, Sarcophilus harrisii (Marsupialia: Dasyuridae)
Publisher: Oxford University Press (OUP)
Date: 27-05-2019
DOI: 10.1093/BIOLINNEAN/BLZ072
Abstract: Polyandry, a common reproductive strategy in various animal species, has potential female benefits, which include enhanced offspring fitness. Benefits can be direct, such as reduced risk of male infanticide of offspring, or indirect, such as increased genetic ersity of offspring and the acquisition of ‘good genes’. Multiple paternity of litters has been recorded in numerous marsupial species but has not been reported in Tasmanian devils, Sarcophilus harrisii (Boitard). We investigated whether multiple paternity occurred in litters within a wild population of Tasmanian devils. Using major histocompatibility complex-linked and neutral microsatellite markers, the paternity of nine litters was analysed. We found multiple paternity in four out of nine litters and that yearling ( 1, 2 years old) male devils were siring offspring. This is the first record of multiple paternity and of male precocial breeding in wild Tasmanian devils. To date, there are no data relating to the subsequent survival of devils from single- vs. multiple-sired litters therefore, we do not know whether multiple paternity increases offspring survival in the wild. These results have implications for the Tasmanian devil captive insurance programme, because group housing can lead to multiple-sired litters, making the maintenance of genetic ersity over time difficult to manage.
A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi
Publisher: Cold Spring Harbor Laboratory
Date: 08-12-2021
DOI: 10.1101/2021.12.07.471656
Abstract: Bio ersity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie ( Bettongia penicillata ogilbyi ), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.
Future-proofing the koala: Synergising genomic and environmental data for effective species management.
Publisher: Wiley
Date: 19-04-2022
DOI: 10.1111/MEC.16446
Abstract: Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial ergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (~430 to 300 kya), a major climatic reorganisation that increased the litude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of vulnerable populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g., guiding translocations), as existing management isions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.
Addressing Threats and Ecosystem Intactness to Enable Action for Extinct in the Wild Species
Publisher: MDPI AG
Date: 13-07-2020
DOI: 10.3390/D15020268
Abstract: The species listed as Extinct in the Wild (EW) in the IUCN Red List of Threatened Species consist of 84 plants and animals that have been lost from their indigenous range. EW species are therefore restricted to ex situ conservation facilities and often have populations founded with few in iduals. Our analysis demonstrates that 60% of EW species are associated with ecoregions that have very low proportions of intact habitat. Furthermore, threats such as invasive species, pollution, and climate change affect just over half of EW species and compound the obstacles facing their reinstatement to the wild. Despite these bleak assessments, there are various options for EW recovery. We present five scenarios that encapsulate the circumstances facing EW species and suggest potential conservation action for each of these situations. We illustrate these scenarios using case studies of EW species that demonstrate how the various options of ex situ management, reintroduction, and assisted colonisation to new habitat can be used to address the very exacting requirements of EW species. Our aim is to present a broad review of the obstacles facing the recovery of EW species whilst inspiring action to prevent the extinction of the most imperilled species on the planet.
Genomic insights into a critically endangered island endemic songbird provide a roadmap for preventing extinction.
Publisher: Authorea, Inc.
Date: 25-09-2023
A meta-analysis of birth-origin effects on reproduction in diverse captive environments
Publisher: Springer Science and Business Media LLC
Date: 13-03-2018
DOI: 10.1038/S41467-018-03500-9
Abstract: Successfully establishing captive breeding programs is a priority across erse industries to address food security, demand for ethical laboratory research animals, and prevent extinction. Differences in reproductive success due to birth origin may threaten the long-term sustainability of captive breeding. Our meta-analysis examining 115 effect sizes from 44 species of invertebrates, fish, birds, and mammals shows that, overall, captive-born animals have a 42% decreased odds of reproductive success in captivity compared to their wild-born counterparts. The largest effects are seen in commercial aquaculture, relative to conservation or laboratory settings, and offspring survival and offspring quality were the most sensitive traits. Although a somewhat weaker trend, reproductive success in conservation and laboratory research breeding programs is also in a negative direction for captive-born animals. Our study provides the foundation for future investigation of non-genetic and genetic drivers of change in captivity, and reveals areas for the urgent improvement of captive breeding.
Ten simple rules for getting started with command-line bioinformatics
Publisher: Public Library of Science (PLoS)
Date: 18-02-2021
The Value of Reference Genomes in the Conservation of Threatened Species
Publisher: MDPI AG
Date: 25-10-2019
Abstract: Conservation initiatives are now more crucial than ever—over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited ex les of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an ex le of how a reference genome has influenced management actions in the conservation of a species.
Species Management Benchmarking: Outcomes Over Outputs in a Changing Operating Environment
Publisher: Wiley
Date: 13-08-2012
DOI: 10.1002/ZOO.21039
Abstract: Species management has been utilized by the zoo and aquarium industry, since the mid-1990s, to ensure the ongoing genetic and demographic viability of populations, which can be difficult to maintain in the ever-changing operating environments of zoos. In 2009, the Zoo and Aquarium Association Australasia reviewed their species management services, focusing on addressing issues that had arisen as a result of the managed programs maturing and operating environments evolving. In summary, the project examined resourcing, policies, processes, and species to be managed. As a result, a benchmarking tool was developed (Health Check Report, HCR), which evaluated the programs against a set of broad criteria. A comparison of managed programs (n = 98), between 2008 and 2011, was undertaken to ascertain the tool's effectiveness. There was a marked decrease in programs that were designated as weak (37 down to 13) and an increase in excellent programs (24 up to 49) between the 2 years. Further, there were significant improvements in the administration benchmarking area (submission of reports, captive management plan development) across a number of taxon advisory groups. This HCR comparison showed that a benchmarking tool enables a program's performance to be quickly assessed and any remedial measures applied. The increases observed in program health were mainly due to increased management goals being attained. The HCR will be an ongoing program, as the management of the programs increases and goals are achieved, criteria will be refined to better highlight ongoing issues and ways in which these can be resolved.
Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights
Publisher: Authorea, Inc.
Date: 29-11-2022
DOI: 10.22541/AU.166974487.73559017/V1
Abstract: Genomics can play important roles in bio ersity conservation, especially for Extinct-in-the-Wild species where genetic factors can influence total extinction risk and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister’s gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand in iduals however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate contiguous reference genomes for both species, including the XY chromosome pair in the skink. We then analyze patterns of genetic ersity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the blue-tailed skink (0.007) and Lister’s gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the skink reference genome falls within long runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci, whereas we detect only a single ROH in the gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in species’ histories and implications for management. We show how reference genomes can provide evolutionary and conservation insights in the absence of resequencing data, and we provide a resource for future population-level and comparative genomic studies in reptiles.
Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs
Publisher: Wiley
Date: 19-05-2020
DOI: 10.1111/EVA.12981
Do conservation translocations involve or result in hybridization and what are the consequences of hybridization for conservation? A systematic review protocol
Publisher: Center for Open Science
Date: 18-08-2023
Abstract: BackgroundConservation translocations are the intentional movement of plants and animals to another location for the purpose of conservation (IUCN/SSC, 2013). Conservation translocations can have intended and unintended impacts on threatened populations. Conservation translocations can be beneficial, harmful, or both and such impacts can be intended or unintended (Novak et al., 2021). Conservation translocations can result in or involve hybridization. Hybridization is defined as the interbreeding of in iduals from genetically distinct populations and can be intentional or unintentional. Hybridization can be interspecific, intraspecific or between subspecies (Chan et al., 2019). For conservation practitioners, understanding if hybridization might occur and what the consequences are is a key consideration when developing conservation management policies. There is currently no systematic review of (A) the frequency of hybridization after conservation translocations and (B) the consequences of hybridization occurring after conservation translocations. This review will provide critical insight and information for conservation professionals and scientists who are considering conservation translocations. MethodsA thorough search of peer-reviewed journal articles, open-access articles, and grey literature will be conducted. Five different databases will be searched, one open access (BASE) and four subscription based (Web of Science Core Collection, Zoological Record, Scopus, and BIOSIS). Bibliographic information will be recorded using the citation management software Zotero. Two screening stages will be performed (title/abstract, then full text) against predefined inclusion and exclusion criteria. The retained relevant literature will be subjected to coding and meta-data extraction. Each relevant study will then be critically appraised, based on a set of predefined validity criteria. Relevant knowledge gaps and emergent themes will be identified and discussed further.
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