ORCID Profile
0000-0003-3035-2827
Current Organisations
Smithsonian Institution
,
University of Sydney
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Genomics | Other Biological Sciences | Access to Justice | Forensic Biology |
Criminal Justice | Flora, Fauna and Biodiversity at Regional or Larger Scales | Trade and Environment
Publisher: Public Library of Science (PLoS)
Date: 10-04-2018
Publisher: California Digital Library (CDL)
Date: 28-06-2019
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-07-2022
Abstract: High-quality reference genomes for non–model species can benefit conservation
Publisher: The Royal Society
Date: 24-02-2021
Abstract: X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is an iconic ex le of epigenetic regulation. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here, we examine genome-wide signatures of DNA methylation across fives tissues from a male and female koala ( Phascolarctos cinereus ), and present the first whole-genome, multi-tissue marsupial ‘methylome atlas’. Using these novel data, we elucidate ergent versus common features of representative marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in koalas primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx , the primary lnc RNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-specific (and presumably inactive X chromosome-specific) expression. Finally, we use the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5%) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily ergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.
Publisher: Springer Science and Business Media LLC
Date: 20-11-2017
DOI: 10.1038/S41598-017-16171-1
Abstract: The koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus) . KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an in idual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites. Most integrations contain full-length, endogenous provirus KoRV-A subtype. The second most frequent integrations contain an endogenous recombinant element (recKoRV) in which most of the KoRV protein-coding region has been replaced with an ancient, endogenous retroelement. A third set of integrations, with very low sequence coverage, may represent somatic cell integrations of KoRV-A, KoRV-B and two recently designated additional subgroups, KoRV-D and KoRV-E. KoRV-D and KoRV-E are missing several genes required for viral processing, suggesting they have been transmitted as defective viruses. Our results represent the first comprehensive analyses of KoRV integration and variation in a single animal and provide further insights into the process of retroviral-host species interactions.
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2023
DOI: 10.1101/2023.08.22.554353
Abstract: In an era of global climate change and massive environmental disturbance, bio ersity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic ersity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic ersity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna ( Acridotheres tristis ) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a erse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low- ersity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic ersity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.
Publisher: Wiley
Date: 09-2015
DOI: 10.1890/15.WB.014
Publisher: Springer Science and Business Media LLC
Date: 08-2004
Publisher: Elsevier BV
Date: 12-2017
Publisher: Elsevier BV
Date: 11-2003
DOI: 10.1016/S1055-7903(03)00114-3
Abstract: The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been lost once. A maximum likelihood analysis showed that loss of the metapleural gland is significantly associated with the weaver life-pattern. The graph of the frequencies with which trees were discovered versus their likelihood indicates that trees with high likelihoods have much larger basins of attraction than those with lower likelihoods. While this result indicates that single searches are more likely to find high- than low-likelihood tree islands, it also indicates that searching only for the single best tree may lose important information.
Publisher: Proceedings of the National Academy of Sciences
Date: 18-01-2022
Abstract: Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic ersification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of bio ersity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes—about 2 million species—should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing ergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.FORSCIINT.2018.11.019
Abstract: The illegal trade in wild animals being sold as 'captive bred' is an emerging issue in the pet and zoo industry and has both animal welfare and conservation implications. DNA based methods can be a quick, inexpensive, and definitive way to determine the source of these animals, thereby assisting efforts to combat this trade. The short beaked echidna (Tachyglossus aculeatus) is currently one of the species suspected to be targeted in this trade. As this species is distributed throughout Australia and in New Guinea (currently comprising of five recognised sub-species), this project aimed to develop a DNA based method to definitively determine the source country of an echidna and explore the use of non-invasive s ling techniques. Here we use non-invasively s led echidna quills and demonstrate the extraction of mitochondrial DNA and lification of a region of the mitochondrial genome. Phylogenetically informative markers for analysis of a 322bp segment of the D-loop region were developed, and subsequently validated, using animals with known source locations allowing us to reliably distinguish between echidnas from New Guinea, and Australia. This research presents the first validated forensic protocols for short beaked echidnas and will be an integral tool in understanding the movement of animals in this emerging trade.
Publisher: Wiley
Date: 20-06-2021
DOI: 10.1111/ACV.12603
Publisher: Springer Science and Business Media LLC
Date: 14-06-2018
Publisher: Oxford University Press (OUP)
Date: 22-09-2017
Abstract: A fundamental challenge in resolving evolutionary relationships across the tree of life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinct clusters of loci, each providing an estimate of the species tree that matches previously proposed resolutions of the marsupial phylogeny. We also identify a well-supported placement for the enigmatic marsupial moles (Notoryctes) that contradicts previous molecular estimates but is consistent with morphological evidence. The pattern of gene-tree variation across tree-space is characterized by changes in information content, GC content, substitution-model adequacy, and signatures of purifying selection in the data. In a simulation study, we show that incomplete lineage sorting can explain the ision of loci into the two tree-topology clusters, as found in our phylogenomic analysis of marsupials. We also demonstrate the potential benefits of minimizing uncertainty from phylogenetic conflict for molecular dating. Our analyses reveal that Australasian marsupials appeared in the early Paleocene, whereas the ersification of present-day families occurred primarily during the late Eocene and early Oligocene. Our methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome-scale data.
Publisher: Springer Science and Business Media LLC
Date: 17-01-2012
Publisher: Wiley
Date: 16-12-2012
Publisher: Springer Science and Business Media LLC
Date: 02-07-2018
Publisher: CRC Press
Date: 23-05-2013
DOI: 10.1201/B14553
Publisher: PeerJ
Date: 14-06-2019
DOI: 10.7717/PEERJ.7138
Abstract: Processed seafood products are not readily identifiable based on physical characteristics, which leaves the industry vulnerable to high levels of product mislabelling (globally estimated at 5–30% mislabelled). This is both a food safety issue and a consumer protection issue as cheaper species could be substituted for more expensive species. DNA barcoding is proving to be a valuable tool for authentication of fish products. We worked with high school students to perform a market survey and subsequent species assessment via DNA barcoding to investigate the accuracy of fish product names used by retailers in Sydney, Australia. Sixty-eight fish s les, sold under 50 different common names, were purchased anonymously from two retailers in Sydney. Each product name was recorded and reconciled with the Australian Fish Names Standard (AFNS). S les were DNA barcoded and resulting sequences were deposited in the online Barcode of Life Data system using the simplified Student Data Portal interface. Forty percent of the fish names did not comply with the AFNS, however, half of these were either spelling errors or vendors supplied more information than the standard requires. The other half of the non-compliant s les were given common names not listed on the AFNS. Despite this lack of standardization, DNA barcode data confirmed the retailers’ identifications for 93% of s les and 90% of species s led. The level of mislabelling we report for Sydney retailers (7% of s les or 10% of species) compares favorably with the global rates of 5–30%, but unfavorably with the only previous DNA barcode fish authentication study for Australia, which found no confirmed mislabelling in Hobart. Our study s led mostly Australian produce, only two retailers and no restaurants. Results of our limited s le suggest that although many Sydney fish retailers attempt to implement the voluntary fish name standards, the standards are inadequate. As Australia imports 75% of its seafood, and in other countries restaurants generally show lower levels of compliance than retailers, broader surveys are needed before generalizing these results. DNA barcoding is a powerful yet simple method supported by accessible online analytical tools. Incorporation of fish barcoding into high school science classes provided students with valuable firsthand experience in scientific research and drew together different strands of the NSW curriculum relating to genetics and sustainability. Given the techniques, equipment, and reagents are now readily accessible, we expect to see greater uptake of DNA barcoding technology by high schools, citizen scientists and consumer groups in Australia in future. However, there remains much scope for further development of DNA barcode diagnostics (both data and analytical methods) for commercial fish species.
Publisher: Public Library of Science (PLoS)
Date: 02-09-2016
Publisher: Wiley
Date: 27-11-2014
DOI: 10.1111/COBI.12177
Abstract: The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was ergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action.
Publisher: Wiley
Date: 26-06-2021
DOI: 10.1111/CSP2.483
Abstract: As the global bio ersity crisis deepens, with increasing habitat fragmentation and a changing climate, innovative options for conserving species are being explored. One such conservation action is genetic rescue: introduction of new alleles to promote population fitness. However, for critically endangered species where only one viable population remains, options for introducing new alleles are limited. Interspecies hybridization offers a potential solution but requires resolution of evolutionary relationships, a sound understanding of species biology, social license, and permissive legislative frameworks. Here, we show how phylogenetics and species biology can inform genetic rescue options for the orange‐bellied parrot (OBP Neophema chrysogaster ), a critically endangered Australian bird with one small remaining wild population. Our phylogenetic analysis of mitochondrial genomes and nuclear loci for all congeneric species provided strong support for OBPs being the sister species to a group comprising elegant, rock, and blue‐winged parrots. Accounting for species distribution, behavior, and ecology, a captive trial of interspecific hybridization with the blue‐winged parrot is recommended, including assessment of the fitness of hybrid in iduals. Introduction of new alleles into the OBP genome would achieve the conservation goal of improving genetic ersity in a critically endangered species. Concurrently, legislative issues will need to be resolved.
Publisher: Australian Museum
Date: 13-12-2017
Publisher: Springer Science and Business Media LLC
Date: 09-01-2015
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.FSIGEN.2013.12.007
Abstract: Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Ex les are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.
Publisher: Oxford University Press (OUP)
Date: 11-2012
Abstract: Using next-generation sequencing technology, we describe the complete mitochondrial genomes for 5 Australian passerine birds (Epthianura albifrons, Petroica phoenicea, Petroica goodenovii, Petroica boodang, and Eopsaltria australis). We successfully assemble each mitogenome de novo using just 1/8th of a Roche GL FSX 454 pyrosequencing plate. From the assembled mitogenomes, we identify 2 different mitochondrial gene arrangements in the region spanning 5'-3' from Cytochrome B to 12s RNA. These gene arrangements represent 2 of the 4 known avian mitochondrial gene arrangements. Our results, together with other previously described avian mitogenomes, highlight that certain mitochondrial rearrangements appear to have arisen multiple times.
Publisher: Springer Science and Business Media LLC
Date: 17-05-2023
DOI: 10.1038/S41437-023-00621-W
Abstract: The common myna ( Acridotheres tristis ) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic ersity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 in iduals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by in iduals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by in iduals from other localities in India. Our findings suggest that New Zealand mynas were founded by in iduals from Melbourne, which, in turn, were founded by in iduals from Maharashtra. We identified two genetic clusters among New Zealand mynas, ided by New Zealand’s North Island’s axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/ZO16081
Abstract: Habitat loss and fragmentation are key threats to local koala (Phascolarctos cinereus) populations. Broad-scale management is suboptimal for koalas because distribution models are not easily generalised across regions. Therefore, it is imperative that data relevant to local management bodies are available. Genetic data provides important information on gene flow and potential habitat barriers, including anthropogenic disturbances. Little genetic data are available for nationally significant koala populations in north-eastern New South Wales, despite reported declines due to urbanisation and habitat loss. In this study, we develop 14 novel microsatellite loci to investigate koala populations in north-eastern New South Wales (Port Macquarie, Coffs Harbour, Tyagarah, Ballina) and south-eastern Queensland (Coomera). All locations were significantly differentiated (FST = 0.096–0.213 FʹST = 0.282–0.582), and this pattern was not consistent with isolation by distance (R2 = 0.228, P = 0.058). Population assignment clustered the more northern populations (Ballina, Tyagarah and Coomera), suggesting contemporary gene flow among these sites. For all locations, low molecular variation among (16%) rather than within (84%) sites suggests historical connectivity. These results suggest that koala populations in north-eastern New South Wales and south-eastern Queensland are experiencing contemporary impediments to gene flow, and highlight the importance of maintaining habitat connectivity across this region.
Publisher: Wiley
Date: 19-09-2019
Abstract: Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome-wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such s les. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum s les (i.e. s les that were not collected with the primary intent of DNA analysis) and 113 fresh tissue s les (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq
Publisher: Springer Science and Business Media LLC
Date: 17-07-2010
DOI: 10.1007/S12024-010-9174-9
Abstract: The use of genetic identification techniques in wildlife forensic investigations has increased significantly in recent years. The utilization of DNA is especially important when species identification using other methods are inconclusive. Australia has strict laws against illegal importation of wildlife as well as laws to protect its unique bio ersity from pests and diseases of quarantine concern. Two separate case studies in which genetic identification was essential for species identification are presented-the first involved illegally held shark fins, the second illegally imported live bird eggs. In the latter case genetic identification enabled charges to be laid for illegal importation of CITES Appendix I species. Australian laws allow for some of the highest penalties for illegal trade of wildlife compared to other countries, however only a fraction of cases are prosecuted and penalties applied to date have been lower than the maximum permitted. Both of the reported cases resulted in fines, and one in imprisonment of the offender, which provides a persuasive precedent for future prosecutions.
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/ZO13059
Abstract: The bush stone-curlew (Burhinus grallarius Latham), a ground-nesting nocturnal bird, is endangered in southern Australia due to habitat modification and introduced predators. To provide tools for conservation, ecological and behavioural studies, we isolated variable microsatellite repeat sequences and designed primers for PCR lification in this species. Primer pairs were developed and levels of ersity were assessed for eight microsatellite loci, including one locus linked to the gene encoding Microtubule-Associated Protein 2, a protein important for behavioural imprinting in birds, and one sex-linked locus. Isolated loci contained allelic ersity of between 5 and 17 alleles.
Publisher: Wiley
Date: 1997
Abstract: Social insects present many phenomena seen in all organisms but in more extreme forms and with larger s le sizes than those observable in most natural populations of vertebrates. Microsatellites are proving very much more informative than allozymes for the analysis of population biological problems, and prolifically polymorphic markers are fairly readily developed. In addition, the male-haploid genetic system of many social insects facilitates genetic analysis. The ability to lify DNA from sperm stored in a female's sperm storage device enables the determination of mating types long after the death of the short-lived males, in addition to information on the degree of mixing of sperm from different males. Mitochondrial (mt) DNA sequences are also proving important, not only in phylogenetic studies but also in molecular population genetics, as a tracer of female movements. Mitochondrial markers have definitively shown the movement of females between colonies, challenging models giving exclusive primacy to kin selection as the explanation for multiqueen colonies, in Australian meat ants, Iridomyrmex purpureus, and the aridzone queenless ant Rhytidoponera sp. 12. Microsatellite and mtDNA variation are being studied in C onotus consobrinus sugar ants, showing an unexpected ersity of complexity in colony structure, and microsatellites have shown that transfer of ants between nests of the weaver ant Polyrhachis doddi must be slight, despite an apparent lack of hostility.
Publisher: Proceedings of the National Academy of Sciences
Date: 18-01-2022
Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: S le Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.FSIGEN.2017.10.003
Abstract: Rhinoceros (rhino) numbers have dwindled substantially over the past century. As a result, three of the five species are now considered to be critically endangered, one species is vulnerable and one species is near-threatened. Poaching has increased dramatically over the past decade due to a growing demand for rhino horn products, primarily in Asia. Improved wildlife forensic techniques, such as validated tests for species identification of seized horns, are critical to aid current enforcement and prosecution efforts and provide a deterrent to future rhino horn trafficking. Here, we present an internationally standardized species identification test based on a 230 base pair cytochrome-b region. This test improves on previous nested PCR protocols and can be used for the discrimination of s les with <20pg of template DNA, thus suitable for DNA extracted from horn products. The assay was designed to lify water buffalo s les, a common 'rhino horn' substitute, but to exclude human DNA, a common contaminant. Phylogenetic analyses using this partial cytochrome-b region resolved the five extant rhino species. Testing successfully returned a sequence and correct identification for all of the known rhino horn s les and vouchered rhino s les from museum and zoo collections, and provided species level identification for 47 out of 52 unknown s les from seizures. Validation and standardization was carried out across five different laboratories, in four different countries, demonstrating it to be an effective and reproducible test, robust to inter laboratory variation in equipment and consumables (such as PCR reagents). This is one of the first species identification tests to be internationally standardized to produce data for evidential proceedings and the first published validated test for rhinos, one of the flagship species groups of the illegal wildlife trade and for which forensic tools are urgently required. This study serves as a model for how species identification tests should be standardized and disseminated for wildlife forensic testing.
Publisher: Springer Science and Business Media LLC
Date: 05-06-2019
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.FORSCIINT.2016.05.011
Abstract: Illegal poaching causes great harm to species ersity and conservation. A vast amount of money is involved in the trade of illegal or forged animal parts worldwide. In many cases, the suspected animal part is unidentifiable and requires costly and invasive laboratory analysis such as isotopic fingerprinting or DNA testing. The lack of rapid and accurate methods to identify wildlife parts at the point of detection represents a major hindrance in the enforcement and prosecution of wildlife trafficking. The ability of wildlife detector dogs to alert to different wildlife species demonstrates that there is a detectable difference in scent profile of illegally traded animal parts. This difference was exploited to develop a rapid, non-invasive screening method for distinguishing rhinoceros horns of different species. The method involved the collection of volatile organic compounds (VOC) by headspace solid-phase microextraction (HS-SPME) and analysis by comprehensive two-dimensional gas chromatography - time-of-flight mass spectrometry (GC×GC-TOFMS). It was hypothesised that the use of the specific odour profile as a screening method could separate and differentiate geographic origin or exploit the difference in diets of different species within a family (such as white rhinoceros and black rhinoceros from the Rhinocerotidae family). Known black and white rhinoceros horn s les were analysed using HS-SPME-GC×GC-TOFMS and multivariate statistics were applied to identify groupings in the data set. The black rhinoceros horn s les were distinctly different from the white rhinoceros horn s les. This demonstrated that seized rhinoceros horn s les can be identified based on their distinct odour profiles. The chemical odour profiling method has great potential as a rapid and non-invasive screening method in order to combat and track illegal trafficking of wildlife parts.
Publisher: Public Library of Science (PLoS)
Date: 14-06-2018
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/PC19037
Abstract: Basic knowledge of species ersity and distributions underpins the study of island biogeography and is fundamental for conservation planning. In Solomon Islands, new mammals continue to be described and several lineages are yet to be documented from large islands where, presumably, they should occur. On Malaita and Makira, no giant rats (Solomys or Uromys), or monkey-faced bats (Pteralopex) have been documented by scientists, but traditional knowledge suggests they exist. In East Kwaio, Malaita, we combined traditional knowledge and scientific methods to survey mammals and search for these taxa. Camera traps, mist nets, spotlight surveys, echolocation call recorders, rat traps and active searches were used to produce an inventory of the island’s mammals. No Solomys, Uromys or Pteralopex were captured. However, detailed accounts suggest that giant rats and monkey-faced bats were present as recently as 1996 and 2002 respectively. Moreover, we consider the presence of gnawed Canarium nuts an indicator that giant rats still persist. The human population of Malaita is dense, hunting pressure appears high, feral cats are common, and logging is rapidly reducing primary forests. A notable feature of this work has been the commitment towards collaboration and upskilling landowners in mammal survey techniques. This collaboration has helped fuel a growing conservation movement on Malaita and led to the designation of three large conservation areas. Gathering evidence for the existence of undescribed mammals on Malaita is paramount for reducing further extinctions in Melanesia. Continued support for skilled community members in East Kwaio will be key to collecting this evidence.
Publisher: Springer Science and Business Media LLC
Date: 24-04-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 26-09-2022
Abstract: Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For ex le, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
Publisher: Informa UK Limited
Date: 26-02-2019
Publisher: Wiley
Date: 14-10-2021
DOI: 10.1002/WFS2.1397
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
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.YMPEV.2018.05.030
Abstract: Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue s les from 36 in idual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia (D. lumholtzi, D. bennettianus) and five in New Guinea (D. inustus, D. ursinus, a Goodfellow's group, D. mbaiso and a Doria's group). Two major episodes of ersification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All s led subspecies showed high levels of genetic ergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.
Publisher: Oxford University Press (OUP)
Date: 21-07-2005
Publisher: Springer Science and Business Media LLC
Date: 21-07-2020
Publisher: Springer Science and Business Media LLC
Date: 05-08-2020
Publisher: Wiley
Date: 25-02-2014
DOI: 10.1111/ACV.12108
Abstract: Urbanization represents the most extreme form of land cover transformation and is expected to restrict dispersal of animals, both because of the structural unsuitability of the novel habitat, as well as through mechanisms associated with human activity, such as disturbance. Fragmentation of populations by urbanization is considered to be a significant threat to several endangered bird populations, although isolation has seldom been demonstrated genetically. The aim of this study was to explore the utility of genetic criteria for identifying at‐risk populations, using a salt‐marsh‐inhabiting bird, the white‐fronted chat E pthianura albifrons , as a case study. DNA was extracted from feathers from 78 in iduals from five sites, including two salt marsh remnants situated within the intensively urbanized zone of a city of more than three million people, and three sites up to 500 km distant. Microsatellite markers were used to measure genetic ersity and compare genetic structure between populations. Analyses of population structure demonstrated that the two populations surrounded by intensive urban development were genetically distinct from each other despite being separated by less than 20 km. They were also distinct from larger populations beyond the urban zone that showed much lower levels of genetic differentiation and no evidence of isolation by distance, despite being separated by continuous forest, which is not a recognized habitat for this species. The two endangered populations had low levels of genetic ersity reflected in the number of alleles and heterozygosity. Two immigrants were detected in one of the isolated populations, but their reproductive success was very low and they failed to effect genetic rescue. This study demonstrates that the endangered population satisfies the genetic criteria for listing, and although the population is unlikely to have special evolutionary significance in itself, flagging the population highlights the vulnerability of some coastal fauna to the impacts of urbanization.
Publisher: Elsevier BV
Date: 05-2009
DOI: 10.1016/J.YMPEV.2009.02.001
Abstract: A species flock of the freshwater isopod genus Eophreatoicus Nicholls lives in seeps, springs and perched aquifers at the base of the Arnhem Plateau and associated sandstone outliers in Australia's Northern Territory. These species have been found to have surprisingly high levels of genetic ergence and narrow range endemism, despite potential opportunities for dispersion during the summer monsoon season when streams flow continuously and have connectivity. Species of Eophreatoicus were identified morphologically as distinct taxa, sometimes with two or three species occurring at the same site. DNA sequence data from the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes corroborate our morphological concepts to a high level of resolution, with the exception of two distinct species that are identical genetically. The value of mtDNA data for identification of these species, therefore, is limited. These isopods disperse downstream from their home springs to a limited extent during the wet season, but the genetic data show that migration to non-natal springs, and reproduction there, may be rare. We argue that the multiplication of the narrow-range endemic species is the result of their homing behaviour combined with monsoonal alternation between aridity and flooding over recent and geological time scales since the Miocene period.
Publisher: Springer Science and Business Media LLC
Date: 12-05-2020
Publisher: MDPI AG
Date: 10-01-2020
DOI: 10.3390/SEPARATIONS7010005
Abstract: Globally, the rapid decline in wildlife species has many causes. The illegal trafficking of fauna and flora is a major contributor to species decline and continues to grow at an alarming rate. To enable the prosecution of those involved in the trafficking of illegal wildlife, accurate and reliable identification is paramount. Traditionally, morphology and DNA lification are used. This paper investigates a novel application of volatilome profiling using comprehensive two-dimensional gas chromatography coupled with time of flight mass spectrometry for wildlife s le detection. Known s les of elephant-derived ivory, other dentine s les, and bone (a common ivory substitute) were used as reference s les for volatilome profiling. Subsequently, specimens that were suspected ivory from border control seizures were obtained and analysed. Confirmatory DNA analyses were conducted on seized s les to establish the reliability parameters of volatilome profiling. The volatilome method correctly identified six of the eight seized s les as elephant ivory, which was confirmed through DNA analysis. There was also clear distinction of African elephant ivory parts from the bone and dentine s les from other species, as shown through PCA and discriminant analyses. These preliminary results establish volatilome profiling through GC×GC-TOFMS as a novel screening method used for the identification of unknown wildlife contraband.
Publisher: Springer Science and Business Media LLC
Date: 08-2005
Publisher: Informa UK Limited
Date: 2005
Publisher: Proceedings of the National Academy of Sciences
Date: 06-08-2018
Abstract: Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs are degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate that recombination with an ancient koala retroelement disables KoRV, and that recombination occurs frequently and early in the invasion process. Recombinant KoRVs (recKoRVs) are then able to proliferate in the koala germ line. This may in part explain the generally degraded nature of ERVs in vertebrate genomes and suggests that degradation via recombination is one of the earliest processes shaping retroviral genomic invasions.
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.
Publisher: Wiley
Date: 06-11-2020
DOI: 10.1002/JWMG.21777
Publisher: Wiley
Date: 24-11-2018
DOI: 10.1111/JBI.13473
Publisher: Springer Science and Business Media LLC
Date: 15-05-2012
Publisher: Magnolia Press
Date: 04-03-2019
DOI: 10.11646/ZOOTAXA.4564.1.7
Abstract: Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al. (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al. (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al. (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al. (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply ergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al. (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis—by demonstrating deep evolutionary ergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al. (2019) have not done this instead they have misrepresented the content and conclusions of Jackson et al. (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al. (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature.
Publisher: Springer Science and Business Media LLC
Date: 09-03-0009
DOI: 10.1038/S41598-017-00137-4
Abstract: The virulence of chlamydial infection in wild koalas is highly variable between in iduals. Some koalas can be infected (PCR positive) with Chlamydia for long periods but remain asymptomatic, whereas others develop clinical disease. Chlamydia in the koala has traditionally been studied without regard to coinfection with other pathogens, although koalas are usually subject to infection with koala retrovirus (KoRV). Retroviruses can be immunosuppressive, and there is evidence of an immunosuppressive effect of KoRV in vitro . Originally thought to be a single endogenous strain, a new, potentially more virulent exogenous variant (KoRV-B) was recently reported. We hypothesized that KoRV-B might significantly alter chlamydial disease outcomes in koalas, presumably via immunosuppression. By studying sub-groups of Chlamydia and KoRV infected koalas in the wild, we found that neither total KoRV load (either viraemia or proviral copies per genome), nor chlamydial infection level or strain type, was significantly associated with chlamydial disease risk. However, PCR positivity with KoRV-B was significantly associated with chlamydial disease in koalas ( p = 0.02961). This represents an ex le of a recently evolved virus variant that may be predisposing its host (the koala) to overt clinical disease when co-infected with an otherwise asymptomatic bacterial pathogen ( Chlamydia ).
Publisher: PeerJ
Date: 28-03-2016
DOI: 10.7717/PEERJ.1847
Abstract: Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala s les collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical s les. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
Publisher: Oxford University Press (OUP)
Date: 07-2004
Publisher: Springer Science and Business Media LLC
Date: 05-09-2007
Publisher: Informa UK Limited
Date: 20-11-2020
Start Date: 05-2016
End Date: 12-2017
Amount: $250,000.00
Funder: Australian Research Council
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