%0 Journal Article %J Endangered Species Research %D 2021 %T Life history of the Critically Endangered largetooth sawfish: a compilation of data for population assessment and demographic modelling %A PM Kyne %A Oetinger, M %A Michael I. Grant %A Pierre Feutry %K age and growth %K Demography %K Pristis pristis %K reproductive biology %K threatened species %X

The largetooth sawfish Pristis pristis is a Critically Endangered, once widespread shark-like ray. The species is now extinct or severely depleted in many former parts of its range and is protected in some other range states where populations persist. The likelihood of collecting substantial new biological information is now low. Here, we review all available life history information on size, age and growth, reproductive biology, and demography as a resource for population assessment and demographic modelling. We also revisit a subset of historical data from the 1970s to examine the maternal size−litter size relationship. All available information on life history is derived from the Indo-West Pacific (i.e. northern Australia) and the Western Atlantic (i.e. Lake Nicaragua-Río San Juan system in Central America) subpopulations. P. pristis reaches a maximum size of at least 705 cm total length (TL), size-at-birth is 72−90 cm TL, female size-at-maturity is reached by 300 cm TL, male size-at-maturity is 280−300 cm TL, age-at-maturity is 8−10 yr, longevity is 30−36 yr, litter size range is 1−20 (mean of 7.3 in Lake Nicaragua), and reproductive periodicity is suspected to be biennial in Lake Nicaragua (Western Atlantic) but annual in Australia (Indo-West Pacific). There was a weak relationship between litter size and maternal size in Lake Nicaragua, and lifetime reproductive output for an individual female from Lake Nicaragua was estimated as 73 pups. Future demographic models should aim to capture the variability and uncertainty in life history parameters for P. pristis and we encourage a conservative approach to any application for conservation and management.

%B Endangered Species Research %V 44 %P 79 - 88 %8 28 Jan 2021 %G eng %U https://www.int-res.com/abstracts/esr/v44/p79-88/ %9 Journal %! Endang. Species. Res. %R 10.3354/esr01090 %0 Report %D 2021 %T Molecular analysis of newly-discovered geographic range of the threatened river shark Glyphis glyphis reveals distinct populations %A PM Kyne %A Christy Davies %A Floriaan Devloo-Delva %A Grant Johnson %A Yolarnie Amepou %A Michael I. Grant %A Aaran Green %A R. Gunasekera %A Alistair V Harry %A Theresa Lemon %A Rob Lindsay %A Travis Maloney %A James Marthick %A Richard D. Pillans %A Thor Saunders %A Amos Shields %A Matthew Shields %A Pierre Feutry %K connectivity %K DArTseq %K euryhaline %K mitogenomics %K Population structure %K Speartooth shark %X

This technical report is aimed at providing policy makers, fisheries managers, and conservation agencies with information on the population structure of a threatened shark of northern Australia, the Speartooth Shark. The identification of population boundaries is key to determining the appropriate spatial scale for the conservation and management of wildlife. The major river drainages (Wenlock River, Alligator Rivers, Adelaide River) comprising the species’ known range have been shown previously to be distinct genetic populations. Recent surveys have revealed a wider range than previously documented with newly-identified populations in the Daly River of the Northern Territory and the Ord River of Western Australia as well as the species’ rediscovery in Papua New Guinea (PNG). Here we aimed to test the hypothesis that the newly identified rivers (Daly and Ord Rivers), along with the Kikori River in southern PNG, also represent distinct populations given their isolation from known populations. The analysis revealed that the Ord and Kikori Rivers represent distinct populations. Results from the Daly River also suggest that this is a distinct population, although sample size was small and power limited to infer statistical significance. Each river system within the range of the Speartooth Shark should be treated as a separate management unit.

%8 30 Jul 2021 %G eng %0 Journal Article %J Frontiers in Conservation Science %D 2021 %T Papua New Guinea: A potential refuge for threatened Indo–Pacific river sharks and sawfishes %A Grant, Michael I. %A White, William T. %A Amepou, Yolarnie %A Appleyard, Sharon A. %A Baje, Leontine %A Floriaan Devloo-Delva %A Pierre Feutry %A Ibana, Dotty %A Jogo, Dick J. %A Jogo, Stanley %A PM Kyne %A Mana, Ralph %A Mapmani, Nigel %A Nagul, Anthony %A Roeger, Darcy %A Simpfendorfer, Colin A. %A Chin, Andrew %K Glyphis %K Pristidae %K riverine %K small-scale fisheries %K swim bladder %K threatened species %X

The conservation of threatened elasmobranchs in tropical regions is challenging due to high local reliance on aquatic and marine resources. Due primarily to fishing pressure, river sharks (Glyphis) and sawfishes (Pristidae) have experienced large population declines in the Indo-Pacific. Papua New Guinea (PNG) may offer a refuge for these species, as human population density is low, and river shark and sawfish populations are thought to persist. However, few data are available on these species in PNG, and risk posed by small-scale fishers is poorly understood. This study observed elasmobranch catches in small-scale fisheries in riverine and coastal environments in the East Sepik (northern region), Gulf, and Western Provinces (southern region) of PNG. Surveys were conducted over a period of weeks to months in each region, during the dry season across seven field trips from 2017 to 2020. We observed a total of 783 elasmobranchs encompassing 38 species from 10 families. River sharks made up 29.4% of observations in the southern region, while sawfishes made up 14.8 and 20.3% in the northern and southern regions, respectively. River sharks were commonly caught by small-scale fishers in lower riverine environments in southern PNG, while sawfishes were generally less common and mainly observed through dried rostra. The primary threat to river shark and sawfish populations is their capture by small-scale fishers targeting teleosts for swim bladder. Persisting populations of river sharks and sawfishes indicate that PNG is the second known nation with viable populations of multiple species in the Indo-Pacific. However, populations are declining or at high risk of decline, and fisheries management and conservation are required to realize the potential of PNG as a long-term refuge.

%B Frontiers in Conservation Science %V 2 %8 6 Sep 2021 %G eng %U https://www.frontiersin.org/articles/10.3389/fcosc.2021.719981/full %9 Journal %! Front. Conserv. Sci. %R 10.3389/fcosc.2021.719981 %0 Generic %D 2020 %T Northern River Shark project summary fact sheet %A PM Kyne %A Bryony Bennett %A Pierre Feutry %K Glyphis garricki; close-kin mark-recapture; northern river shark; Van Diemen Gulf; Northern Territory; population size; population structure; threatened species %X

A fact sheet synthesising Marine Biodiversity Hub research on the Northern River Shark.

A decade of Marine Biodiversity Hub Research led by Charles Darwin University shows the Northern River Shark to be more wide-ranging than previously thought, with new populations documented in several northern rivers. In 2010, the species was known from only 32 records in six rivers/estuaries; now more than 600 individuals have been recorded in 12 rivers/estuaries. Five genetically distinct populations were identified: four in Australia and one in Papua New Guinea. CSIRO close-kin mark-recapture analyses enabled the first population size estimates for one of these populations: the Northern Territory’s Van Diemen Gulf population size was estimated to be only ~600–1100 adults. The research provides monitoring and population assessment capability directly relevant to managing the recovery of the Northern River Shark and underpins environmental assessments under the EPBC Act in the context of northern Australia’s development.

%8 6 Aug 2020 %0 Generic %D 2020 %T Northern River Shark project summary poster %A PM Kyne %A Bell, L %A Bryony Bennett %A Pierre Feutry %K Glyphis garricki; close-kin mark-recapture; northern river shark; Van Diemen Gulf; Northern Territory; population size; population structure; threatened species %X

A poster providing a summary of the Marine Biodiversity Hub research on the Northern River Shark.

A poster summarising Northern River Shark research findings

A decade of Marine Biodiversity Hub Research led by Charles Darwin University shows the Northern River Shark to be more wide-ranging than previously thought, with new populations documented in several northern rivers. In 2010, the species was known from only 32 records in six rivers/estuaries; now more than 600 individuals have been recorded in 12 rivers/estuaries. Five genetically distinct populations were identified: four in Australia and one in Papua New Guinea. CSIRO close-kin mark-recapture analyses enabled the first population size estimates for one of these populations: the Northern Territory’s Van Diemen Gulf population size was estimated to be only ~600–1100 adults. The research provides monitoring and population assessment capability directly relevant to managing the recovery of the Northern River Shark and underpins environmental assessments under the EPBC Act in the context of northern Australia’s development.

%G eng %0 Journal Article %J Molecular Ecology Resources %D 2020 %T One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark %A Pierre Feutry %A Floriaan Devloo-Delva %A Adrien Tran Lu Y %A Mona, Stefano %A R. Gunasekera %A Grant Johnson %A Richard D. Pillans %A Jaccoud, Damian %A Kilian, Andrzej %A David L Morgan %A Thor Saunders %A Nicholas J. Bax %A PM Kyne %K Close‐Kin Mark‐Recapture %K coalescent simulations %K connectivity %K Glyphis garricki %K RAD %K sequence capture %X

With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close‐Kin Mark‐Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost‐efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost‐effectiveness.

%B Molecular Ecology Resources %V 20 %P 1470 - 1485 %8 04 Nov 2020 %G eng %U https://onlinelibrary.wiley.com/toc/17550998/20/6 %N 6 %9 Journal %! Mol Ecol Resour %R 10.1111/1755-0998.13204 %0 Report %D 2019 %T Close-Kin Mark-Recapture population size estimate of Glyphis garricki in the Northern Territory %A Mark Bravington %A Pierre Feutry %A Richard D. Pillans %A Hillary, Rich %A Grant Johnson %A Thor Saunders %A R. Gunasekera %A Nicholas J. Bax %A PM Kyne %K close-kin mark-recapture %K Northern River Shark %K Northern Territory %K population size %K threatened species %K Van Diemen Gulf %X

The Endangered Northern River Shark Glyphis garricki (family Carcharhinidae) is found only in northern Australia and southern Papua New Guinea. It is a euryhaline species inhabiting tidal rivers and estuaries with all life stages (neonates to adults) recorded in rivers, while adults have also been recorded in marine waters. During surveys under the National Environmental Research Program (NERP) and the National Environmental Science Program (NESP), samples were collected in the Northern Territory in the rivers of Van Diemen Gulf (VDG) and the Daly River, and in the Kimberley region of Western Australia, from Cambridge Gulf and King Sound. Previously, the species was only known from a very limited number of records (~40) and these surveys have shown its range to be more widespread than initially documented. It is also likely that the species will be recorded in other rivers and estuaries with suitable habitat as more surveys are undertaken. For the purpose of this report, the VDG encompasses the Alligator Rivers region west to the Adelaide River. Based on recent genetic population structure research, the VDG population appears demographically separate from other known populations in the western part of its range, which in turn are separate to each other.

The aim of this study was to apply Close-Kin Mark-Recapture (CKMR) to G. garricki to estimate population size within the Northern Territory. Samples were collected from six rivers and creeks flowing into VDG (from east to west): East Alligator River, South Alligator River, West Alligator River (collectively, these three rivers make up the ‘Alligator Rivers’), Wildman River, Sampan Creek, and the Adelaide River. While sampling has been conducted across the Australian range of the species (i.e. Daly River, Cambridge Gulf, King Sound), limited sample size outside the VDG prohibited the application of a CKMR model and therefore the focus of this study is the VDG.

%8 4 Dec 2019 %G eng %0 Report %D 2018 %T A close-kin mark-recapture estimate of the population size and trend of east coast grey nurse shark %A R. W. Bradford %A Russell J. Thomson %A Mark Bravington %A Foote, D %A R. Gunasekera %A Barry Bruce %A David Harasti %A Otway, N %A Pierre Feutry %K close-kin mark-recapture %K grey nurse shark %X

A close-kin mark-recapture estimate of the population size and trend of east coast grey nurse shark - was initiated to provide a contemporary population estimate of the eastern grey nurse shark (Carcharias taurus) using emerging genetic and statistical techniques. It follows on from the successful National Assessment of the Status of White Sharks (A3) project and uses a modification of the population-dynamics model used to derive a population estimate for white sharks. Importantly, due to the absence of age estimates as well as the unreliable length estimates of the sampled grey nurse shark (GNS), the GNS model had to be more elaborate to account for greater kinship possibilities.

The grey nurse shark, Carcharias taurus (GNS), is distributed primarily within the continental shelf zones of tropical and temperate regions of the North and South Atlantic, Indian and western Pacific oceans (Last & Stevens, 2009) to depths of at least 230 m (Otway and Ellis 2011). In Australia, two distinct subpopulations are recognised, one along the eastern seaboard of Australia, the other along the western seaboard. Within Australia the distribution of the eastern population extends approximately 2,700 km from central Queensland south to at least the New South Wales (NSW)/Victorian border (Otway et al. 2003; Bansemer 2009; Otway and Ellis 2011). The western population extends across a similar distance of the West Australian coastline from the North West Shelf south to at least Cocklebiddy in the Great Australian Bight (McAuley et al. 2002; Cavanagh et al. 2003; Chidlow et al. 2005). This project was focussed on deriving an abundance estimate of the eastern Australian GNS population.
 
The species is listed as “vulnerable” on the IUCN Red List of Threatened Species (Pollard & Smith 2009) as a result of observed declines in GNS numbers worldwide. The eastern Australian population has been declared “critically endangered” under the Australian Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act) and as such is the subject of an on-going recovery plan. This publication addresses Objective 1 of the 2014 recovery plan: Develop and apply quantitative monitoring of the population status (distribution and abundance) and potential recovery of the grey nurse shark in Australian waters (Australian Government Department of the Environment 2014).

 

 

%8 19 Nov 2018 %G eng %0 Journal Article %J Scientific Reports %D 2018 %T Genetic relatedness reveals total population size of white sharks in eastern Australia and New Zealand %A R. M. Hillary %A Mark Bravington %A T. A. Patterson %A Grewe, P. %A R. W. Bradford %A Pierre Feutry %A R. Gunasekera %A Peddemors, V. %A Werry, J. %A Malcolm P. Francis %A Duffy, C. A. J. %A Bruce, B. D. %X

Conservation concerns exist for many sharks but robust estimates of abundance are often lacking. Improving population status is a performance measure for species under conservation or recovery plans, yet the lack of data permitting estimation of population size means the efficacy of management actions can be difficult to assess, and achieving the goal of removing species from conservation listing challenging. For potentially dangerous species, like the white shark, balancing conservation and public safety demands is politically and socially complex, often leading to vigorous debate about their population status. This increases the need for robust information to inform policy decisions. We developed a novel method for estimating the total abundance of white sharks in eastern Australia and New Zealand using the genetic-relatedness of juveniles and applying a close-kin mark-recapture framework and demographic model. Estimated numbers of adults are small (ca. 280–650), as is total population size (ca. 2,500–6,750). However, estimates of survival probability are high for adults (over 90%), and fairly high for juveniles (around 73%). This represents the first direct estimate of total white shark abundance and survival calculated from data across both the spatial and temporal life-history of the animal and provides a pathway to estimate population trend.

News story - Sibling DNA matches provide key data for white shark population estimates - 8 February 2018

%B Scientific Reports %V 8 %8 08 Feb 2018 %G eng %U http://www.nature.com/articles/s41598-018-20593-w %N 1 %! Sci Rep %R 10.1038/s41598-018-20593-w %0 Report %D 2018 %T A national assessment of the status of white sharks %A B Bruce %A R. W. Bradford %A Mark Bravington %A Pierre Feutry %A P Grewe %A R. Gunasekera %A David Harasti %A R. M. Hillary %A T. A. Patterson %X

This report provides an overview of the key findings on Australasian white shark (Carcharodon
carcharias) abundance and population dynamics which have superseded the initial estimates in
Hillary et al. (2018). Both the submitted paper and the updated work detailed herein constitute the
first robust estimates of Australasian white shark abundance and demographic rates (survival and
trend) ever undertaken, and employ a variety of cutting-edge methods and novel data from across
the Australian/New Zealand range of the species. Importantly, these estimates do not rely on the
highly uncertain historical catch data for this species. To our knowledge, no similar study has been
conducted worldwide. The results and methods employed, represent a step-change in capacity to
assess otherwise difficult to monitor species, such as white sharks.

%I National Environmental Science Program Marine Biodiversity Hub %C Hobart %8 08 Feb 2018 %G eng %U https://www.nespmarine.edu.au/document/national-assessment-status-white-sharks %9 Report %0 Journal Article %J Mitochondrial DNA Part B %D 2018 %T The phylogenomic position of the Critically Endangered Largetooth Sawfish Pristis pristis (Rhinopristiformes, Pristidae), inferred from the complete mitochondrial genome %A PM Kyne %A Wang, Jun-Jie %A Xiang, Dan %A Chen, Xiao %A Pierre Feutry %K Mitochondrial genome %K Pristidae %K Pristis pristis %K threatened species %X

The complete mitogenome of the Critically Endangered Largetooth Sawfish Pristis pristis (Rhinopristiformes, Pristidae) is presented in this study. The genome is 16,912 bp in length with a nucleotide base composition of 32.0% A, 26.5% C, 13.2% G, and 28.3% T, containing 37 genes typical of vertebrates. Two start (GTG and ATG) and two stop (TAG and TAA/T) codons are found in the protein-coding genes. The 22 tRNA genes range from 66 bp (tRNA-Ser2) to 75 bp (tRNA-Leu1). The tRNA-Pro gene is duplicated with an unknown sequence between the two copies. Bayesian phylogenetic reconstruction showed that P. pristis clusters with the Pristis clade with strong posterior probability (100%).

%B Mitochondrial DNA Part B %V 3 %P 972 - 973 %8 10 Sep 2018 %G eng %U https://www.tandfonline.com/doi/full/10.1080/23802359.2018.1501315 %N 2 %! Mitochondrial DNA Part B %R 10.1080/23802359.2018.1501315 %0 Journal Article %J Ecological Management & Restoration %D 2017 %T Recreational fishing impacts on threatened river sharks: A potential conservation issue %A PM Kyne %A Pierre Feutry %K Adelaide River %K DNA barcoding %K Glyphis garricki %K Glyphis glyphis %K protected species. %X

The Adelaide River in Australia's Northern Territory is a popular recreational fishing area, as well as habitat for threatened and protected river sharks (Glyphis species). Both the Critically Endangered Speartooth Shark (Glyphis glyphis) and Endangered Northern River Shark (Glyphis garricki) are identified here in illegal catches from recreational angling. The identification of a decayed shark specimen using a DNA barcoding-like approach is the first such application to the identification of protected sharks in a recreational fishery. While the extent of catches by recreational anglers is unknown, the threatened status of these sharks, their suspected low population sizes, restricted distributions and importance of the Adelaide River as a nursery area call for the consideration of this as a potential conservation issue. As such, appropriate measures should be taken to reduce interactions with recreational anglers. The primary target species in the river is the iconic sportfish, Barramundi, which is predominantly caught by unbaited lure. Sharks are rarely caught on lure, allowing an opportunity for mitigation to focus on a fishing activity (baited hooks) which would limit any regulatory impact on popular lure fishing. Potential mitigation measures range from increased angler education and compliance checks, to the implementation of a spatial closure to baited hook fishing (a lure-only zone). Such measures may assist in meeting a stated objective of the Australian Government's river shark Recovery Plan to ‘reduce and, where possible, eliminate adverse impacts of recreational fishing'.

%B Ecological Management & Restoration %V 18 %8 09 Aug 2017 %G eng %U http://onlinelibrary.wiley.com/doi/10.1111/emr.12266/full %N 3 %! Ecol Manag Restor %R 10.1111/emr.12266 %0 Journal Article %J Molecular Ecology %D 2016 %T Inferring contemporary and historical genetic connectivity from juveniles %A Pierre Feutry %A Berry, Oliver %A PM Kyne %A Richard D. Pillans %A R. M. Hillary %A Grewe, Peter M. %A Marthick, James R. %A Grant Johnson %A R. Gunasekera %A Nicholas J. Bax %A Mark Bravington %X

Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeting sampling in nurseries and juveniles aggregation should be included in the genomic toolbox of threatened species management.
 

%B Molecular Ecology %8 19 Nov 2016 %G eng %U http://doi.wiley.com/10.1111/mec.13929 %! Mol Ecol %R 10.1111/mec.13929 %0 Journal Article %J Mitochondrial DNA Part B %D 2016 %T The phylogenomic position of the Winghead Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the mitochondrial genome %A Pierre Feutry %A PM Kyne %A Xiao Chen %K Eusphyra blochii %K Mitochondrial genome %K Sphyrnidae %K threatened species %X

The complete mitogenome of the Winghead Shark Eusphyra blochii (Carcharhiniformes: Sphyrnidae) is determined in this study, which is 16,727 bp with a nucleotide base composition: 31.6% A, 25.7% C, 13.0% G and 29.7% T, containing 37 genes with the typical gene arrangement pattern and translate orientation in vertebrates. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) are found in the protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic position showed that E. blochii clustered with the Sphyrna clade with strong posterior probability (100%).

The hammerhead sharks (family Sphyrnidae) are a small but a highly distinctive group of tropical to temperate coastal and pelagic sharks. The family faces an elevated risk of extinction with several species assessed as threatened on the IUCN Red List of Threatened Species (IUCN 2015). There is also evidence for cryptic species in the Atlantic Ocean (Abercrombie et al. 2005), which presents issues for the identification and monitoring of catches. Molecular identification of hammerhead products can assist catch identification (Abercrombie et al. 2005; Chapman et al. 2009 ) and is becoming increasingly important as conservation and management measures are implemented for these species, such as the 2013 listing of the three larger-bodied species on the Convention on International Trade in Endangered Species (CITES 2013).

%B Mitochondrial DNA Part B %V 1 %P 386 - 387 %8 20 Jun 2016 %G eng %U http://www.tandfonline.com/doi/full/10.1080/23802359.2016.1172049 %N 1 %! Mitochondrial DNA Part B %R 10.1080/23802359.2016.1172049 %0 Journal Article %J Mitochondrial DNA %D 2015 %T Complete mitochondrial genome of the Critically Endangered Smalltooth Sawfish Pristis pectinata (Rajiformes: Pristidae) %A Xiao Chen %A Wiley, Tonya %A PM Kyne %A Pierre Feutry %K Mitochondrial genome %K Pristis pectinata %K threatened species %X

In this study we describe the first complete mitochondrial sequence of the Critically Endangered Smalltooth Sawfish Pristis pectinata. It is 16,802 bp in length and contains all 37 genes found in typical vertebrate mitogenomes. The nucleotide composition of the coding strand is 31.1% A, 26.0% C, 13.1% G and 28.9% T. There are 29 bp overlaps and 38 short intergenic spaces dispersed in the mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were found in the protein-coding genes. The length of the 22 tRNA genes range from 67 bp (tRNASer2) to 75 bp (tRNALeu1). The control region is 1102 bp in length with high A + T (62.0%) and poor G (13.5%) content.

%B Mitochondrial DNA %P 1 - 2 %8 05 Nov 2015 %G eng %U http://www.tandfonline.com/doi/full/10.3109/19401736.2015.1018208 %! Mitochondrial DNA %R 10.3109/19401736.2015.1018208 %0 Journal Article %J Mitochondrial DNA %D 2015 %T Complete mitochondrial genome of the Endangered Narrow Sawfish Anoxypristis cuspidata (Rajiformes: Pristidae) %A Xiao Chen %A PM Kyne %A Richard D. Pillans %A Pierre Feutry %K Mitochondrial genome %K noxypristis cuspidata %K threatened species %X

In this study, we describe the first complete mitochondrial sequence for the Endangered Narrow Sawfish Anoxypristis cuspidata. It is 17,243 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region with the common vertebrate mitogenomic organization. A total of 30 bp overlaps and 28 bp short intergenic spaces are located between all genes. The overall base composition is 32.7% A, 25.7% C, 12.9% G, and 28.6% T. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in all protein-coding genes. The origin of L-strand replication (OL) sequence (38 bp) formed a hairpin structure (13 bp stem and 12 bp loop) to initiate the replication of L-strand.
Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2014.1003898


 

%B Mitochondrial DNA %P 1 - 2 %8 20 Jan 2015 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2014.1003898 %! Mitochondrial DNA %R 10.3109/19401736.2014.1003898 %0 Journal Article %J Marine Ecology Progress Series %D 2015 %T Whole mitogenome sequencing refines population structure of the Critically Endangered sawfish Pristis pristis %A Pierre Feutry %A PM Kyne %A Richard D. Pillans %A Chen, X %A Marthick, J %A David L Morgan %A Grewe, PM %X

The Largetooth Sawfish Pristis pristis is a highly threatened euryhaline elasmobranch that in recent times has undergone a significant range contraction. It now only remains in a few areas with northern Australia being the main stronghold. Previous work using a single mitochondrial gene approach suggested the existence of regional barriers to gene flow in northern Australia. In this study, whole mitochondrial sequences of 92 P. pristis from seven river drainages across northern Australia were used to refine the population structure. This approach revealed barriers to gene flow at a scale as fine as between adjacent river drainages. Except for those flowing into the Gulf of Carpentaria, all river drainages appeared to host a genetically distinct population. The apparent genetic homogeneity in the Gulf is probably due to freshwater connectivity between river drainages, either during the last glaciation event when the Gulf was a freshwater lake or through contemporary wet season flooding. These results suggest that each river drainage across the species’ range should be considered a discrete management unit unless there is evidence of freshwater connectivity. More broadly, the improved resolution of population structure obtained with whole mitogenome analysis compared to single mitochondrial gene approaches, suggests that female reproductive philopatry may have been overlooked in previous studies of some elasmobranch species.
 

%B Marine Ecology Progress Series %V 533 %P 237 - 244 %8 06 Aug 2015 %G eng %U http://www.int-res.com/abstracts/meps/v533/p237-244/ %! Mar. Ecol. Prog. Ser. %R 10.3354/meps11354 %0 Journal Article %J Mitochondrial DNA %D 2014 %T Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis %A Pierre Feutry %A PM Kyne %A Peng, Zaiqing %A Pan, Lianghao %A Xiao Chen %K Dasyatidae %K Himantura dalyensis %K mitochondrion %X

The complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis is presented in this study. It is 17,693 bp in length and contains 37 genes in typical gene order and transcriptional orientation observed in vertebrates. There were a total of 86 bp short intergenic spacers and 22 bp overlaps in the genome. The overall base composition was 31.4% A, 25.5% C, 13.2% G and 29.9% T. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were found in 13 protein-coding genes. The length of 22 tRNA genes ranged from 68 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1). The origin of L-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes. The base composition of the control region (1940 bp) was similar to the whole mitogenome.

Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2014.958682


 

%B Mitochondrial DNA %P 1 - 2 %8 18 Sep 2014 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2014.958682 %! Mitochondrial DNA %R 10.3109/19401736.2014.958682 %0 Journal Article %J Mitochondrial DNA %D 2014 %T Complete mitochondrial genome of the Pigeye Shark Carcharhinus amboinensis (Carcharhiniformes: Carcharhinidae) %A Pierre Feutry %A Every, Sharon L. %A PM Kyne %A Sun, Renjie %A Xiao Chen %K Carcharhinus amboinensis %K genome %K mitochondrion %X

In this manuscript we describe the first complete mitochondrial sequence for the Data Deficient Pigeye Shark Carcharhinus amboinensis. The mitogenome is 16,704 bp long and consists of 1 control region, 2 rRNA genes, 22 tRNA genes and 13 protein-coding genes with an overall base composition of 31.6% A, 24.9% C, 13.1% G and 30.4% T. The gene arrangement pattern and transcriptional direction were typical for a vertebrate species. The tRNA-Ser2 lacks the dihydrouridine arm and forms a simple loop, therefore it cannot be folded into the typical cloverleaf secondary structures like other tRNAs.

Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2014.982590


 

%B Mitochondrial DNA %P 1 - 2 %8 24 Nov 2014 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2014.982590 %! Mitochondrial DNA %R 10.3109/19401736.2014.982590 %0 Journal Article %J Mitochondrial DNA %D 2014 %T Complete mitogenome of the Graceful Shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae) %A Pierre Feutry %A Richard D. Pillans %A PM Kyne %A Xiao Chen %K Carcharhinus amblyrhynchoides %K genome %K mitochondrion %X

In this manuscript we describe the first complete mitochondrial sequence for the Near
Threatened Graceful Shark Carcharhinus amblyrhynchoides. It is 16,705 bp in length, consists of
two rRNA genes, 22 tRNA genes, 13 protein-coding genes and one control region with the
typical gene arrangement pattern and translate orientation in vertebrates. The overall base
composition is 31.4% A, 25.1% C, 13.2% G and 30.3% T. The shortest tRNA-Ser2 cannot fold into
a clover-leaf secondary structure due to the lack of the dihydrouridine arm.

%B Mitochondrial DNA %P 1 - 2 %8 03 Nov 2014 %G eng %U http://www.tandfonline.com/doi/abs/10.3109/19401736.2014.892094 %! Mitochondrial DNA %R 10.3109/19401736.2014.892094 %0 Journal Article %J Mitochondrial DNA %D 2014 %T Complete mitogenomic sequence of the Critically Endangered Northern River Shark Glyphis garricki (Carcharhiniformes: Carcharhinidae). %A Pierre Feutry %A Grewe, Peter M. %A PM Kyne %A Xiao Chen %K Glyphis garricki %K Mitochondrial genome %K threatened species %X

In this study we describe the first complete mitochondrial sequence for the Critically Endangered Northern River shark Glyphis garricki. The complete mitochondrial sequence is 16,702 bp in length, contains 37 genes and one control region with the typical gene order and transcriptional direction of vertebrate mitogenomes. The overall base composition is 31.5% A, 26.3% C, 12.9% G and 29.3% T. The length of 22 tRNA genes ranged from 68 (tRNA-Ser2 and tRNA-Cys) to 75 (tRNA-Leu1) bp. The control region of G. garricki was 1067 bp in length with high A + T (67.9%) and poor G (12.6%) content. The mitogenomic characters (base composition, codon usage and gene length) of G. garricki were very similar to Glyphis glyphis.


Read More: http://informahealthcare.com/doi/abs/10.3109/19401736.2013.861428

%B Mitochondrial DNA %P 1 - 2 %8 01 Oct 2014 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2013.861428 %! Mitochondrial DNA %R 10.3109/19401736.2013.861428 %0 Journal Article %J BMC Evolutionary Biology %D 2014 %T Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing %A Pierre Feutry %A PM Kyne %A Richard D. Pillans %A Xiao Chen %A Gavin J. P. Naylor %A Grewe, Peter M. %K D-loop %K Dispersal %K Elasmobranchs %K IUCN Red List %K Low genetic diversity %K Philopatry %K Population genetics %X

Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark Glyphis glyphis from the last three river drainages they inhabit in northern Australia.

%B BMC Evolutionary Biology %V 14 %8 12 Jan 2014 %G eng %U http://www.biomedcentral.com/1471-2148/14/232 %! BMC Evol Biol %& 232 %R 10.1186/s12862-014-0232-x %0 Journal Article %J Mitochondrial DNA %D 2013 %T Complete mitochondrial genome of the Critically Endangered speartooth shark Glyphis glyphis (Carcharhiniformes: Carcharhinidae) %A Xiao Chen %A Liu, Min %A Grewe, Peter M. %A PM Kyne %A Pierre Feutry %K Glyphis glyphis %K mitogenome %K river sharks %K threatened species %X

In this study we present the first complete mitogenome for the speartooth shark Glyphis
glyphis, a rare euryhaline elasmobranch from northern Australia and Papua New Guinea.
The mitogenome is 16,702 bp in length and the overall base composition is 31.5% A; 26.0% C;
13.0% G and 29.5% T. It includes 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes,
13 protein-coding genes and a putative 1066 bp long control region. The COI gene is initiated
by GTG codon whereas the remaining protein-coding genes started with the ATG codon.
This study will help elucidate the taxonomy of this poorly known group of sharks.

%B Mitochondrial DNA %P 1 - 2 %8 01 Jul 2013 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2013.809443 %! Mitochondrial DNA %R 10.3109/19401736.2013.809443 %0 Journal Article %J Mitochondrial DNA %D 2013 %T Whole mitogenome of the Endangered dwarf sawfish Pristis clavata (Rajiformes: Pristidae). %A Pierre Feutry %A PM Kyne %A Grewe, Peter M. %A Xiao Chen %A Liu, Min %K Mitochondrial genome %K Pristis clavata %K threatened species %X

In this study, we describe the first complete mitochondrial sequence for the Endangered dwarf sawfish Pristis clavata. The base composition of the 16,804 bp long mitogenome is 31.9% A, 26.5% C, 13.3% G and 28.3% T and the gene arrangement and transcriptional direction are the same as those found in most vertebrates. All protein-coding genes start with ATG except the COI gene, which starts with GTG. Stop codons include incomplete T, AGG and TAA; however, TAG is not found in the mitogenome of this euryhaline elasmobranch species.

%B Mitochondrial DNA %P 1 - 2 %G eng %U http://informahealthcare.com/doi/abs/10.3109/19401736.2013.830297 %! Mitochondrial DNA %R 10.3109/19401736.2013.830297