ORCID Profile
0000-0003-2886-1614
Current Organisation
NSW Department of Primary Industries
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Publisher: Public Library of Science (PLoS)
Date: 10-08-2016
Publisher: Springer Science and Business Media LLC
Date: 29-07-2009
DOI: 10.1038/HDY.2009.102
Abstract: Recent advances in the statistical analysis of microsatellite data permit calculation of sex-specific dispersal rates through sex- and age-specific comparisons of genetic variation. This approach, developed for the analysis of data derived from co-dominant autosomal markers, should be applicable to a sex-specific marker such as mitochondrial DNA. To test this premise, we lified a 449 bp control region DNA sequence from the mitochondrial genome of the collared peccary (Pecari tajacu), and estimated intra-class correlations among herds s led from three Texas populations. Analyses on data partitioned by breeding group showed a clear signal of male-biased dispersal sex-specific fixation indices associated with genetic variation among social groups within populations yielded values for females (F(GP)=0.91), which were significantly larger than values for males (F(GP)=0.24 P=0.0015). The same general pattern emerged when the analyses were conducted on age classes (albeit nonsignificantly), as well as categories of in iduals that were predicted a posteriori to be dispersers (adult males) and philopatric (adult females and all immatures). By extending a previously published methodology based on biparentally inherited markers to matrilineally inherited haploid data, we calculated sex-specific rates of contemporary dispersal among social groups within populations (m(male symbol)=0.37). These results support the idea that mitochondrial DNA haplotype frequency data can be used to estimate sex-specific instantaneous dispersal rates in a social species.
Publisher: Magnolia Press
Date: 03-10-2013
DOI: 10.11646/ZOOTAXA.3718.2.5
Abstract: Light trap surveys of adult Culicoides Latreille in the Republic of Korea (ROK) resulted in the capture of three previously unreported species, C. nasuensis Kitaoka, C. pallidulus Yu and C. jacobsoni Macfie. These new records are supported by supplementary morphological descriptions and DNA barcodes (mitochondrial cytochrome oxidase I or COI). An updated checklist of species reported from the ROK is provided.
Publisher: Wiley
Date: 24-05-2022
DOI: 10.1111/AEN.12601
Abstract: Serpentine leafminer Liriomyza huidobrensis is a highly polyphagous insect pest that threatens vegetable and ornamental horticultural production globally as a function of feeding and egg laying damage to plants. Although this species has been periodically intercepted at Australia's border, the pest had not been recorded as established on the mainland. A population of L. huidobrensis was identified in the Sydney Basin, New South Wales (NSW), Australia, in late 2020 affecting a variety of vegetable crops. Delimiting surveillance revealed L. huidobrensis to be widespread in the Sydney Basin and present in several regional locations, impacting vegetable, ornamental and weed hosts. This article documents the first report of L. huidobrensis in Australia and the ensuing biosecurity response that was triggered at its detection.
Publisher: Wiley
Date: 06-2008
DOI: 10.1111/J.1558-5646.2008.00364.X
Abstract: Microsatellites and mitochondrial DNA (mtDNA) have traditionally been used in population genetics because of their variability and presumed neutrality, whereas genes of the major histocompatibility complex (MHC) are increasingly of interest because strong selective pressures shape their standing variation. Despite the potential for MHC genes, microsatellites, and mtDNA sequences to complement one another in deciphering population history and demography, the three are rarely used in tandem. Here we report on MHC, microsatellite, and mtDNA variability in a single large population of the eastern tiger salamander (Ambystoma tigrinum tigrinum). We use the mtDNA mismatch distribution and, on microsatellite data, the imbalance index and bottleneck tests to infer aspects of population history and demography. Haplotype and allelic variation was high at all loci surveyed, and heterozygosity was high at the nuclear loci. We find concordance among neutral molecular markers that suggests our study population originated from post-Pleistocene expansions of multiple, fragmented sources that shared few migrants. Differences in N(e) estimates derived from haploid and diploid genetic markers are potentially attributable to secondary contact among source populations that experienced rapid mtDNA ergence and comparatively low levels of nuclear DNA ergence. We find strong evidence of natural selection acting on MHC genes and estimate long-term effective population sizes (N(e)) that are very large, making small selection intensities significant evolutionary forces in this population.
Publisher: Informa UK Limited
Date: 03-08-2022
Publisher: Public Library of Science (PLoS)
Date: 15-02-2023
DOI: 10.1371/JOURNAL.PONE.0281759
Abstract: Insect identification and preservation of voucher specimens is integral to pest diagnostic and surveillance activities yet bulk-trapped insects are a diagnostic challenge due to high catch numbers and the susceptibility of s les to environmental damage. Many insect trap catches rely on examination of morphological characters for species identifications, which is a time consuming and highly skilled task, hence there is a need for more efficient molecular approaches. Many bulk DNA extraction methods require destructive s ling of specimens, resulting in damaged, or fully destroyed, voucher specimens. We developed an inexpensive, rapid, bulk DNA isolation method that preserves specimens as pinned vouchers to a standard that allows for post-extraction morphological examination and inclusion in insect reference collections. Our protocol was validated using a group of insects that are time-consuming to identify when trapped in large numbers–the dacine fruit flies (Diptera: Tephritidae: Dacinae). In developing our method, we evaluated existing protocols against the following criteria: effect on morphology suitability for large trap catches cost ease of handling and application to downstream molecular diagnostic analyses such as real-time PCR and metabarcoding. We found that the optimum method for rapid isolation of DNA extraction was immersing flies in a NaOH:TE buffer at 75°C for 10 minutes, without the need for proteinase K or detergents. This HotSOAK method produced sufficient high-quality DNA whilst preserving morphological characters suitable for species-level identification with up to 20,000 flies in a s le. The lysates performed well in down-stream analyses such as loop-mediated isothermal lification (LAMP) and real-time PCR applications, while for metabarcoding PCR the lysate required an additional column purification step. Development of this method is a key step required for upscaling our capacity to accurately detect insects captured in bulk traps, whether for bio ersity, biosecurity, or pest management objectives.
Publisher: Springer Science and Business Media LLC
Date: 10-08-2007
Publisher: Wiley
Date: 27-07-2009
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/SB16027
Abstract: Camel melon (Citrullus lanatus), colocynth (Citrullus colocynthis) and prickly paddy melon (Cucumis myriocarpus) are summer-growing invasive weeds distributed throughout Australia. We used DNA-sequence information from s les collected across Australia and morphological data from glasshouse-grown plants to determine diagnostic features of these species, and to determine the infraspecific identity of Australian Citrullus lanatus and Cucumis myriocarpus. All species possessed distinct genotypes and haplotypes at nuclear G3pdh and chloroplast ycf6–psbM gene regions and could be easily identified on the basis of molecular phylogenetic analysis. A combination of vegetative, floral, fruit and seed characters also allowed for species identification at all developmental stages. On the basis of our morphological and molecular analyses, Australian camel melon and prickly paddy melon populations were identified as Citrullus lanatus var. citroides and Cucumis myriocarpus subsp. myriocarpus respectively.
Publisher: Public Library of Science (PLoS)
Date: 11-04-2017
Publisher: Elsevier BV
Date: 08-2017
Publisher: Magnolia Press
Date: 27-02-2014
DOI: 10.11646/ZOOTAXA.3768.4.1
Abstract: The monophyly of the Imicola complex, a natural species complex within subgenus C. subgen. Avaritia Fox of the biting midge genus Culicoides Latreille, is supported using morphological and molecular analyses. A diagnosis for the group along with comparative redescriptions of the male and female of the species represented in Australasia, C. brevitarsis Kieffer and C. nudipalpis Delfinado and a description of C. asiatica Bellis sp. nov., are presented together with keys for their specific determination and molecular support for their status.
Publisher: Wiley
Date: 16-03-2006
Publisher: Frontiers Media SA
Date: 26-04-2017
Publisher: Springer Science and Business Media LLC
Date: 28-04-2022
Publisher: Korean Society for Parasitology
Date: 25-08-2015
Publisher: Springer Science and Business Media LLC
Date: 08-04-2015
Publisher: Wiley
Date: 09-2016
DOI: 10.1111/AEN.12224
Publisher: CSIRO Publishing
Date: 2002
DOI: 10.1071/MF01225
Abstract: The population genetic structure of the estuarine crab, Scylla serrata (Forskål, 1775), was examined among shelf-connected locations and across a historical bio-geographic barrier. Over 300 in iduals were s led from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at a mitochondrial coding gene (COI). Analysis of molecular variance indicated mitochondrial haplotypes to be structured regionally (P 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow are absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. Two distinct clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation is concordant with a number of other marine species across northern Australia and may indicate a shared history of vicariance induced by eustasy. Alternatively, we suggest that sundering of S. serrata populations resulting in cladogenesis may have its origins outside of the northern Australian region.
Publisher: Magnolia Press
Date: 18-06-2013
Publisher: Springer Science and Business Media LLC
Date: 16-03-2017
DOI: 10.1038/SREP44787
Abstract: Scientific Reports 7: Article number: 42792 published online: 17 February 2017 updated: 16 March 2017 In the original version of this Article, the legend of Figure 4 was incorrect: “Figure 4: There are two spelling problem in this image. Please use the revised image uploaded with this proof”. Now reads:
Publisher: Wiley
Date: 03-10-2019
DOI: 10.1111/PPA.12936
Publisher: Springer Science and Business Media LLC
Date: 17-02-2017
DOI: 10.1038/SREP42792
Abstract: Echium plantagineum and E. vulgare are congeneric exotics first introduced to Australia in the early 1800 s. There, E. plantagineum is now highly invasive, whereas E. vulgare has a limited distribution. Studies were conducted to evaluate distribution, ecology, genetics and secondary chemistry to shed light on factors associated with their respective invasive success. When s led across geographically erse locales, E. plantagineum was widespread and exhibited a small genome size (1 C = 0.34 pg), an annual life cycle, and greater genetic ersity as assessed by DNA sequence analysis. It was found frequently in areas with temperature extremes and low rainfall. In contrast, E. vulgare exhibited a larger genome size (1 C = 0.43 pg), a perennial lifecycle, less chloroplast genetic ersity, and occurred in areas with lower temperatures and higher rainfall. Twelve chloroplast haplotypes of E. plantagineum were evident and incidence aligned well with reported historical introduction events. In contrast, E. vulgare exhibited two haplotypes and was found only sporadically at higher elevations. Echium plantagineum possessed significantly higher levels of numerous pyrrolizidine alkaloids involved in plant defence. We conclude that elevated genetic ersity, tolerance to environmental stress and capacity for producing defensive secondary metabolites have contributed to the successful invasion of E. plantagineum in Australia.
Publisher: Wiley
Date: 27-07-2021
DOI: 10.1111/AEN.12559
Abstract: Economically important cacao ( Theobroma cacao Linnaeus 1753) plantations in South East Asia and Papua New Guinea (PNG) are significantly affected by the cocoa pod borer (CPB) moth. Species identity of the pest is attributed to Conopomorpha cramerella (Snellen 1904), a gracillariid moth endemic to Australasian and Oriental tropic regions that has evolved a host preference for introduced cacao. Suspected presence of cryptic CPB biotypes is largely unsupported by earlier genetic work but remains a concern to organisations developing species‐specific lure and/or control tools for managing this pest. We report the use of DNA barcoding to investigate population and species genetic ersity of CPB infecting cacao plantations in PNG at the eastern periphery of the pest's distribution. DNA barcodes from 94.4% of 179 moths from three disjunct PNG provinces (East Sepik, Bougainville and East New Britain) matched to reported C. cramerella sequence accessions. Genetic ersity among C. cramerella in PNG was limited to four closely related haplotypes, two of which were common in PNG and have previously been reported in the Malay Archipelago at different frequencies. We found evidence of significant population genetic structure between mainland and eastern offshore PNG provinces marked by a reduction of genetic ersity at the offshore provinces. We suggest C. cramerella populations in these offshore island provinces likely arose recently from a genetically depauperate cohort of founders from western sources. Ten moths were genetically unmatched to C. cramerella . Of these, six incidentally captured and degraded adults had novel unmatched DNA barcodes. Four larvae infesting cacao pods were genetically matched to Thaumatotibia zophophanes (Turner 1946) (Lepidoptera: Tortricidae) and an undefined Conopomorpha species distantly related to C. cramerella . The extent to which these two additional moth species affect the cacao industry in PNG (and potentially elsewhere) remains unknown. However, their low representation here ( .3% of s les) indicates they may be of lesser prominence than the widespread C. cramerella . Nevertheless, organisations designing and/or implementing CPB controls tailored specifically for C. cramerella will need to ensure empirical evidence of control efficiency is monitored with respect to species identity of the captured pests.
Publisher: Informa UK Limited
Date: 17-10-2017
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/MF03033
Abstract: Mud crabs (Portunidae Scylla spp.) have become established recently in some south-west Australian estuaries – almost 1000 km south of their recorded distribution. Colonisation may have occurred by a natural range expansion from the north-west or by translocation from source(s) within the Indo-West Pacific. To identify the species and the potential source population(s), genetic analyses was used to compare south-west crabs (N = 32) to other populations. Levels of ersity at two independent genetic markers were also compared to obtain relative estimates of effective population size between colonist and suspected source population(s). Comparisons of mitochondrial DNA sequences (COI) indicated that all south-west crabs were Scylla serrata. Indeed, the sole haplotype found among colonists was identical to one prevalent but endemic to more erse north-west Australian populations. In contrast, source and colonist populations had equally high levels of genetic ersity at two microsatellite loci. It is argued that the south-west region was colonised by large numbers of S. serrata from north-west Australia through a recruitment event enhanced by the strong 1999/2000 Leeuwin Current. Differences in ersity among nuclear and mitochondrial loci may reflect different responses to the colonisation process it is predicted that such differences are prevalent among plankton-dispersed species.
Publisher: Elsevier BV
Date: 04-2020
Publisher: Wiley
Date: 17-10-2002
Publisher: The Royal Society
Date: 07-2008
Abstract: Inbreeding may lead to morphological malformations in a wide variety of taxa. We used genetic markers to evaluate whether malformed urodeles were more inbred and/or had less genetic ersity than normal salamanders. We captured 687 adult and 1259 larval tiger salamanders ( Ambystoma tigrinum tigrinum ), assessed each in idual for gross malformations, and surveyed genetic variation among malformed and normal in iduals using both cytoplasmic and nuclear markers. The most common malformations in both adults and larvae were brachydactyly, ectrodactyly and polyphalangy. The overall frequency of adults with malformations was 0.078 compared to 0.081 in larval s les. Genetic ersity was high in both normal and malformed salamanders, and there were no significant difference in measures of inbreeding ( f and F ), allele frequencies, mean in idual heterozygosity or mean internal relatedness. Environmental contaminants or other extrinsic factors may lead to genome alternations that ultimately cause malformations, but our data indicate that inbreeding is not a causal mechanism.
Publisher: Springer Science and Business Media LLC
Date: 04-08-2023
DOI: 10.1007/S11033-023-08673-1
Abstract: Khapra beetle (Dermestidae: Trogoderma granarium Everts, 1898) is an internationally significant pest of grain crops and stored grain products. Wheat germ traps, routinely used in surveillance s ling of Khapra beetle provide feed-substrates used by the pest throughout its life cycle. However, Khapra beetle larvae, eggs and other traces of the pest, such as larval frass and exuviae, in wheat germ traps are difficult to sort and taxonomically identify. Additionally, high levels of polysaccharides in wheat germ can inhibit PCR based molecular detection of this pest captured in the traps. We have developed a sensitive and low-cost protocol for extracting trace levels of Khapra beetle DNA from an entire wheat germ trap. Overnight digestion of entire trap contents in 6 mL of ATL buffer, followed by a 40 min lysis step was optimal for DNA extraction. Paired with reported qPCR assays, this protocol allows the detection of a few hairs of T. granarium in a typical 2-gram wheat germ trap. This DNA extraction protocol makes it possible to perform a more rapid identification of the pest following wheat germ s le collection. The protocol has potential to improve international efforts for Khapra beetle surveillance.
Publisher: Oxford University Press (OUP)
Date: 16-12-2010
Publisher: Magnolia Press
Date: 31-01-2017
DOI: 10.11646/ZOOTAXA.4227.1.2
Abstract: The biting midge fauna of Dongzhaigang Mangrove Forest, Hainan Province, China was s led on 14 October 2015 using three methods: a pan light trap operated from dusk until dawn the following morning and sweep net and human landing collections performed between 16:15–17:15 hr. Eight species, including two new records for China, Culicoides palawanensis and C. niphanae, and one new record for Hainan, C. circumbasalis, were collected. A key to assist with identification of specimens of these species is provided. DNA barcodes supported the morphological identification of some of these species and identified the potential presence of cryptic species and/or deep population structure in others. The newly recorded species were morphologically similar to species previously reported from Hainan, highlighting the need for further investigation into the taxonomy of biting midges in this region. Species composition and abundance varied considerably between the three collection techniques suggesting that multiple techniques likely provide a more comprehensive s le of biting midge fauna.
Publisher: Springer Science and Business Media LLC
Date: 24-12-2008
DOI: 10.1007/S10709-008-9341-Z
Abstract: Microsatellites are commonly used for mapping and population genetics because of their high heterozygosities and allelic variability (i.e., polymorphism). Microsatellite markers are generally more polymorphic than other types of molecular markers such as allozymes or SNPs because the insertions/deletions that give rise to microsatellite variability are relatively common compared to nucleotide substitutions. Nevertheless, direct evidence of microsatellite mutation rates (MMRs) is lacking in most vertebrate groups despite the importance of such estimates to key population parameters (e.g., genetic differentiation or theta = 4N (e)micro). Herein, we present empirical data on MMRs in eastern tiger salamanders (Ambystoma tigrinum tigrinum). We conducted captive breeding trials and genotyped over 1,000 offspring at a suite of microsatellite loci. These data on 7,906 allele transfers provide the first direct estimates of MMRs in hibians, and they illustrate that MMRs can vary by more than an order of magnitude across loci within a given species (one locus had ten mutations whereas the others had none).
Publisher: Springer Science and Business Media LLC
Date: 25-11-2016
DOI: 10.1038/SREP37746
Abstract: Phytoplasmas are a group of insect-vectored bacteria responsible for disease in many plant species worldwide. Among the crop species affected is the economically valuable forage species lucerne. Here we provide comprehensive molecular evidence for infection in multiple lucerne plants by a phytoplasma not previously known from this plant species. This phytoplasma had a % genetic similarity to an unclassified 16S rRNA subgroup previously reported as Stylosanthes little leaf from Stylosanthes spp. and was genetically and symptomatically distinct from a co-occurring but less common 16SrIIA group phytoplasma. Neighbour-joining analyses with publicly available sequence data confirmed the presence of two distinct phytoplasma lineages in the plant population. No PCR detections were made among 38 in iduals of 12 co-occurring weed species. Sequence analysis revealed that all nine PCR detections from among 106 in iduals of five Hemiptera insect species from the site, three of which had previously been reported as likely vectors, were false positives. This study demonstrates the importance of sequencing to complement PCR detection and avoid potentially inaccurate conclusions regarding vectors, highlights that s ling over a wide spatio-temporal scale is important for vector and alternative host studies, and extends to eight the number of phytoplasma 16 Sr groups known from lucerne.
Publisher: Public Library of Science (PLoS)
Date: 19-09-2019
Publisher: Western Australian Museum
Date: 2013
Publisher: Wiley
Date: 03-2022
DOI: 10.1111/AEN.12590
Abstract: Larval habitats of the pest biting midge Culicoides ornatus were identified and characterised in a macrotidal mangrove creek system in Darwin Harbour in the wet‐dry tropics of northern Australia. S ling was undertaken during the mid to late dry season using submersible emergence traps to indicate larval activity. Substantial emergence was found in two well separated and distinctly different habitats: open creekbanks covered in Avicennia marina (Grey Mangrove) pneumatophores in the upper reaches of small tidal creeks and broad relatively flat areas dominated by Sonneratia alba (Mangrove Apple) at the mouth of the creek system. Intervening areas along creeklines were lined by C tostemon schultzii (Kapok Mangrove) and did not support emergence activity. Adults emerging from each habitat were conspecific, based on comparison of mitochondrial COI gene sequences and a range of morphological characters. Nine different haplotypes were identified from 26 adults, with four haplotypes common to both habitats. Neighbour‐joining analysis resolved all the haplotypes as a single highly supported clade with an average sequence difference of 1.6%. Features common to the two habitats included occurrence in sheltered mangrove‐lined estuaries occurrence in soft, fine, silt mud presence of mangrove pneumatophores and an open vegetation structure providing partial shade. Dense vegetation appeared to be a limiting factor. The tidal creek habitat was similar to C. ornatus habitats previously described from the east coast of Australia, but neither the Sonneratia zone nor other habitats at such a low tidal elevation have been previously associated with C. ornatus . This is the first detailed account of the larval biology of this important mangrove breeding pest species. The identification of likely C. ornatus breeding sites in Darwin Harbour and other similar ria coastlines of northern Australia should be possible from aerial photographs using the habitat descriptions presented in this paper.
Publisher: American Society for Microbiology
Date: 22-11-2017
Abstract: Nassella hyalina (cane needle grass) is on the Alert List for Environmental Weeds in Australia. We present here the first complete chloroplast sequence of N. hyalina reconstructed from Illumina whole-genome sequencing. The complete chloroplast sequence is 137,606 bp in size and has a gene content and structure similar to those of other published chloroplast genomes of Stipeae.
Publisher: Springer Science and Business Media LLC
Date: 07-07-1999
Publisher: Springer International Publishing
Date: 2015
Publisher: Elsevier BV
Date: 02-2017
Publisher: Springer Science and Business Media LLC
Date: 23-07-2022
DOI: 10.1038/S41598-022-16901-0
Abstract: The cue-lure-responding New Guinea fruit fly, Bactrocera trivialis , poses a biosecurity risk to neighbouring countries, e.g., Australia. In trapping programs, lure caught flies are usually morphologically discriminated from non-target species however, DNA barcoding can be used to confirm similar species where morphology is inconclusive, e.g., Bactrocera breviaculeus and B. rufofuscula . This can take days—and a laboratory—to resolve. A quicker, simpler, molecular diagnostic assay would facilitate a more rapid detection and potential incursion response. We developed LAMP assays targeting cytochrome c oxidase subunit I (COI) and Eukaryotic Translation Initiation Factor 3 Subunit L (EIF3L) both assays detected B. trivialis within 25 min. The BtrivCOI and BtrivEIF3L assay anneal derivatives were 82.7 ± 0.8 °C and 83.3 ± 1.3 °C, respectively, detecting down to 1 × 10 1 copies/µL and 1 × 10 3 copies/µL, respectively. Each assay lified some non-targets from our test panel however notably, BtrivCOI eliminated all morphologically similar non-targets, and combined, the assays eliminated all non-targets. Double-stranded DNA gBlocks were developed as positive controls anneal derivatives for the COI and EIF3L gBlocks were 84.1 ± 0.7 °C and 85.8 ± 0.2 °C, respectively. We recommend the BtrivCOI assay for confirmation of suspect cue-lure-trapped B. trivialis , with BtrivEIF3L used for secondary confirmation when required.
Publisher: Wiley
Date: 09-12-2014
DOI: 10.1111/AEN.12131
No related grants have been discovered for David Gopurenko.