Pierre Feutry

Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource.

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. Here we demonstrate heterogeneous population structure among yellowfin tuna sampled at three locations across the Pacific Ocean (western, central, and eastern) via analysis of double digest restriction-site associated DNA using Next Generation Sequencing technology. The differences among locations are such that individuals sampled from one of the three regions examined can be assigned with close to 100% accuracy demonstrating the power of this approach for providing practical markers for fishery independent verification of catch provenance in a way not achieved by previous techniques. Given these results, an extended pan-tropical survey of yellowfin tuna using this approach will not only help combat the largest threat to sustainable fisheries (i.e. illegal, unreported, and unregulated fishing) but will also provide a basis to transform current monitoring, assessment, and management approaches for this globally significant species.

Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing

BackgroundMitochondrial 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.ResultsGenetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA ΦST =0.28283, P <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages.ConclusionsThis study strongly supports the use of single river drainages as discrete management units for the conservation of G. glyphis. Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies.

Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish

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 the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L–1) of the freshwater resulted in the Sr : Ca being substantially higher than the marine water. Importantly, the otolith Sr : Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr : Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr : Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element : Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr : Ca alone can be problematic without an understanding of water chemistry.

Evolution of Diadromy in Fish: Insights from a Tropical Genus (Kuhlia Species)

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 multiple character state changes prevented unequivocal conclusions. The Kuhliidae family consists of 12 fish species that inhabit tropical islands in the Indo-Pacific region. The species have marine, partially catadromous, or fully catadromous life histories (i.e., they migrate from rivers to the sea to reproduce). The evolution of migratory behavior was traced on a well-resolved phylogeny. Catadromous Kuhlia species were basal, and partially catadromous and marine species formed derived monophyletic groups. This is, to our knowledge, the first time that a clear origin and polarity for the diadromous character has been demonstrated. We propose that the relative lack of resources in tropical, inshore, marine habitats and the ephemeral and isolated nature of freshwater environments of tropical islands, combined with phenotypic plasticity of migratory traits, play key roles in driving the evolution of diadromy in the Kuhliidae and probably in other groups. This work is an important starting point to understand the role of diadromy in speciation and adaptation in unstable habitats.

Stretched to the limit; can a short pelagic larval duration connect adult populations of an Indo-Pacific diadromous fish (Kuhlia rupestris)?

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 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 divergence 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.

Complete mitochondrial genome of the Critically Endangered speartooth shark Glyphis glyphis (Carcharhiniformes: Carcharhinidae)

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 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.

Genetic relatedness reveals total population size of white sharks in eastern Australia and New Zealand

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.

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.

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

Abstract 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.

Whole mitogenome of the Endangered dwarf sawfish Pristis clavata (Rajiformes: Pristidae)

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 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.