ORCID Profile
0000-0001-7538-1504
Current Organisation
University of Queensland
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Population, Ecological and Evolutionary Genetics | Marine and Estuarine Ecology (incl. Marine Ichthyology) | Aquaculture | Population Ecology | Ecology | Invertebrate Biology | Fisheries Sciences
ANZSRC Socio-Economic Objective (SEO)
Ecosystem Adaptation to Climate Change | Aquaculture Rock Lobster | Tourism not elsewhere classified | Marine Flora, Fauna and Biodiversity |
Related Links
Publications
Contrasting Genetic Structure among Populations of Two Amphidromous Fish Species (Sicydiinae) in the Central West Pacific
Publisher: Public Library of Science (PLoS)
Date: 09-10-2013
The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)
Publisher: Wiley
Date: 18-10-2007
Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia
Publisher: Springer Science and Business Media LLC
Date: 15-09-2012
Stretched to the limit; Can a short pelagic larval duration connect adult populations of an Indo-Pacific diadromous fish (Kuhlia rupestris)?
Publisher: Wiley
Date: 07-01-2013
DOI: 10.1111/MEC.12192
Abstract: Freshwater species on tropical islands face localized extinction and the loss of genetic ersity. Their habitats can be ephemeral due to variability in freshwater run-off and erosion. Even worse, anthropogenic effects on these ecosystems are intense. Most of these species are hidromous or catadromous (i.e. their life cycle includes a marine larval phase), which buffers them against many of these effects. A long pelagic larval duration (PLD) was thought to be critical to ensure the colonization and persistence in tropical islands, but recent findings indicated that several species with short PLDs are successful in those ecosystems. To test the potential of a short PLD in maintaining genetic connectivity and forestalling extirpation, we studied Kuhlia rupestris, a catadromous fish species with an extensive distribution in the western Pacific and Indian Oceans. Using a combination of molecular genetic markers (13 microsatellite loci and two gene regions from mtDNA) and modelling of larval dispersal, we show that a short PLD constrains genetic connectivity over a wide geographical range. Molecular markers showed that the short PLD did not prevent genetic ergence through evolutionary time and speciation has occurred or is occurring. Modelling of larvae dispersal suggested limited recent connectivity between genetically homogeneous populations across the Coral Sea. However, a short PLD can maintain connectivity on a subocean basin scale. Conservation and management of tropical diadromous species needs to take into account that population connectivity may be more limited than previously suspected in those species.
Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the indo-pacific ocean basin
Publisher: The Royal Society
Date: 07-2017
DOI: 10.1098/RSOS.170309
Abstract: Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST 0.14, p 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks s led in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger s le sizes used here negated any weak population sub ision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .
Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia
Publisher: Oxford University Press (OUP)
Date: 08-05-2016
Abstract: We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the s led area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the s led populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.
The complete validated mitochondrial genome of the black marlin Istiompax indica (Cuvier, 1832)
Publisher: Informa UK Limited
Date: 24-03-2016
DOI: 10.3109/19401736.2014.898285
Abstract: Two complete mitochondrial genomes of the black marlin Istiompax indica were assembled from approximately 3.5 and 2.5 million reads produced by Ion Torrent next generation sequencing. The complete genomes were 16,531 bp and 16,532 bp in length consisting of 2 rRNA, 13 protein-coding genes, 22tRNA and 2 coding regions. They demonstrated a similar A + T base (52.6%) to other teleosts. Intraspecific sequence variation was 99.5% for three I. indica mitogenomes and 99.7% for X. gladius. A lower value (85%) was found for the I. platypterus mitogenomes from genbank and accredited to inadvertent inclusion of gene regions from a con-familial species in one record, highlighting the need for cautious downstream use of genbank data.
Pelagic larval duration of two diadromous species of Kuhliidae (Teleostei: Percoidei) from Indo-Pacific insular systems
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/MF11243
Abstract: Diadromous fish species in the family Kuhliidae are able to colonise freshwater systems in Indo-Pacific islands, but their life cycle and the mechanisms involved in the colonisation of such ecosystems are poorly documented. After validating the daily rate of increment deposition in otoliths of Kuhlia rupestris, we estimated the pelagic larval duration (PLD) of K. rupestris, widely distributed in the Indo-Pacific area, and K. sauvagii, endemic to the Indian Ocean. Median PLD of K. rupestris was significantly longer than that of K. sauvagii (40.6 ± 6.9 and 32.3 ± 3.4 days (± s.d.), respectively), implying that the PLD is probably one factor controlling the extent of distribution range in Kuhlia. Within K. rupestris, in iduals from New Caledonia had longer PLDs than those from Réunion Island (44.3 ± 6.7 and 37.3 ± 4.7 days (± s.d.) respectively). Further research on larval migration is needed to determine whether this was due to different environmental conditions or is population-specific. Interestingly, the PLD of these Kuhlia species is shorter than the PLD of other tropical diadromous fishes. These results improve our understanding of the dispersal strategies of freshwater fauna, to colonise and persist in tropical islands.
Genetic correlations and genome-wide associations of cortical structure in general population samples of 22,824 adults
Publisher: Springer Science and Business Media LLC
Date: 22-09-2020
DOI: 10.1038/S41467-020-18367-Y
Abstract: Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery s le comprises 22,824 in iduals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging.
Polymorphic microsatellite loci for the zebra shark Stegostoma fasciatum
Publisher: Wiley
Date: 31-07-2006
A review of the application of molecular genetics for fisheries management and conservation of sharks and rays
Publisher: Wiley
Date: 04-2012
DOI: 10.1111/J.1095-8649.2012.03265.X
Abstract: Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, ex les from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.
Negligible evidence for regional genetic population structure for two shark species Rhizoprionodon acutus (Rüppell, 1837) and Sphyrna lewini (Griffith & Smith, 1834) with contrasting biology
Publisher: Springer Science and Business Media LLC
Date: 02-04-2011
Genetic population structure of grey mackerel Scomberomorus semifasciatus in northern Australia
Publisher: Wiley
Date: 09-2011
DOI: 10.1111/J.1095-8649.2011.03055.X
Abstract: This study used mtDNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from 12 widespread s ling locations in Australia. S les (n = 544) were genotyped with nine microsatellite loci, and 353 were sequenced for the control (384 bp) and ATPase (800 bp) mtDNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, north-west coast of the Northern Territory, Gulf of Carpentaria and the eastern coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the eastern coast of Queensland was high (mean F(ST) = 0·003 for the microsatellite data and Φ(ST) = 0·033 and 0·009 for control region and ATPase, respectively) leading to some uncertainty about stock boundaries. In contrast, there was a clear genetic break between the stock in Western Australia compared to the rest of northern Australia (mean F(ST) = 0·132 for the microsatellite data and Φ(ST) = 0·135 and 0·188 for control region and ATPase, respectively). This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (north Western Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that authorities in Queensland and Northern Territory should co-ordinate the management of the Gulf of Carpentaria stock.
Variability in multiple paternity rates for grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini)
Publisher: Springer Science and Business Media LLC
Date: 08-05-2017
DOI: 10.1038/S41598-017-01416-W
Abstract: This study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef sharks ( Carcharhinus amblyrhynchos ) and scalloped hammerheads ( Sphyrna lewini ) opportunistically caught in Papua New Guinea (PNG). Litter size between species were significantly different with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 14 and 10 microsatellite loci respectively, we identified MP in 66% of grey reef sharks (4 out of 6 litters) and 100% MP in scalloped hammerheads (5 litters). We found high paternal skew (the uneven contribution of sires per litter) and a positive correlation between female adult size and litter size in scalloped hammerheads but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew may be linked with mating strategies and post-copulatory mechanisms. Multiple paternity is thought to benefit populations by enhancing genetic ersity therefore increasing the population’s genetic resilience to extrinsic pressures. The identification of MP in two shark species reported here, further elucidates the complex breeding strategies elasmobranchs undertake.
Population genetic structure of the brown tiger prawn, Penaeus esculentus, in tropical northern Australia
Publisher: Springer Science and Business Media LLC
Date: 28-09-2006
The complete validated mitochondrial genome of the silver gemfish Rexea solandri (Cuvier, 1832) (Perciformes, Gempylidae)
Publisher: Informa UK Limited
Date: 12-03-2016
DOI: 10.3109/19401736.2014.898279
Abstract: The silver gemfish Rexea solandri is an important economic resource but Vulnerable to overfishing in Australian waters. The complete mitochondrial genome sequence is described from 1.6 million reads obtained via next generation sequencing. The total length of the mitogenome is 16,350 bp comprising 2 rRNA, 13 protein-coding genes, 22 tRNA and 2 non-coding regions. The mitogenome sequence was validated against sequences of PCR fragments and BLAST queries of Genbank. Gene order was equivalent to that found in marine fishes.
Evidence of stock separation in southern hemisphere organge roughy (Hoplostethus atlanticus, Trachichthyidae) from restriction-enzyme analysis of mitochondrial DNA
Publisher: Springer Science and Business Media LLC
Date: 1993
DOI: 10.1007/BF00350011
The complete mitochondrial genome of the black jewfish Protonibea diacanthus (Perciformes: Sciaenidae)
Publisher: Informa UK Limited
Date: 19-05-2016
DOI: 10.3109/19401736.2014.915538
Abstract: We describe the complete mitochondrial genome of the black Jewfish Protonibea diacanthus. It was assembled from approximately 1.6 million reads produced by Ion Torrent next generation sequencing. The complete genome was 16,521 bp in length consisting of 13 protein-coding regions, 22 tRNA, 12S and 16S rRNA as well as two non-coding regions. The A+T base content (52.8%) is similar to other teleosts.
Development and characterization of ten microsatellite loci for the reef manta ray Manta alfredi
Publisher: Springer Science and Business Media LLC
Date: 08-07-2012
Can estimates of genetic effective population size contribute to fisheries stock assessments?
Publisher: Wiley
Date: 11-10-2016
DOI: 10.1111/JFB.13129
Abstract: Sustainable exploitation of fisheries populations is challenging to achieve when the size of the population prior to exploitation and the actual numbers removed over time and across fishing zones are not clearly known. Quantitative fisheries' modeling is able to address this problem, but accurate and reliable model outcomes depend on high quality input data. Much of this information is obtained through the operation of the fishery under consideration, but while this seems appropriate, biases may occur. For ex le, poorly quantified changes in fishing methods that increase catch rates can erroneously suggest that the overall population size is increasing. Hence, the incorporation of estimates of abundance derived from independent data sources is preferable. We review and evaluate a fisheries-independent method of indexing population size inferring adult abundance from estimates of the genetic effective size of a population (N
The phylogenetic position of the roughskin skate Dipturus trachyderma (Krefft & Stehmann, 1975) (Rajiformes, Rajidae) inferred from the mitochondrial genome
Publisher: Informa UK Limited
Date: 30-06-2016
DOI: 10.3109/19401736.2015.1060462
Abstract: The complete mitochondrial genome of the roughskin skate Dipturus trachyderma is described from 1 455 724 sequences obtained using Illumina NGS technology. Total length of the mitogenome was 16 909 base pairs, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Phylogenetic analysis based on mtDNA revealed low genetic ergence among longnose skates, in particular, those dwelling the continental shelf and slope off the coasts of Chile and Argentina.
Breaking the myths (or how to have a successful career in science)
Publisher: Oxford University Press (OUP)
Date: 29-10-2019
Abstract: The article is a recollection of the ups and downs of my career as a research scientist. It does not chronicle my career in the standard way there is no timeline of events and only a few details of the type of research that I have devoted my life to. I feel the take-home messages are relevant no matter what type of science you do. The narrative jumps around between periods of my life, uses anecdotes freely and attempts to be informative, forthright, and entertaining. Although science is perceived as a profession, the career pathway can be uneven and forked. In addition to discipline-specific knowledge and experience, successful scientists need a multitude of skills for instance, human management, logistics, and social media—to name a few. The field often attracts talented introverts for whom working in teams is challenging. The complexity of science is fascinating and powerful. In the fervour for discoveries, care is needed not to become isolated from friends and family by long working hours. For those of you who have gone part or full way down this path, there will be value in comparing your experiences to mine. Mostly I hope that younger scientists who are beginning on this path, or considering whether to enter, will take away some messages that will help them stand on our shoulders.
A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis
Publisher: Wiley
Date: 12-05-2011
DOI: 10.1111/J.1755-0998.2011.03023.X
Abstract: Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays lify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue s les by full mtDNA ND4 sequencing.
Development and characterization of 17 polymorphic microsatellite markers for the reef manta ray (Mobula alfredi)
Publisher: Springer Science and Business Media LLC
Date: 22-04-2019
Restriction fragment length polymorphisms in chloroplast DNA from six species of Eucalyptus
Publisher: CSIRO Publishing
Date: 1991
DOI: 10.1071/BT9910399
Abstract: Chloroplast DNA was extracted from six species of Eucalyptus (E. perriniana, E. nitens, E. ovata, E. regnans, E. amygdalina and E. risdonii). Digests with four restriction enzymes (Hind III, Xho I, Nco I and Eco RV) revealed restriction fragment length polymorphisms (RFLPs) between subgenera, between species and within species. However, no variation in fragment pattern was detected with Sac II or Pst I. The subgenera Monocalyptus and Symphyomyrtus were clearly differentiated by their RFLP patterns where, with the exception of one outlying specimen of E. amygdalina, 45% of all polymorphic fragments were specific to one or other subgenus. While species from different subgenera and series were well differentiated, it was more difficult to differentiate species within series with the low s le sizes used. However, the average net ergence between species increased with increasing taxonomic distance between species, from 0.02% within series and 0.20% between species from different series within subgenera, to 0.99% of nucleotides per nucleotide site for species from different subgenera. Based on Eco RV digests, the eucalypt chloroplast genome was estimated at 143 kb.
The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago
Publisher: Springer Science and Business Media LLC
Date: 2009
Towards better management of Australias shark fishery: Genetic analyses reveal unexpected ratios of cryptic blacktip species Carcharhinus tilstoni and C. limbatus
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/MF09151
Abstract: The common blacktip shark (Carcharhinus limbatus) and the Australian blacktip shark (C. tilstoni) are morphologically similar species that co-occur in subtropical and tropical Australia. In striking contrast to what has been previously reported, we demonstrate that the common blacktip shark is not rare in northern Australia but occurs in approximately equal frequencies with the Australian blacktip shark. Management of shark resources in northern Australia needs to take account of this new information. Species identification was performed using nucleotide sequences of the control, NADH dehydrogenase subunit 4 (ND4) and cytochrome oxidase I (COI) regions in the mitochondrial genome. The proportion of overall genetic variation (FST) between the two species was small (0.042, P 0.01) based on allele frequencies at five microsatellite loci. We confirm that a third blacktip species (C. amblyrhynchoides, graceful shark) is closely related to C. tilstoni and C. limbatus and can be distinguished from them on the basis of mtDNA sequences from two gene regions. The Australian blacktip shark (C. tilstoni) was not encountered among 20 s les from central Indonesia that were later confirmed to be common blacktip and graceful sharks. Fisheries regulators urgently need new information on life history, population structure and morphological characters for species identification of blacktip shark species in Australia.
Stock structure of Grey Mackerel, Scomberomorus semifasciatus (Pisces: Scombridae) across northern Australia, based on otolith stable isotope chemistry
Publisher: Springer Science and Business Media LLC
Date: 22-06-2010
Differential use of Alcian blue and toluidine blue dyes for the quantification and isolation of anionic glycoconjugates from cell cultures: Application to proteoglycans and a high-molecular-weight glycoprotein synthesized by articular chondrocytes
Publisher: Elsevier BV
Date: 10-2000
Characterization of four tetranucleotide and six dinucleotide microsatellite markers for use in the tropical freshwater fish Telmatherina antoniae and related species
Publisher: Wiley
Date: 20-12-2007
Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: Implications for fisheries management
Publisher: Wiley
Date: 08-10-2009
Integrating different approaches in the definition of biological stocks: A northern Australian multi-jurisdictional fisheries example using grey mackerel, Scomberomorus semifasciatus
Publisher: Elsevier BV
Date: 05-2015
Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle
Publisher: Wiley
Date: 26-05-2004
Genetic population structure of red snappers (Lutjanus malabaricus Bloch & Schneider, 1801 and Lutjanus erythropterus Bloch, 1790) in central and eastern Indonesia and northern Australia
Publisher: Wiley
Date: 06-2006
New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)
Publisher: Wiley
Date: 02-05-2013
Abstract: Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA s les from three s ling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled s le of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172,837 raw reads (17.4 Mbp) were retrieved, 95,500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA s les genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern s ling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard s le sizes of 50 and validated subsets of available markers.
Assessment of genetic structure among Australian east coast populations of snapper Chrysophrys auratus (Sparidae)
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MF18146
Abstract: Snapper Chrysophrys auratus is a high-value food fish in Australia targeted by both commercial and recreational fisheries. Along the east coast of Australia, fisheries are managed under four state jurisdictions (Queensland, Qld New South Wales, NSW Victoria, Vic. and Tasmania, Tas.), each applying different regulations, although it is thought that the fisheries target the same biological stock. An allozyme-based study in the mid-1990s identified a weak genetic disjunction north of Sydney (NSW) questioning the single-stock hypothesis. This study, focused on east-coast C. auratus, used nine microsatellite markers to assess the validity of the allozyme break and investigated whether genetic structure exists further south. Nine locations were s led spanning four states and over 2000km, including sites north and south of the proposed allozyme disjunction. Analyses confirmed the presence of two distinct biological stocks along the east coast, with a region of genetic overlap around Eden in southern NSW, ~400km south of the allozyme disjunction. The findings indicate that C. auratus off Vic. and Tas. are distinct from those in Qld and NSW. For the purpose of stock assessment and management, the results indicate that Qld and NSW fisheries are targeting a single biological stock.A
Mitochondrial and allozyme genetics of two tasmanian galaxiids (Galaxias auratus and g. tanycephalus, pisces: Galaxiidae) with restricted lacustrine distributions
Publisher: Springer Science and Business Media LLC
Date: 03-1993
DOI: 10.1038/HDY.1993.33
Characterisation and cross-amplification of 19 novel microsatellite loci for the sandbar shark, Carcharhinus plumbeus
Publisher: Springer Science and Business Media LLC
Date: 19-10-2015
Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci: a conservation alert?
Publisher: Springer Science and Business Media LLC
Date: 2001
Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific
Publisher: Public Library of Science (PLoS)
Date: 25-09-2013
Likelihood-based genetic mark-recapture estimates when genotype samples are incomplete and contain typing errors
Publisher: Elsevier BV
Date: 11-2011
DOI: 10.1016/J.TPB.2011.06.006
Abstract: Genotypes produced from s les collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark-recapture methodology in wildlife species can therefore be prone to misidentifications leading to both 'true non-recaptures' being falsely accepted as recaptures (Type I errors) and 'true recaptures' being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standard error of recapture estimates can be minimised through our algorithms. Interestingly, the precision of our recapture estimates actually improved when we included in iduals with missing genotypes, as this increased the number of pairwise comparisons potentially uncovering more recaptures. Simulations suggest that the method is tolerant to per locus error rates of up to 5% per locus and can theoretically work in datasets with as little as 60% of loci genotyped. Our methods can be implemented in datasets where standard mismatch analyses fail to distinguish recaptures. Finally, we show that by assigning a low Type I error rate to our matching algorithms we can generate a dataset of in iduals of known capture histories that is suitable for the downstream analysis with traditional mark-recapture methods.
Mitochondrial DNA restriction site map for Gadopsis marmoratus
Publisher: Elsevier BV
Date: 04-1988
Fine scale population structure of dugongs (Dugong dugon) implies low gene flow along the southern Queensland coastline
Publisher: Springer Science and Business Media LLC
Date: 13-06-2014
Analysis of whole mitochondrial genome sequences increases phylogenetic resolution of istiophorid billfishes
Publisher: Bulletin of Marine Science
Date: 2018
Telomere dynamics in the Sydney rock oyster (Saccostrea glomerata): an investigation into the effects of age, tissue type, location and time of sampling
Publisher: Springer Science and Business Media LLC
Date: 16-09-2011
Population genetics of Southern Hemisphere tope shark (Galeorhinus galeus): Intercontinental divergence and constrained gene flow at different geographical scales
Publisher: Public Library of Science (PLoS)
Date: 07-09-2017
Mitochondrial DNA variation and phylogenetic relationships of Jasus spp. (Decapoda: Palinuridae)
Publisher: Wiley
Date: 05-1992
Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material
Publisher: Wiley
Date: 29-08-2017
Abstract: Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from s les of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the s les. No clear relationships between age of s les, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
Habitat segregation and mosaic sympatry of the two species of manta ray in the Indian and Pacific Oceans: Manta alfredi and M. birostris
Publisher: Cambridge University Press (CUP)
Date: 10-06-2011
The genetic signature of recent speciation in manta rays (Manta alfredi and M. birostris)
Publisher: Elsevier BV
Date: 07-2012
DOI: 10.1016/J.YMPEV.2012.03.020
Abstract: Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondrial CO1 (574 bp) and ND5 genes (1188 bp). The assay with CO1 sequences, widely used in DNA barcoding, failed to distinguish the two species. The two species were clearly distinguishable, however, with no shared RAG1 or ND5 haplotypes. The species were reciprocally monophyletic for RAG1, but paraphyletic for ND5 sequences. Qualitative evidence and statistical inferences using the 'Isolation-with-Migration models' indicated that these results were better explained with post- ergence gene flow in the recent past rather than incomplete lineage sorting with zero gene flow since speciation. An estimate of ergence time was less than 0.5 Ma with an upper confidence limit of within 1 Ma. Recent speciation of highly mobile species in the marine environment is of great interest, as it suggests that speciation may have occurred in the absence of long-term physical barriers to gene flow. We propose that the ecologically driven forces such as habitat choice played a significant role in speciation in manta rays.
Lack of multiple paternity in the oceanodromous tiger shark (Galeocerdo cuvier)
Publisher: The Royal Society
Date: 2018
DOI: 10.1098/RSOS.171385
Abstract: Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark ( Galeocerdo cuvier ) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci lifying for this in idual, results were inconclusive. In summary, it appears that the tiger sharks s led in this study were genetically monogamous. These findings may have implications for the genetic ersity and future sustainability of this population.
Genetic and phenotypic diversity in the wedgefish Rhynchobatus australiae, a threatened ray of high value in the shark fin trade
Publisher: Inter-Research Science Center
Date: 21-04-2016
DOI: 10.3354/MEPS11617
Isolation and characterisation of 18 polymorphic microsatellite loci for black marlin (Istiompax indica) and their utility for Pacific billfish species
Publisher: Elsevier BV
Date: 06-2015
Stock structure of Lethrinus laticaudis (Lethrinidae) across northern Australia determined using genetics, otolith microchemistry and parasite assemblage composition
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/MF17087
Abstract: The grass emperor Lethrinus laticaudis is a conspicuous element of the commercial and recreational catch from nearshore reef systems across northern Australia. The nearshore reef systems across northern Australia are exposed to increasing levels of fishing pressure from commercial and recreational fishers. To inform ongoing management of this species, the present study examined the stock structure of L. laticaudis across northern Australia using a combination of complementary techniques. In all, 342 L. laticaudis s les were collected from 13 locations in the coastal waters of northern Australia ranging from the Pilbara region of Western Australia to Moreton Bay in south-east Queensland. Population genetic analyses using microsatellite markers demonstrated that there were at least four genetically distinct populations across northern Australia with gene flow between management jurisdictions (with significantly more separation between Western Australian and Northern Territory locations than between Northern Territory and Queensland locations). An isolation by distance effect was evident (genetic differences increasing linearly with distance). Otolith microchemistry and parasitology analyses indicated some spatial structuring of populations within broader regions. These findings of restricted connectivity at small spatial scales suggest that L. laticaudis is vulnerable to localised depletion in areas where fishing effort is concentrated. This conclusion is consistent with recent observations of fishery declines in heavily fished locations.
Spatial genetic subdivision among populations of the highly migratory black marlin Istiompax indica within the central Indo-Pacific
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/MF14370
Abstract: The black marlin Istiompax indica is a highly migratory species and as a result is expected to show little genetic population structure throughout its broad geographic range. Tissue s les from 183 I. indica were collected from three geographic regions within the central Indo-Pacific and analysed using mitochondrial and nuclear DNA markers. Nuclear genetic heterogeneity was found among populations in the south-western Pacific Ocean, eastern Indian Ocean and South China Sea (significant FST values of 0.013–0.037). Combining information from nuclear markers with published movement and reproductive data suggests that reproductive philopatry plays a role in maintaining contemporary I. indica population structure. Analyses of the mitochondrial control region did not reflect this pattern however, it identified historical population structure. Differing patterns of genetic population structure revealed by mitochondrial and nuclear markers demonstrated that a transition must have occurred between historical and contemporary population structures. This restructuring presumably reflects a species whose populations have become genetically isolated before experiencing a period of secondary contact. The spatial sub ision evident among populations indicates that I. indica in this central Indo-Pacific region should be managed as three independent stocks, to guide the sustainability of this fisheries resource.
Mitochondrial DNA analyses of the red rock lobster Jasus edwardsii supports an apparent absence of population subdivision throughout Australasia
Publisher: Springer Science and Business Media LLC
Date: 06-1992
DOI: 10.1007/BF00702478
Novel multimarker comparisons address the genetic population structure of silvertip sharks (Carcharhinus albimarginatus)
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MF18296
Abstract: The silvertip shark (Carcharhinus albimarginatus) is a reef-associated shark, with an intermittent distribution across the Indo-Pacific Ocean. Owing to global declines, the species is listed as Vulnerable under the International Union of Conservation for Nature Red List. S les from 152C. albimarginatus were collected from three locations: Papua New Guinea (PNG), east Australia and Seychelles. S les were analysed using mitochondrial, microsatellite and double-digest restriction-associated DNA (ddRAD) generated single nucleotide polymorphism markers. As expected across a vast oceanic expanse, no gene flow was identified between south-west Pacific locations and Seychelles for any marker (population differentiation measured using ΦST values 0.92–0.98, FST values 0.036–0.059). Mitochondrial DNA indicated significant population structuring between PNG and east Australia (ΦST=0.102), but nuclear markers suggested connectivity between these geographically close regions (FST=0.000–0.001). In combination with known telemetry movements for C. albimarginatus, our results suggest stepping-stone patterns of movement between regions is likely driven by reproductive requirements. The use of three distinct marker types in this study has facilitated a powerful genetic description of the population connectivity of C. albimarginatus between the three s led regions. Importantly, the connectivity described between PNG and east Australia should be used as a guide for managing the south-west Pacific stock of C. albimarginatus.
Erratum: Habitat segregation and mosaic sympatry of the two species of manta ray in the Indian and Pacific Oceans: Manta alfredi and M. birostris(Marine Biodiversity Records (2011) 4 (e53) DOI: 10.1017/S1755267211000479)
Publisher: Cambridge University Press (CUP)
Date: 11-2011
Characterisation and cross-amplification of 21 novel microsatellite loci for the dusky shark, Carcharhinus obscurus
Publisher: Springer Science and Business Media LLC
Date: 22-10-2015
locuseater and shadowboxer: programs to optimize experimental design and multiplexing strategies for genetic mark-recapture
Publisher: Wiley
Date: 25-08-2005
Stock Identity of the Red (Jasus edwardsii) and Green (Jasus verreauxi) Rock Lobsters Inferred from Mitochondrial DNA Analysis
Publisher: Wiley
Date: 11-10-2008
The complete mitochondrial genome of the golden snapper Lutjanus johnii (Perciformes: Lutjanidae)
Publisher: Informa UK Limited
Date: 20-05-2016
DOI: 10.3109/19401736.2014.919457
Abstract: We describe the complete mitochondrial genome of the golden snapper Lutjanus johnii. It was assembled from approximately 1.4 million reads produced by Ion Torrent next generation sequencing. The complete genome was 16,596 bp in length consisting of 13 protein-coding regions, 22 tRNA, 12S and 16S rRNA as well as two non-coding regions. The A+T base content (52.8%) is similar to other teleosts.
Application of environmental DNA to detect an endangered marine skate species in the wild
Publisher: Public Library of Science (PLoS)
Date: 07-06-2017
The complete mitochondrial genome of the dusky shark Carcharhinus obscurus
Publisher: Informa UK Limited
Date: 04-04-2013
DOI: 10.3109/19401736.2013.772154
Abstract: The dusky shark Carcharhinus obscurus is economically important but vulnerable to overharvesting. The complete C. obscurus mitogenome was assembled from approximately 1 million whole genome shotgun sequences using a combination of reference mapping and de novo assembly (mean coverage 59x). This resulted in a 16,706 bp double-stranded circular mitochondrial sequence. Following the consensus vertebrate mtDNA genome, it comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and has 2 non-coding areas. The A + T (56.9%) versus G + C (43.1%) composition confirmed an A + T bias previously noted for sharks. This genome is the first for the speciose Carcharhinus genus and provides a valuable resource for studies of shark molecular systematics, phylogeography, conservation genetics, and stock structure.
Identification of small juvenile scombrids from northwest tropical Australia using mitochondrial DNA cytochrome b sequences
Publisher: Springer Science and Business Media LLC
Date: 25-08-2007
Genetic population structure of mangrove jack, Lutjanus argentimaculatus (Forsskål)
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/MF02142
Abstract: Translocations of mangrove jack, Lutjanus argentimaculatus (Forsskål 1775), to increase angling opportunities in artificial impoundments are foreshadowed in Queensland. To evaluate genetic population structure before translocations occur, mangrove jack were collected from three sites on the Queensland coast and from one site on the north-western coast of Western Australia. Allelic variation at four dinucleotide microsatellite loci was high: gene ersity (heterozygosity) ranged from 0.602 to 0.930 and allelic counts from 10 to 24. Genetic differentiation among collection sites was weak: estimates of FST were 0.002 for all four sites, and less (FST = 0.001) across a major biogeographical boundary (the Torres Strait region). Nucleotide sequence from two mitochondrial regions (control, 375 base pairs, and ATPase, 415 base pairs) was obtained from a subset of the Australian and additional Indo-Pacific (Indonesian and Samoan) mangrove jack. Haplotype ersity was high (control region, 33 haplotypes for 34 fish ATPase region, 13 haplotypes for 56 fish). Phylogenetic analysis of mitochondrial DNA sequence data could not discern a relationship between tree topology and geography. These results suggest that mangrove jack in Queensland, and possibly throughout Australia, experience high levels of gene flow. The artificial gene flow caused by permitted translocations is unlikely to exceed natural levels. Fine-scale ecological matching between donor and recipient populations may increase stocking success, and is important if translocation is needed as a species recovery tool in the future.
Genetype and phylogenomic position of the frilled shark Chlamydoselachus anguineus inferred from the mitochondrial genome
Publisher: Informa UK Limited
Date: 2016
Parental contribution to progeny during experimental spawning of jungle perch, Kuhlia rupestris
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/MF13313
Abstract: When releasing captive-bred animals into wild populations, it is essential to maintain the capacity for adaptation and resilience by minimising the effect on population genetic ersity. Populations of the jungle perch (Kuhlia rupestris) have become reduced or locally extinct along the Queensland coast thus, captive breeding of K. rupestris for restocking is presently underway. Currently, multiple in iduals are placed in a tank to produce larvae, yet the number of adults contributing to larval production is unknown. We performed a power analysis on pre-existing microsatellite loci to determine the minimum number of loci and larvae required to achieve accurate assignment of parentage. These loci were then used to determine the number of contributing participants during a series of four spawning events through the summer breeding season in 2012–2013. Not all fish contributed to larval production and no relationship was found between male body size and parentage success. In most cases, there was a high skew of offspring to one mating pair (62% was the average contribution of the most successful pair per tank). This has significant implications for the aquaculture, restocking and conservation of K. rupestris.
Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: A case study on spanish mackerel (Scomberomorus commerson)
Publisher: Oxford University Press (OUP)
Date: 04-2013
Abstract: Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. However, pitfalls are predicted when the effective size is large because estimates require large numbers of s les from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with s le sizes of approximately 5000. This number was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow-barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest SD of Ne estimates occurred when low-frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently s led from cryptic species or nonbreeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife res ling were greater than 24,000.
Harnessing the Power of Genomics to Secure the Future of Seafood
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.TREE.2017.06.010
Abstract: Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.
Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes
Publisher: Inter-Research Science Center
Date: 30-05-2012
DOI: 10.3354/MEPS09659
The relationship between abundance and genetic effective population size in elasmobranchs: an example from the globally threatened zebra shark Stegostoma fasciatum within its protected range
Publisher: Springer Science and Business Media LLC
Date: 15-07-2015
Mitochondrial dna restriction site variation in tasmanian populations of orange roughy (Hoplostethus atlanticus), a deep-water marine teleost
Publisher: CSIRO Publishing
Date: 1989
DOI: 10.1071/MF9890001
Abstract: The orange roughy, Hoplostethus atlanticus, forms the basis of an important trawl fishery in Australia and New Zealand which is currently being over-exploited. To gain information about the stock structure of an Australian orange roughy population, ten restriction enzymes were used to survey the restriction- site variation in the mitochondrial genome of 23 in iduals collected from the east coast and 26 in iduals collected from the west coast of Tasmania. The mean ersity between all 49 genomes was a low 0.19%. Of the eleven haplotypes identified, only one was present in both the east and west coast s les. Four haplotypes were found only in the east coast s le and six were found only in the west coast s le. Eight haplotypes were related to the haplotype found on both coasts by the gain or loss of one restriction site. One haplotype collected in the east coast s le was related to one other east coast haplotype by one site change. One haplotype collected from the west coast was related to a west coast haplotype by one site change. If this pattern is confirmed by further mitochondrial DNA studies, it could be inferred that gene flow between the orange roughy populations on the east and west coasts of Tasmania is low.
Distribution of Jasus spp. (Decapoda: Palinuridae) phyllosomas in southern waters: Implications for larval recruitment
Publisher: Inter-Research Science Center
Date: 2000
DOI: 10.3354/MEPS200241
Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification
Publisher: PeerJ
Date: 31-08-2016
DOI: 10.7717/PEERJ.2418
Abstract: Thirty-four microsatellite loci were isolated from three reef fish species golden snapper Lutjanus johnii , blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the lification of the golden snapper and the blackspotted croaker loci, as well as post- lification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.
Towards sustainable fishery management for skates in South America: The genetic population structure of Zearaja chilensis and Dipturus trachyderma (Chondrichthyes, Rajiformes) in the south-east Pacific Ocean
Publisher: Public Library of Science (PLoS)
Date: 16-02-2017
Detection of interspecies hybridisation in Chondrichthyes: Hybrids and hybrid offspring between Australian (Carcharhinus tilstoni) and common (C. limbatus) blacktip shark found in an Australian fishery
Publisher: Springer Science and Business Media LLC
Date: 17-12-2012
Mitochondrial DNA nucleotide sequence variation in Atlantic salmon (Salmo salar), brown trout (S. trutta), rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis) from Tasmania, Australia
Publisher: Elsevier BV
Date: 08-1993
Comparison of the reproductive ecology of two sympatric blacktip sharks (Carcharhinus limbatus and Carcharhinus tilstoni) off north-eastern Australia with species identification inferred from vertebral counts
Publisher: Wiley
Date: 15-08-2012
DOI: 10.1111/J.1095-8649.2012.03400.X
Abstract: Precaudal vertebral counts were used to distinguish between 237 morphologically similar Carcharhinus limbatus and Carcharhinus tilstoni and were congruent with differences in reproductive ecology between the species. In addition to differing lengths at maturity and adult body size, the two species had asynchronous parturition, were born at different sizes and the relative frequencies of neonates differed in two coastal nursery areas. Despite evidence that hybridization can occur, these differences suggest the species are largely reproductively isolated.
Accuracy of species identification by fisheries observers in a north Australian shark fishery
Publisher: Elsevier BV
Date: 09-2012
Switch from sexual to parthenogenetic reproduction in a zebra shark
Publisher: Springer Science and Business Media LLC
Date: 16-01-2017
DOI: 10.1038/SREP40537
Abstract: Parthenogenesis is a natural form of asexual reproduction in which embryos develop in the absence of fertilisation. Most commonly found in plants and invertebrate organisms, an increasing number of vertebrate species have recently been reported employing this reproductive strategy. Here we use DNA genotyping to report the first demonstration of an intra-in idual switch from sexual to parthenogenetic reproduction in a shark species, the zebra shark Stegostoma fasciatum . A co-housed, sexually produced daughter zebra shark also commenced parthenogenetic reproduction at the onset of maturity without any prior mating. The demonstration of parthenogenesis in these two conspecific in iduals with different sexual histories provides further support that elasmobranch fishes may flexibly adapt their reproductive strategy to environmental circumstances.
The phylogenomic position of the grey nurse shark Carcharias taurus Rafinesque, 1810 (Lamniformes, Odontaspididae) inferred from the mitochondrial genome
Publisher: Informa UK Limited
Date: 14-10-2016
DOI: 10.3109/19401736.2015.1089486
Abstract: The complete mitochondrial genome of the grey nurse shark Carcharias taurus is described from 25 963 828 sequences obtained using Illumina NGS technology. Total length of the mitogenome is 16 715 bp, consisting of 2 rRNAs, 13 protein-coding regions, 22 tRNA and 2 non-coding regions thus updating the previously published mitogenome for this species. The phylogenomic reconstruction inferred from the mitogenome of 15 species of Lamniform and Carcharhiniform sharks supports the inclusion of C. taurus in a clade with the Lamnidae and Cetorhinidae. This complete mitogenome contributes to ongoing investigation into the monophyly of the Family Odontaspididae.
Genetic subdivision of Australian and New Zealand populations of Jasus verreauxi (Decapoda: Palinuridae)—preliminary evidence from the mitochondrial genome
Publisher: Informa UK Limited
Date: 03-1992
Preliminary investigation of mitochondrial dna variation in jack mackerel (Trachurus declivis, carangidae) from south-eastern australian waters
Publisher: CSIRO Publishing
Date: 1994
DOI: 10.1071/MF9940495
Abstract: A preliminary investigation of the genetic structure of jack mackerel (Trachurus declivis, Carangidae) in south-eastern Australian waters was conducted by using restriction enzyme analysis of mitochondrial DNA (mtDNA). Seventy-five jack mackerel s les were collected from two localities: off Eden in New South Wales and off south-eastern Tasmania. Fish were s led twice at each locality. Mitochondrial DNA was extracted from developing ovary tissue and heart tissue. The 75 jack mackerel s les were screened with 11 six-base and four four-base enzymes. The level of genetic ersity in jack mackerel was low. The six-base enzyme analysis found limited evidence of reproductive isolation between New South Wales and Tasmanian s les of jack mackerel. However, an analysis of a subset of 42 jack mackerel with four four-base enzymes found evidence of temporal differences in the mtDNA ersities of two Tasmanian s les of jack mackerel.
Population genetic evidence for the east-west division of the narrow-barred Spanish mackerel (Scomberomorus commerson, Perciformes: Teleostei) along Wallace's Line
Publisher: Springer Science and Business Media LLC
Date: 07-08-2010
Accounting for missing data in the estimation of contemporary genetic effective population size (Ne )
Publisher: Wiley
Date: 29-12-2013
Abstract: Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing in iduals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized s le size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random s ling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective s le size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-s le and two-s le (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus s le size components.
Evolutionary relationships of Gadopsis spp. inferred from restriction enzyme analysis of their mitochondrial DNA
Publisher: Wiley
Date: 1988
Evidence for a stock discontinuity of snapper (Pagrus auratus) on the east coast of Australia
Publisher: Elsevier BV
Date: 10-2008
Multi-gene barcoding to discriminate sibling species within a morphologically difficult fish genus (Sillago)
Publisher: Elsevier BV
Date: 06-2013
The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus
Publisher: Informa UK Limited
Date: 18-06-2016
DOI: 10.3109/19401736.2014.926487
Abstract: The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one in idual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.
Venereal transmission of Sindbis virus between individuals of Aedes australis (Diptera: Culicidae).
Publisher: Oxford University Press (OUP)
Date: 30-05-1984
The stock structure of grey mackerel Scomberomorus semifasciatus in Australia as inferred from its parasite fauna
Publisher: Elsevier BV
Date: 2010
The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome
Publisher: Informa UK Limited
Date: 11-08-2015
DOI: 10.3109/19401736.2015.1074208
Abstract: The giant devil ray, Mobula mobular, is a member of one of the most distinct groups of cartilaginous fishes, the Mobulidae (manta and devil rays), and is the only mobulid assessed as Endangered due its restricted distribution, high bycatch mortality and suspected population decline. The complete mitochondrial genome is 18 913 base pairs in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison with the partial mitogenome of M. japanica suggests a sister-cryptic species complex and two different taxonomic units. However, the limited ergence within the species (>99.9% genetic identity) may be the result of a geographically and numerically restricted population of M. mobular within the Mediterranean Sea.
Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized fishery collapse in a large Sciaenid fish, Protonibea diacanthus
Publisher: Wiley
Date: 12-07-2017
DOI: 10.1111/EVA.12499
Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite “tiny” Ne /N ratios elsewhere
Publisher: Wiley
Date: 06-2019
DOI: 10.1111/MEC.15130
Abstract: A landmark study published in 2002 estimated a very small N
Misidentification of istiophorid billfishes by fisheries observers raises uncertainty over stock status
Publisher: Wiley
Date: 08-2018
DOI: 10.1111/JFB.13738
Abstract: We investigated whether commercially landed black marlin Istiompax indica were being misidentified by fisheries observers operating throughout the Pacific Ocean. Of 83 s les reported by observers as I. indica, 77% were genetically identified to be blue marlin Makaira nigricans and 2% to be striped marlin Kajikia audax. The high rate of misidentification by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin and stock assessments relying on the validity of these data.
Population genetics of the endangered Maugean skate (Zearaja maugeana) in Macquarie Harbour, Tasmania
Publisher: Springer Science and Business Media LLC
Date: 30-10-2018
Translocation between freshwater catchments has facilitated the spread of tilapia in eastern Australia
Publisher: Springer Science and Business Media LLC
Date: 31-10-2015
Genetic structure and diversity of two highly vulnerable carcharhinids in Australian waters
Publisher: Inter-Research Science Center
Date: 09-04-2014
DOI: 10.3354/ESR00580
Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.MITO.2013.06.002
Abstract: Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.
Telomere length analysis in crustacean species: Metapenaeus macleayi, Sagmariasus verreauxi, and Jasus edwardsii
Publisher: Oxford University Press (OUP)
Date: 15-09-2011
Abstract: Godwin, R. M., Frusher, S., Montgomery, S. S., and Ovenden, J. 2011. Telomere length analysis in crustacean species: Metapenaeus macleayi, Sagmariasus verreauxi, and Jasus edwardsii. – ICES Journal of Marine Science, 68: 2053–2058. Estimates of age and growth in crustaceans have been historically problematic and presented significant challenges to researchers. Current techniques of age determination provide valuable data, but also suffer from disadvantages. Telomeric DNA has been proposed as an age biomarker because it shortens with age in some species. In this study, the feasibility of using telomere length (TL) to estimate age was examined in the school prawn Metapenaeus macleayi and the spiny lobsters Sagmariasus verreauxi and Jasus edwardsii. Carapace length (CL) was used as a surrogate for age, and terminal restriction fragment assays were used to test the relationship between TL and size. Degradation of telomeric DNA with time during storage significantly influenced TL estimates, particularly for M. macleayi. TLs obtained from species in this study were 10–20 kb. No relationship between CL and TL was detected for any of the test species, and TL did not differ between male and female M. macleayi. TLs of J. edwardsii pueruli were unexpectedly shorter than those of J. edwardsii adults. The suitability of TL as an age biomarker in crustaceans may be limited, but further research is needed to elucidate telomere dynamics in these species with their different life histories and lifespans.
NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data
Publisher: Wiley
Date: 31-08-2014
Abstract: NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-s le estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-s le (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data (ii) options for screening out rare alleles (iii) confidence intervals for all methods (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more) (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data and (vi) correction for temporal estimates when in iduals s led are not removed from the population (Plan I s ling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.
Crinkles in connectivity: Combining genetics and other types of biological data to estimate movement and interbreeding between populations
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/MF12314
Abstract: Marine species generally have large population sizes, continuous distributions and high dispersal capacity. Despite this, they are often sub ided into separate populations, which are the basic units of fisheries management. For ex le, populations of some fisheries species across the deep water of the Timor Trench are genetically different, inferring minimal movement and interbreeding. When connectivity is higher than the Timor Trench ex le, but not so high that the populations become one, connectivity between populations is crinkled. Crinkled connectivity occurs when migration is above the threshold required to link populations genetically, but below the threshold for demographic links. In future, genetic estimates of connectivity over crinkled links could be uniquely combined with other data, such as estimates of population size and tagging and tracking data, to quantify demographic connectedness between these types of populations. Elasmobranch species may be ideal targets for this research because connectivity between populations is more likely to be crinkled than for finfish species. Fisheries stock-assessment models could be strengthened with estimates of connectivity to improve the strategic and sustainable harvesting of biological resources.
Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei
Publisher: Wiley
Date: 2011
DOI: 10.1111/J.1095-8649.2010.02865.X
Abstract: Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49 P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling s les provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught s les showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor however, temporal shifts in allele frequencies suggest sw ing with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.
Fifteen microsatellite loci for the jungle perch, Kuhlia rupestris
Publisher: Wiley
Date: 12-10-2009
DOI: 10.1111/J.1755-0998.2009.02735.X
Abstract: We developed and optimized 15 polymorphic microsatellite loci in the jungle perch, Kuhlia rupestris. Loci were screened in a single population (n = 24) from Fraser Island, Queensland, Australia. Number of alleles per locus ranged from 3 to 19 and observed heterozygosity from 0.25 to 1. No significant linkage disequilibrium was detected between any pair of loci. Genotype proportions for these loci in the population s led were in Hardy-Weinberg equilibrium.
New microsatellite loci for Carcharhinid sharks (Carcharhinus tilstoni and C. sorrah) and their cross-amplification in other shark species
Publisher: Wiley
Date: 27-03-2006
Characterization of 26 new microsatellite loci in the dugong (Dugong dugon)
Publisher: Wiley
Date: 15-06-2007
neogen: A tool to predict genetic effective population size (N e ) for species with generational overlap and to assist empirical N e study design
Publisher: Wiley
Date: 16-10-2019
Abstract: Molecular genetic estimates of population effective size (N
Spatial genetic subdivision between northern Australian and southeast Asian populations of Pristipomoides multidens: A tropical marine reef fish species
Publisher: Elsevier BV
Date: 12-2002
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits
Publisher: Wiley
Date: 03-03-2022
Abstract: Targeted sequencing is an increasingly popular next‐generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three erse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern s les. The workflow used for designing these three bait sets has been implemented in the R‐package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R‐package is user‐friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: github.com/BelenJM/supeRbaits
Evidence for reproductive philopatry in the bull shark Carcharhinus leucas
Publisher: Wiley
Date: 13-04-2012
DOI: 10.1111/J.1095-8649.2012.03228.X
Abstract: Reproductive philopatry in bull sharks Carcharhinus leucas was investigated by comparing mitochondrial (NADH dehydrogenase subunit 4, 797 base pairs and control region genes 837 base pairs) and nuclear (three microsatellite loci) DNA of juveniles s led from 13 river systems across northern Australia. High mitochondrial and low microsatellite genetic ersity among juveniles s led from different rivers (mitochondrial φ(ST) = 0·0767, P 0·05) supported female reproductive philopatry. Genetic structure was not further influenced by geographic distance (P > 0·05) or long-shore barriers to movement (P > 0·05). Additionally, results suggest that C. leucas in northern Australia has a long-term effective population size of 11 000-13 000 females and has undergone population bottlenecks and expansions that coincide with the timing of the last ice-ages.
A novel field method to distinguish between cryptic carcharhinid sharks, A ustralian blacktip shark Carcharhinus tilstoni and common blacktip shark C. limbatus, despite the pre
Publisher: Wiley
Date: 24-10-2016
DOI: 10.1111/JFB.13102
Abstract: Multivariate and machine-learning methods were used to develop field identification techniques for two species of cryptic blacktip shark. From 112 specimens, precaudal vertebrae (PCV) counts and molecular analysis identified 95 Australian blacktip sharks Carcharhinus tilstoni and 17 common blacktip sharks Carcharhinus limbatus. Molecular analysis also revealed 27 of the 112 were C. tilstoni × C. limbatus hybrids, of which 23 had C. tilstoni PCV counts and four had C. limbatus PCV counts. In the absence of further information about hybrid phenotypes, hybrids were assigned as either C. limbatus or C. tilstoni based on PCV counts. Discriminant analysis achieved 80% successful identification, but machine-learning models were better, achieving 100% successful identification, using six key measurements (fork length, caudal-fin peduncle height, interdorsal space, second dorsal-fin height, pelvic-fin length and pelvic-fin midpoint to first dorsal-fin insertion). Furthermore, pelvic-fin markings could be used for identification: C. limbatus has a distinct black mark >3% of the total pelvic-fin area, while C. tilstoni has markings with diffuse edges, or has smaller or no markings. Machine learning and pelvic-fin marking identification methods were field tested achieving 87 and 90% successful identification, respectively. With further refinement, the techniques developed here will form an important part of a multi-faceted approach to identification of C. tilstoni and C. limbatus and have a clear management and conservation application to these commercially important sharks. The methods developed here are broadly applicable and can be used to resolve species identities in many fisheries where cryptic species exist.
Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries
Publisher: Wiley
Date: 27-08-2015
DOI: 10.1111/FAF.12052
Evidence for extensive population structure in the white-spotted eagle ray within the Indo-Pacific inferred from mitochondrial gene sequences
Publisher: Wiley
Date: 22-04-2010
Extensive genetic population structure in the Indo-West Pacific spot-tail shark, Carcharhinus sorrah
Publisher: Bulletin of Marine Science
Date: 2014
A PCR assay for gender assignment in dugong (Dugong dugon) and West Indian manatee (Trichechus manatus)
Publisher: Wiley
Date: 05-2008
DOI: 10.1111/J.1471-8286.2007.02041.X
Abstract: Gender assignment for some aquatic mammals in the field is difficult. Molecular sexing from tissue biopsies is possible as males are heterogametic. Here we describe a multiplex PCR assay that lifies the male specific SRY gene and differentiates ZFX and ZFY gametologues in two sirenian species, dugong (Dugong dugon) and West Indian manatee (Trichechus manatus). The assay was validated with animals of known gender and proved accurate and robust to experimental failure.
A perfect storm of genetic drift and divergence may prevent the rebuilding of the gemfish (Rexea solandri) stock on the east Australian coast
Publisher: Elsevier BV
Date: 10-2020
Effect of DNA extraction on ageing success in coral trout (Plectropomus leopardus) otoliths
Publisher: Wiley
Date: 24-09-2007
Improved confidence intervals for the linkage disequilibrium method for estimating effective population size
Publisher: Springer Science and Business Media LLC
Date: 23-03-2016
DOI: 10.1038/HDY.2016.19
Mitochondrial DNA phylogeny of red and green rock lobsters (genus Jasus)
Publisher: CSIRO Publishing
Date: 1997
DOI: 10.1071/MF97192
Abstract: A cladistic analysis of nucleotide substitutions in the 16S ribosomal RNA and cytochrome oxidase subunit I genes of mitochondrial DNA does not support the monophyly of species within each of the ‘lalandii’ and ‘frontalis’ subgroups of Jasus the subgroupings may need revision. The recently described species J. caveorum is most closely related to J. tristani and J. paulensis, and not to J. frontalis with which it shares an eastern South Pacific distribution and morphological similarity. Two species, J. tristani and J. paulensis, are so genetically similar that further genetic, morphological and behavioural analyses are needed to assess their status as separate species.
The complete mitochondrial genome of the grass emperor, Lethrinus laticaudis (Perciformes: Lethrinidae)
Publisher: Informa UK Limited
Date: 2016
Integrated analyses of SNP-genotype and environmental data in a continuously distributed snapper species (Lutjanus johnii, Bloch, 1792) reveals a mosaic of populations and a challenge for susta
Publisher: Oxford University Press (OUP)
Date: 10-2021
Abstract: Understanding population structure is important for predicting the outcomes of anthropogenic development, harvest, and environmental change on the abundance of fisheries species. Logically, the use of several data sources is best for delineating population structure, but combining across data types adds extra challenges as results can be incongruent. Here, genetic and environmental markers were used to test hypotheses about population structure in a collection of 523 tropical inshore finfish (Lutjanus johnii) across northern Australia from 20 locations. Redundancy analyses (RDA) were used to statistically test for correlations among data sources providing a basis for reconciliation and insights into ecological and evolutionary processes. Genomic data (10349 SNP loci) revealed low, but significant genetic ergence (max FST 0.0402) between 16 locations. A total of 12 putative contiguous biological stocks were proposed whose distributions were correlated with IMCRA bioregions but not to existing regions used for management of the fishery. RDA showed a significant correlation between environmental markers (otolith chemistry and parasite abundances) and SNP genotype in two of three region-wide analyses supporting the proposed stock structure, and suggesting that L. johnii may be locally adapted to the heterogeneous environment. These findings are significant for the conservation of the commercially and recreationally important L. johnii and can be used to guide future fisheries management actions.
A Program for the Estimation of Restriction Endonuclease Sote Positions from Restriction Fragment Size and Number: An Aid for Mitochondrial DNA Analysis
Publisher: Oxford University Press (OUP)
Date: 06-1992
DOI: 10.1093/OXFORDJOURNALS.JHERED.A111206
Abstract: We examined the physiology of continence in 12 patients at least four months after colectomy, mucosal proctectomy, and endorectal ileo-anal anastomosis for ulcerative colitis and familial polyposis. The mean fecal output (+/-SEM) was 598 +/- 60 gm, passed as 12 +/- 4 movements/24 hr, of which 4 +/- 1 were passed at night. The patients were generally continent during the day and could distinguish gas from stool, but 11 of 12 leaked stools at night. Anal sphincter resting pressures (71 +/- 8 cm H2O) and squeeze pressures (171 +/- 15 cm H2O) of patients were similar to those of ten healthy controls (P greater than 0.05), although the rectal inhibitory reflex was absent in the patients. After operation, the distal bowel had a pressure-volume curve of greater slope (0.15 +/- 0.05 ml/cm H2O) than it had in controls (0.07 +/- 0.01 ml/cm H2O, P less than 0.05) and a lesser maximum capacity (patients, 248 +/- 31 ml controls, 406 +/- 26 ml P less than 0.05). The greater the capacity of the neorectum, the fewer was the number of bowel movements/day (r = 0.91, P less than 0.001). We concluded that the operation preserved the anal sphincter, although it decreased the capacity and compliance of the distal bowel and impaired continence.
IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo‐West Pacific
Publisher: Wiley
Date: 2009
The complete validated mitochondrial genome of the yellownose skate Zearaja chilensis (Guichenot 1848) (Rajiformes, Rajidae)
Publisher: Informa UK Limited
Date: 04-08-2016
DOI: 10.3109/19401736.2014.945530
Abstract: The yellownose skate Zearaja chilensis is endemic to South America. The species is the target of a valuable commercial fishery in Chile, but is highly susceptible to over-exploitation. The complete mitochondrial genome was described from 694,593 sequences obtained using Ion Torrent Next Generation Sequencing. The total length of the mitogenome was 16,909 bp, comprising 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison between the proposed mitogenome and one previously described from "raw fish fillets from a skate speciality restaurant in Seoul, Korea" resulted in 97.4% similarity, rather than approaching 100% similarity as might be expected. The 2.6% dissimilarity may indicate the presence of two separate stocks or two different species of, ostensibly, Z. chilensis in South America and highlights the need for caution when using genetic resources without a taxonomic reference or a voucher specimen.
Population genetic diversity in the Australian 'seascape': A bioregion approach
Publisher: Public Library of Science (PLoS)
Date: 16-09-2015
Effective number of white shark (Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand
Publisher: Wiley
Date: 09-12-2021
DOI: 10.1002/ECE3.7007
Abstract: Population size is a central parameter for conservation however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data‐poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case for the white shark ( Carcharodon carcharias ), a highly mobile apex predator for whom recent and substantial population declines have been recorded in many globally distributed populations. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle ( Nb ) to provide a snapshot of recent reproductive effort in an east Australian–New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, and 2013) using two genetic estimators (linkage disequilibrium LD and sibship assignment SA) based on genetic data derived from two types of genetic markers (single nucleotide polymorphisms SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable for ex le, the 2013 age cohort Nb ( SA ) was 289 (95% CI 200–461) and Nb ( LD ) was 208.5 (95% CI 116.4–712.7). We show that over the time period studied, Nb was stable and ranged between 206.1 ( SD ± 45.9) and 252.0 ( SD ± 46.7) per year using a combined estimate of Nb ( LD+SA ) from SNP loci. In addition, a simulation approach showed that in this population the effective population size ( Ne ) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data‐poor species of conservation concern.
Related Organisations
Related Funding Activities
Linkage Projects - Grant ID: LP110200793
Start Date: 07-2011
End Date: 06-2014
Amount: $405,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP150100669
Start Date: 03-2016
End Date: 06-2020
Amount: $315,236.00
Funder: Australian Research Council
View Funded Activity