Pierre Feutry

Pierre Feutry
The Commonwealth Scientific and Industrial Research Organisation | CSIRO · Oceans and Atmosphere

PhD

About

75
Publications
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Publications

Publications (75)
Article
Neritic tunas and tuna-like species are an important resource for many coastal nations1 worldwide supporting both commercial and artisanal fisheries, but little is known about their population structure at a spatial scale required for effective fisheries management. In this study, we use Next Generation Sequencing methods to investigate the genetic...
Article
Full-text available
Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function...
Article
Full-text available
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32....
Article
Full-text available
Reliable information on population size is fundamental to the management of threatened species. For wild species, mark-recapture methods are a cornerstone of abundance estimation. Here, we show the first application of the close-kin mark-recapture (CKMR) method to a terrestrial species of high conservation value; the Christmas Island flying-fox (CI...
Article
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Abstract Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life‐history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distribut...
Article
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Abstract The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessme...
Article
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Sample cross-contamination remains a pervasive issue in genetics and genomics. With growing reliance on molecular methods for managing marine resources, the need to ensure the integrity of tissue samples that underpin these methods has never been more pressing. We conducted an experiment on wild-caught bigeye tuna (Thunnus obesus) to assess cross-c...
Article
Full-text available
The viability of spatially structured populations depends on the abundance and connectivity between subpopulations of breeding adults. Yet, for many species, both are extremely difficult to assess. The speartooth shark is a critically endangered elasmobranch inhabiting tropical rivers with only three adults ever recorded in Australia. Close-kin mar...
Article
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The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible...
Preprint
Full-text available
Understanding the population structure of a species is important to accurately assess its conservation status and manage the risk of local extinction. The Bull Shark ( Carcharhinus leucas ) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its...
Preprint
The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species, yet classified as critically endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population across the worldwide species range. Blue shar...
Preprint
Full-text available
Identifying sex-linked markers from genomic data has both theoretical and applied importance, especially in conservation. Yet, few methods and tools exist to detect such markers from Restriction-site-Associated DNA sequencing reads and even fewer tools can identify sex-linked markers from existing genotyped data. Here, we describe a new R function...
Preprint
Full-text available
Elasmobranchs are one of the most highly-threatened vertebrate taxa. Estimating abundance of spawning adults is often extremely challenging, yet crucial for prioritization of conservation measures. Emblematic of these challenges, the speartooth shark (Glyphis glyphis, Mulller and Henle, 1839) was initially known only from rare specimens collected i...
Article
Full-text available
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a con...
Article
Full-text available
In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. W...
Article
The last two decades have witnessed rapid developments and increasing interest in use of: (1) genetic methods to estimate effective population size ( N e ) and (2) close‐kin mark–recapture (CKMR) methods to estimate abundance based on the incidence of close relatives. Whereas N e estimation methods have been applied to a wide range of taxa, all CKM...
Article
Full-text available
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, a...
Article
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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 al...
Preprint
Full-text available
The last two decades have witnessed rapid developments and increasing interest in use of (1) genetic methods to estimate effective population size (Ne) and (2) close-kin mark-recapture (CKMR) methods to estimate abundance based on the incidence of close relatives. Whereas Ne-estimation methods have been applied to a wide range of taxa, all CKMR app...
Article
Full-text available
Environmental DNA (eDNA) is recognized as a promising sampling tool for biodiversity monitoring. It has also been proposed as a tool for performing population genetic analyses on target species, but early applications make questionable assumptions, such as assuming that the amount of DNA in the sample is directly related to the number of individual...
Conference Paper
Full-text available
The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide pop...
Technical Report
Full-text available
The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide pop...
Article
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....
Article
Full-text available
Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Depend...
Article
Full-text available
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 T...
Chapter
Carefully designed studies involving thousands of SNP loci can provide new insight into existing questions of evolution and ecology with increased precision and accuracy (Andrews and Luikart, 2014). Determining causal relationships among genomic variation, phenotypes, and the environment allows a better understanding of the genetic basis of adaptiv...
Article
Full-text available
Genetic studies of several marine species with high fecundity have produced “tiny” estimates (≤10⁻³) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 10⁶ for souther...
Article
Delineating naturally occurring and self‐sustaining sub‐populations (stocks) of a species is an important task, especially for species harvested from the wild. Despite its central importance to natural resource management, analytical methods used to delineate stocks are often, and increasingly, borrowed from superficially similar analytical tasks i...
Article
Full-text available
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 g...
Article
Full-text available
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...
Article
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 b...
Article
Full-text available
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 GT...
Article
Full-text available
Tropical tuna fisheries are central to food security and economic development of many regions of the world. Contemporary population assessment and management generally assume these fisheries exploit a single mixed spawning population, within ocean basins. To date population genetics has lacked the required power to conclusively test this assumption...
Article
Full-text available
The largetooth sawfish Pristis pristis (Linnaeus, 1758) 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...
Article
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...
Article
Full-text available
Background 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 approac...
Article
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 s...
Article
Full-text available
Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr : Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, s...
Article
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 arrangem...
Article
Abstract 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 co...
Conference Paper
Reliable and cost-effective assessment and monitoring tools are urgently required for the conservation and management of data-poor, low abundance, threatened species in Australia, including the Largetooth Sawfish and the Speartooth Shark. In these two species, adults are marine and/or estuarine and too rare for any population assessment based on ca...
Conference Paper
Estimated spawning stock biomass is a central measure for management of fisheries stocks and setting total allowable catch (TAC) quotas. For the highly valued and depleted southern bluefin tuna (Thunnus maccoyii), conventional stock assessment methods provided reasonably precise estimates of relative depletion. Absolute abundance estimates however...
Article
Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr:Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr:Ca and Ba:Ca, however, showed...
Article
Abstract 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 vertebrate...
Article
Abstract 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 c...
Article
Full-text available
Abstract 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 gene...
Article
Abstract 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...
Article
Full-text available
Due to the sparse and unstable nature of insular freshwater habitats, marine larval dispersal of amphidromous species is considered a critical element of population persistence. We assessed population genetic structure of freshwater prawn Macrobrachium lar across its range that encompasses two biogeographic barriers: the vast open ocean separating...
Article
Freshwater species on tropical islands face localized extinction and the loss of genetic diversity. 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 amphidromous or catadromous (i.e. their life cycle includes a marine la...
Article
Full-text available
Abstract Diadromous species undergo regular migration between fresh and marine waters. This behavior is found in many species, including fish, mollusks, and crustaceans, some of which are commercially valuable species. Several attempts to trace the evolution of this behavior have been made in Salmonidae and Galaxiidae, but ambiguous phylogenies and...
Article
Full-text available
Otolith microchemistry and microstructure were examined in juveniles of 3 Kuhlia species (Teleostei) from fresh and brackish environments in order to examine their migratory histories. All species presented with strontium: calcium (Sr:Ca) and barium: calcium (Ba:Ca) profiles in the inner region of the otoliths that suggested an obligatory marine la...
Article
Full-text available
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 durat...
Article
Full-text available
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 durat...
Thesis
Full-text available
The Kuhliidae family includes 12 species arising from tropical waters of the Indo-Pacific region. In this family, half of the species are marine, whereas the others are found in rivers and estuaries of insular systems and thus are supposed to be diadromous (i.e. their life cycle include migrations between marine and freshwater biomes). In tropical...
Article
Strontium ⁄ Calcium (Sr ⁄ Ca) and Barium ⁄ Calcium (Ba ⁄ Ca) ratios were measured in 60 otoliths of the French Polynesian flagtail Kuhlia malo. Both elemental ratios were needed to correctly distinguish residence in marine, brackish and fresh water. High Sr ⁄ Ca and low Ba ⁄ Ca around the nucleus of all otoliths provided evidence of marine residenc...
Article
Full-text available
The aim of the present paper is to provide first information on the mangrove fish community of the tropical fjord-like Golfo Dulce (GD), to study its importance for fish diversity and fisheries in the area and to give preliminary results on its spatial–temporal variation. Eighty-two species belonging to 30 families were identified. More than half o...

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