Fishing for oil and meat drives irreversible defaunation of deepwater sharks and rays.

The deep ocean is the last natural biodiversity refuge from the reach of human activities. Deepwater sharks and rays are among the most sensitive marine vertebrates to overexploitation. One-third of threatened deepwater sharks are targeted, and half the species targeted for the international liver-oil trade are threatened with extinction. Steep population declines cannot be easily reversed owing to long generation lengths, low recovery potentials, and the near absence of management. Depth and spatial limits to fishing activity could improve conservation when implemented alongside catch regulations, bycatch mitigation, and international trade regulation. Deepwater sharks and rays require immediate trade and fishing regulations to prevent irreversible defaunation and promote recovery of this threatened megafauna group.

Elemental analysis of vertebrae discerns diadromous movements of threatened non-marine elasmobranchs.

River sharks (Glyphis spp.) and some sawfishes (Pristidae) inhabit riverine environments, although their long-term habitat use patterns are poorly known. We investigated the diadromous movements of the northern river shark (Glyphis garricki), speartooth shark (Glyphis glyphis), narrow sawfish (Anoxypristis cuspidata), and largetooth sawfish (Pristis pristis) using in situ laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) on vertebrae to recover elemental ratios over each individual's lifetime. We also measured elemental ratios for the bull shark (Carcharhinus leucas) and a range of inshore and offshore stenohaline marine species to assist in interpretation of results. Barium (Ba) was found to be an effective indicator of freshwater use, whereas lithium (Li) and strontium (Sr) were effective indicators of marine water use. The relationships between Ba and Li and Ba and Sr were negatively correlated, whereas the relationship between Li and Sr was positively correlated. Both river shark species had elemental signatures indicative of prolonged use of upper-estuarine environments, whereas adults appear to mainly use lower-estuarine environments rather than marine environments. Decreases in Li:Ba and Sr:Ba at the end of the prenatal growth zone of P. pristis samples indicated that parturition likely occurs in fresh water. There was limited evidence of prolonged riverine habitat use for A. cuspidata. The results of this study support elemental-environment relationships observed in teleost otoliths and indicate that in situ LA-ICP-MS elemental characterization is applicable to a wide range of elasmobranch species as a discriminator for use and movement across salinity gradients. A greater understanding of processes that lead to element incorporation in vertebrae, and relative concentrations in vertebrae with respect to the ambient environment, will improve the applicability of elemental analysis to understand movements across the life history of elasmobranchs into the future.

From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator.

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 assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.

Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species.

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 mark-recapture models, informed by sibling pairs among 226 juveniles, were developed to estimate adult abundance and connectivity in two Australian river systems. Sixty-eight sibling pairs were found, and adult abundance was estimated at 892 for the Adelaide River and 1128 for the Alligator Rivers. We found strong evidence for female philopatry, with most females returning to the same river to pup. Adelaide River males appear largely philopatric, whereas Alligator Rivers males are highly connected to the Adelaide River. From only 4 years of sampling, our results demonstrate that juvenile-only kin pairs can inform simultaneous estimates of abundance and connectivity in a rare and threatened species.

Mitochondrial phylogeny within the Yellow Chat (Epthianura crocea) does not support subspecific designation of endangered Alligator Rivers population.

The delineation of subspecies is important in the evaluation and protection of biodiversity. Subspecies delineation is hampered by inconsistently applied criteria and a lack of agreement and shifting standards on how a subspecies should be defined. The Australian endemic Yellow Chat (Epthianura crocea) is split into three subspecies (E. c. crocea, E. c. tunneyi, and E. c. macgregori) based on minor plumage differences and geographical isolation. Both E. c. tunneyi (Endangered) and E. c. macgregori (Critically Endangered) are recognized under Australian legislation as threatened and are the subject of significant conservation effort. We used mitochondrial DNA to evaluate the phylogeny of the Yellow Chat and determine how much genetic variation is present in each of the three subspecies. We found no significant difference in the cytochrome b sequences (833 base pairs) of E. c. crocea and E. c. tunneyi, but approximately 0.70% or 5.83 bp difference between E. c macgregori and both E. c. crocea and E. c. tunneyi. This analysis supports the delineation of E. c. macgregori as a valid subspecies but does not support separation of E. c. crocea from E. c. tunneyi. We also found very low levels of genetic variation within the Yellow Chat, suggesting it may be vulnerable to environmental change. Our results cast doubt upon the geographic isolation of E. c. crocea from E. c. tunneyi, but more advanced genetic sequencing and a robust comparison of plumage are needed to fully resolve taxonomy.

An annotated checklist of the chondrichthyans of South Africa.

An annotated checklist of chondrichthyan fishes (sharks, batoids, and chimaeras) occurring in South African waters is presented. The checklist is the result of decades of research and on-going systematic revisions of the regional fauna. The chondrichthyan fauna of South Africa is one of the richest in the world with 191 species, comprising 50 families and 103 genera. It consists of 30 families, 64 genera, and 111 species of sharks; 17 families, 36 genera, and 72 species of batoids; and, 3 families, 5 genera, and 8 species of chimaeras. The most species-rich shark families are the whaler sharks Carcharhinidae with 20 species followed by the deepwater catsharks Pentanchidae with 13 species. The most species-rich batoid families are the hardnose stakes Rajidae with at least 21 species followed by the stingrays Dasyatidae with 13 species. This monograph represents the first detailed annotated checklist of chondrichthyans from South Africa in over 30 years.

Overfishing and habitat loss drive range contraction of iconic marine fishes to near extinction.

Extinctions on land are often inferred from sparse sightings over time, but this technique is ill-suited for wide-ranging species. We develop a space-for-time approach to track the spatial contraction and drivers of decline of sawfishes. These iconic and endangered shark-like rays were once found in warm, coastal waters of 90 nations and are now presumed extinct in more than half (n = 46). Using dynamic geography theory, we predict that sawfishes are gone from at least nine additional nations. Overfishing and habitat loss have reduced spatial occupancy, leading to local extinctions in 55 of the 90 nations, which equates to 58.7% of their historical distribution. Retention bans and habitat protections are urgently necessary to secure a future for sawfishes and similar species.

Half a century of global decline in oceanic sharks and rays.

Overfishing is the primary cause of marine defaunation, yet declines in and increasing extinction risks of individual species are difficult to measure, particularly for the largest predators found in the high seas1-3. Here we calculate two well-established indicators to track progress towards Aichi Biodiversity Targets and Sustainable Development Goals4,5: the Living Planet Index (a measure of changes in abundance aggregated from 57 abundance time-series datasets for 18 oceanic shark and ray species) and the Red List Index (a measure of change in extinction risk calculated for all 31 oceanic species of sharks and rays). We find that, since 1970, the global abundance of oceanic sharks and rays has declined by 71% owing to an 18-fold increase in relative fishing pressure. This depletion has increased the global extinction risk to the point at which three-quarters of the species comprising this functionally important assemblage are threatened with extinction. Strict prohibitions and precautionary science-based catch limits are urgently needed to avert population collapse6,7, avoid the disruption of ecological functions and promote species recovery8,9.

Social media posts reveal the geographic range of the Critically Endangered clown wedgefish, Rhynchobatus cooki.

The shark-like rays of the family Rhinidae (wedgefishes) are globally threatened with extinction. The poorly known clown wedgefish, Rhynchobatus cooki has historically been recorded only from fish markets in Singapore and Jakarta, Indonesia. Its natural geographic range has until now gone undocumented. Social media posts revealed the first wild records of this Critically Endangered species; six records were located between 2015 and 2020 from small-scale fisheries in Lingga and Singkep Islands, Indonesia. These results demonstrate the utility of social media searches to identify biogeographic records of cryptic and data-poor species.

One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark.

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.

The correct spelling of the nomen of the lost shark Carcharhinus obsolerus White, Kyne amp; Harris, 2019 (Chondrichthyes, Carcharhinidae).

White et al. (2019) described a new species of whaler shark represented by only three specimens from South-east Asia, all collected prior to 1934. They proposed the nomen Carcharhinus obsolerus with the justification of: "The specific name is Latin for 'extinct' (obsolerus) in allusion to the fact that the species has not been recorded in many decades." Dubois Séret (2019) stated that the epithet obsolerus was "doubtless" an incorrect spelling which must be corrected to obsoletus. However, the Dubois Séret (2019) publication becomes confusing in its discussion around the wording of the related Articles in the International Code of Zoological Nomenclature (32.2, 33.2 and 32.5) and lacks a clear conclusion.

Lost before found: A new species of whaler shark Carcharhinus obsolerus from the Western Central Pacific known only from historic records.

Carcharhinus obsolerus is described based on three specimens from Borneo, Thailand and Vietnam in the Western Central Pacific. It belongs to the porosus subgroup which is characterised by having the second dorsal-fin insertion opposite the anal-fin midbase. It most closely resembles C. borneensis but differs in tooth morphology and counts and a number of morphological characters, including lack of enlarged hyomandibular pores which are diagnostic of C. borneensis. The historic range of C. obsolerus sp. nov. is under intense fishing pressure and this species has not been recorded anywhere in over 80 years. There is an urgent need to assess its extinction risk status for the IUCN Red List of Threatened Species. With so few known records, there is a possibility that Carcharhinus obsolerus sp. nov. has been lost from the marine environment before any understanding could be gained of its full historic distribution, biology, ecosystem role, and importance in local fisheries.

The phylogenomic position of the Critically Endangered Largetooth Sawfish Pristis pristis (Rhinopristiformes, Pristidae), inferred from the complete mitochondrial genome.

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%).

Inferring contemporary and historical genetic connectivity from juveniles.

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 shark 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 targeted sampling in nurseries and juvenile aggregations should be included in the genomic toolbox of threatened species management.

Urogymnus acanthobothrium sp. nov., a new euryhaline whipray (Myliobatiformes: Dasyatidae) from Australia and Papua New Guinea.

The Mumburarr Whipray, Urogymnus acanthobothrium sp. nov. is described from a single specimen taken from the Cambridge Gulf, Western Australia, and from images of 10 other specimens from northern Australia and Papua New Guinea (all observed but not collected). It is a very large ray that attains at least 161 cm disc width, making it amongst the largest of the whiprays. The ventral tail below the caudal sting has a low, short-based fold. A ventral tail fold (or a dorsal fold) has not been recorded for any other himanturin stingray in the Indo-West Pacific. Molecular data suggest it is most closely related to a similar but more widely distributed cognate, U. granulatus. Both of these species share a suboval disc shape, similar squamation patterns, and the tail posterior to the sting is entirely white (at least in small individuals). U. acanthobothrium sp. nov. differs from U. granulatus in having a longer and more angular snout, longer tail, more posteriorly inserted caudal sting, lacks white flecks on the dorsal surface, and the ventral disc is uniformly white (rather than white with a broad black margin). It co-occurs with two other morphologically distinct Urogymnus in the region (U. asperrimus and U. dalyensis). Like U. dalyensis it occurs in both brackish and marine waters. A key is proved to the members of the genus Urogymnus.

A new species of wedgefish Rhynchobatus cooki (Rhinopristiformes, Rhinidae) from the Indo-West Pacific.

A new dwarf wedgefish, Rhynchobatus cooki sp. nov. is described from a single female from a Jakarta fish market (Indonesia) and 11 specimens collected at Jurong fish market (Singapore). First collected in 1934, the broader ichthyological community have been aware of this distinctive but little known ray since the late 1990's. Rhynchobatus cooki is the smallest of the wedgefishes (to 81 cm TL) and has the lowest vertebral count (fewer than 107 centra). It is also distinguishable from its congeners based on its long, hastate snout, very strongly undulate anterior pectoral-fin margin, coloration and aspects of its squamation. The dorsal coloration is mainly dark and distinctively marked with white blotches, spots and streaks, and has a dark cruciate marking on the interorbit and a prominent white border around the body margin. Unlike most other wedgefish species, the snout tip lacks dark blotches and there is no black pectoral-fin marking. It shares well-developed rostral spines with a much larger Atlantic species (Rhynchobatus luebberti), but these spines are confined to the snout tip (rather than being more numerous and extending in paired rows along the rostral ridges nearly to the eyes). No additional specimens have been observed since 1996, despite an increased recent effort to survey the chondrichthyan fauna of South-East Asia and collect biological data for species, raising concerns over its conservation status.

Complete mitochondrial genome of the Endangered Narrow Sawfish Anoxypristis cuspidata (Rajiformes: Pristidae).

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.

Complete mitochondrial genome of the Freshwater Whipray Himantura dalyensis.

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.

Complete mitochondrial genome of the Pigeye Shark Carcharhinus amboinensis (Carcharhiniformes: Carcharhinidae).

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.

The phylogenomic position of the Winghead Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the mitochondrial genome.

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%).