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1.
Zootaxa ; 4564(1): zootaxa.4564.1.7, 2019 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-31716520

RESUMO

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 divergent 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 divergence 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.


Assuntos
Lobos , Animais , Austrália , Cães , Nova Guiné
2.
Mol Ecol Resour ; 19(6): 1578-1592, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31484222

RESUMO

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 samples. To achieve this, we generated thousands of SNPs from 47 red-tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site-associated DNA marker approach (DArTseq™ ). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq-based method to produce reliable genome-wide SNP data from traditional museum specimens.

3.
PeerJ ; 7: e7138, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31231598

RESUMO

Background: 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. Methods: Sixty-eight fish samples, 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). Samples were DNA barcoded and resulting sequences were deposited in the online Barcode of Life Data system using the simplified Student Data Portal interface. Results: 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 samples were given common names not listed on the AFNS. Despite this lack of standardization, DNA barcode data confirmed the retailers' identifications for 93% of samples and 90% of species sampled. Discussion: The level of mislabelling we report for Sydney retailers (7% of samples 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 sampled mostly Australian produce, only two retailers and no restaurants. Results of our limited sample 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.

4.
Proc Natl Acad Sci U S A ; 115(34): 8609-8614, 2018 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-30082403

RESUMO

Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.


Assuntos
Retrovirus Endógenos/genética , Phascolarctidae/genética , Recombinação Genética , Animais , Feminino , Masculino , New South Wales
6.
Nat Genet ; 50(8): 1102-1111, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29967444

RESUMO

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.


Assuntos
Adaptação Fisiológica/genética , Phascolarctidae/genética , Animais , Austrália , Infecções por Chlamydia/genética , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Feminino , Genoma , Anotação de Sequência Molecular/métodos , Phascolarctidae/metabolismo , Translocação Genética
7.
PLoS One ; 13(6): e0198565, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29902212

RESUMO

Rhinoceros (rhinos) have suffered a dramatic increase in poaching over the past decade due to the growing demand for rhino horn products in Asia. One way to reverse this trend is to enhance enforcement and intelligence gathering tools used for species identification of horns, in particular making them fast, inexpensive and accurate. Traditionally, species identification tests are based on DNA sequence data, which, depending on laboratory resources, can be either time or cost prohibitive. This study presents a rapid rhino species identification test, utilizing species-specific primers within the cytochrome b gene multiplexed in a single reaction, with a presumptive species identification based on the length of the resultant amplicon. This multiplex PCR assay can provide a presumptive species identification result in less than 24 hours. Sequence-based definitive testing can be conducted if/when required (e.g. court purposes). This work also presents an actual casework scenario in which the presumptive test was successfully utlitised, in concert with sequence-based definitive testing. The test was carried out on seized suspected rhino horns tested at the Institute of Ecology and Biological Resources, the CITES mandated laboratory in Vietnam, a country that is known to be a major source of demand for rhino horns. This test represents the basis for which future 'rapid species identification tests' can be trialed.


Assuntos
Cornos , Tipagem Molecular/métodos , Perissodáctilos/genética , Reação em Cadeia da Polimerase/métodos , Animais , Búfalos , Conservação dos Recursos Naturais , Citocromos b/genética , Humanos , Análise de Sequência de DNA/métodos , Especificidade da Espécie , Vietnã
8.
Mol Phylogenet Evol ; 127: 589-599, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29807156

RESUMO

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 samples from 36 individual 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 diversification 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 sampled subspecies showed high levels of genetic divergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.


Assuntos
Macropodidae/classificação , Animais , Biodiversidade , Evolução Biológica , Macropodidae/genética , Nova Guiné , Filogenia , Análise de Sequência de DNA
9.
PLoS One ; 13(4): e0194908, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29634748

RESUMO

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation.


Assuntos
Quirópteros/genética , Quirópteros/fisiologia , DNA Mitocondrial/genética , Animais , Austrália , Teorema de Bayes , Conservação dos Recursos Naturais , DNA/química , Esmalte Dentário/fisiologia , Genes RAG-1/genética , Geografia , Funções Verossimilhança , Ilhas do Pacífico , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie
10.
Forensic Sci Int Genet ; 32: 33-39, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29035720

RESUMO

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 samples with <20pg of template DNA, thus suitable for DNA extracted from horn products. The assay was designed to amplify water buffalo samples, 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 samples and vouchered rhino samples from museum and zoo collections, and provided species level identification for 47 out of 52 unknown samples 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.


Assuntos
Conservação dos Recursos Naturais/legislação & jurisprudência , Crime , Grupo dos Citocromos b/genética , Impressões Digitais de DNA/normas , Cornos , Perissodáctilos/genética , Animais , Sequência de Bases , Primers do DNA/normas , Genética Forense/normas , Humanos , Internacionalidade , Filogenia , Reação em Cadeia da Polimerase , Reprodutibilidade dos Testes , Especificidade da Espécie
11.
Syst Biol ; 67(3): 400-412, 2018 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-29029231

RESUMO

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 division 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 diversification 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.


Assuntos
Genômica , Marsupiais/classificação , Modelos Genéticos , Filogenia , Animais , Simulação por Computador , Marsupiais/genética
12.
Sci Rep ; 7(1): 15838, 2017 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-29158564

RESUMO

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 individual. 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.


Assuntos
Evolução Molecular , Phascolarctidae/genética , Infecções por Retroviridae/genética , Retroviridae/genética , Animais , Gammaretrovirus , Células Germinativas , Phascolarctidae/virologia , Retroviridae/patogenicidade , Infecções por Retroviridae/virologia , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
13.
PLoS One ; 11(9): e0162207, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27588685

RESUMO

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia's most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.


Assuntos
Conservação dos Recursos Naturais , Variação Genética , Phascolarctidae/genética , Animais , Austrália , Evolução Biológica , DNA Mitocondrial/genética , Ecossistema , Haplótipos , Filogenia , Filogeografia
14.
Forensic Sci Int ; 266: e99-e102, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27240958

RESUMO

Illegal poaching causes great harm to species diversity 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 samples were analysed using HS-SPME-GC×GC-TOFMS and multivariate statistics were applied to identify groupings in the data set. The black rhinoceros horn samples were distinctly different from the white rhinoceros horn samples. This demonstrated that seized rhinoceros horn samples 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.


Assuntos
Conservação dos Recursos Naturais/legislação & jurisprudência , Crime , Cornos , Odorantes , Perissodáctilos , Compostos Orgânicos Voláteis/análise , Animais , Cromatografia Gasosa-Espectrometria de Massas , Humanos , Microextração em Fase Sólida
15.
PeerJ ; 4: e1847, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27069793

RESUMO

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 samples 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 samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

16.
PLoS One ; 10(3): e0121068, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25799012

RESUMO

Toll-like receptors (TLRs) play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous) were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.


Assuntos
Phascolarctidae/genética , Polimorfismo de Nucleotídeo Único , Receptor 10 Toll-Like/genética , Animais , Phascolarctidae/classificação , Filogenia
17.
BMC Genomics ; 15: 786, 2014 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-25214207

RESUMO

BACKGROUND: The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. RESULTS: RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene.Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. CONCLUSIONS: This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org.


Assuntos
Perfilação da Expressão Gênica , Variação Genética , Phascolarctidae/genética , Phascolarctidae/virologia , Retroviridae/genética , Retroviridae/fisiologia , Transcrição Genética , Animais , Sequência de Bases , Evolução Molecular , Feminino , Duplicação Gênica/genética , Genômica , Masculino , Anotação de Sequência Molecular , Processamento de RNA/genética , Análise de Sequência de RNA , Proteínas Virais/genética
18.
Forensic Sci Int Genet ; 10: 1-11, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24680123

RESUMO

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. Examples 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.


Assuntos
Animais Selvagens/genética , DNA/genética , Genética Forense , Acreditação , Animais , Certificação
19.
Conserv Biol ; 28(2): 572-9, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24283832

RESUMO

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 divergent 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.


Assuntos
Biodiversidade , Conservação dos Recursos Naturais , Musaranhos/classificação , Musaranhos/genética , Animais , Austrália , Citocromos b/genética , Espécies em Perigo de Extinção , Ilhas do Oceano Índico , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
20.
J Hered ; 103(6): 882-6, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23125406

RESUMO

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.


Assuntos
Ordem dos Genes , Genoma Mitocondrial , Aves Canoras/genética , Adenosina Trifosfatases/genética , Animais , Citocromos b/genética , Dados de Sequência Molecular , RNA Ribossômico , RNA Ribossômico 16S , RNA de Transferência , Análise de Sequência de DNA/métodos
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