DNA capture reveals transoceanic gene flow in endangered river sharks

An annotated catalogue of selected historical type specimens, including genetic data, housed in the Natural History Museum Vienna

Museum collections are an important source for resolving taxonomic issues and species delimitation. Type specimens as name-bearing specimens, traditionally used in morphology-based taxonomy, are, due to the progress in historical DNA methodology, increasingly used in molecular taxonomic studies. Museum collections are subject to constant deterioration and major disasters. The digitisation of collections offers a partial solution to these problems and makes museum collections more accessible to the wider scientific community. The Extended Specimen Approach (ESA) is a method of digitisation that goes beyond the physical specimen to include the historical information stored in the collection. The collections of the Natural History Museum Vienna represent one of the largest non-university research centres in Europe and, due to their size and numerous type specimens, are frequently used for taxonomic studies by visiting and resident scientists. Recently, a version of ESA was presented in the common catalogue of the Fish and Evertebrata Varia collections and extended to include genetic information on type specimens in a case study of a torpedo ray. Here the case study was extended to a heterogeneous selection of historical type series from different collections with the type locality of Vienna. The goal was to apply the ESA, including genetic data on a selected set of type material: three parasitic worms, three myriapods, two insects, twelve fishes, and one bird species. Five hundred digital items (photographs, X-rays, scans) were produced, and genetic analysis was successful in eleven of the 21 type series. In one case a complete mitochondrial genome was assembled, and in another case ten short fragments (100-230 bp) of the cytochrome oxidase I gene were amplified and sequenced. For five type series, genetic analysis confirmed their taxonomic status as previously recognised synonyms, and for one the analysis supported its status as a distinct species. For two species, genetic information was provided for the first time. This catalogue thus demonstrates the usefulness of ESA in providing digitised data of types that can be easily made available to scientists worldwide for further study.

Mid-Holocene marine faunas from the Bangkok Clay deposits in Nakhon Nayok, the Central Plain of Thailand

Based on several field investigations, many molluscan shells and chondrichthyan teeth, together with other invertebrate and actinopterygian remains were found from the marine Bangkok Clay deposits in Ongkharak, Nakhon Nayok, at a depth of ~ 5-7 m below the topsoil surface. Animal macrofossils recovered from these Holocene marine deposits were identified and their chronological context was investigated in order to reconstruct the paleoenvironments of the area at that time. The majority of marine fossils recovered from the site consist of molluscs, with a total of 63 species identified. Other invertebrate species include a stony coral, a mud lobster, barnacles, and a sea urchin. The vertebrates are represented by fish remains, including carcharhinid shark teeth from at least nine species, stingray and trichiurid teeth, and one sciaenid otolith. The molluscan fauna indicates that the paleoenvironments of the area corresponded to intertidal to sublittoral zones, where some areas were mangrove forests and intertidal mudflats. The fish fauna is dominated by the river shark Glyphis, indicating freshwater influences and possibly occasional brackish conditions. The carbon-14 analysis of mollusc and charcoal remains shows that deposition of the marine sediment sequence began during the mid-Holocene, spanning approximately from 8,800 to 5,300 cal yr BP. This study provides in-depth insights into the diversity of fishes, marine molluscs, and other invertebrates from the Bangkok Clay deposits, supporting the existence of a marine transgression onto the Lower Central Plain of Thailand during the mid-Holocene.

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.

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.

Market surveys and social media provide confirmation of the endangered giant freshwater whipray Urogymnus polylepis in Myanmar

The giant freshwater whipray Urogymnus polylepis is a threatened species that is vulnerable to riverine and coastal marine pressures. Despite its threatened status, the range of U. polylepis is still being determined. In this study, photographic evidence of U. polylepis in Myanmar was provided through market surveys (2017-2018) and social media (Sharks and Rays of Rakhine Facebook page, 2021). Urogymnus polylepis is exposed to fisheries and habitat degradation pressures in Myanmar; therefore, conservation management is likely needed to ensure populations persist into the future.

Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set

A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.

Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae

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 control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.

Defining Management Units for Wild Nile Tilapia Oreochromis niloticus from Nine River Basins in Ghana

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano–Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano–Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term.

Papua New Guinea: A Potential Refuge for Threatened Indo–Pacific River Sharks and Sawfishes

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.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BACKGROUND

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS

In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS

Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches

Background

Delimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group.

Results

Both mtDNA and SNP analyses showed potential delimitation within C. punctatum from the Indo-Australian region and consisted of four operational taxonomic units (OTUs), i.e. those from Indo-Malay region, the west coast of Sumatra, Lesser Sunda region, and the Australian region. Each OTU can be interpreted differently depending on available supporting information, either based on biological, ecological or geographical data. We found that SNP data provided more robust results than mtDNA data in determining the boundary between population and cryptic species.

Conclusion

To split a cryptic species complex and erect new species based purely on the results of genetic analyses is not recommended. The designation of new species needs supportive diagnostic morphological characters that allow for species recognition, as an inability to recognise individuals in the field creates difficulties for future research, management for conservation and fisheries purposes. Moreover, we recommend that future studies use a comprehensive sampling regime that encompasses the full range of a species complex. This approach would increase the likelihood of identification of operational taxonomic units rather than resulting in an incorrect designation of new species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01852-3.

Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens

Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Genomics of Population Differentiation in Humpback Dolphins, Sousa spp. in the Indo-Pacific Ocean

Speciation is a fundamental process in evolution and crucial to the formation of biodiversity. It is a continuous and complex process, which can involve multiple interacting barriers leading to heterogeneous genomic landscapes with various peaks of divergence among populations. In this study, we used a population genomics approach to gain insights on the speciation process and to understand the population structure within the genus Sousa across its distribution in the Indo-Pacific region. We found 5 distinct clusters, corresponding to S. plumbea along the eastern African coast and the Arabian Sea, the Bangladesh population, S. chinensis off Thailand and S. sahulensis off Australian waters. We suggest that the high level of differentiation found, even across geographically close areas, is likely determined by different oceanographic features such as sea surface temperature and primary productivity.

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

'Barcode fishing' for archival DNA from historical type material overcomes taxonomic hurdles, enabling the description of a new frog species

Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne d'Ambre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d'Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this 'barcode fishing' approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.

Integrative taxonomy identifies a new stingray species of the genus Hypanus Rafinesque, 1818 (Dasyatidae, Myliobatiformes), from the Tropical Southwestern Atlantic

An integrative approach by the congruence of genetics, morphology and ecological niche modelling (ENM) was used to delimit a new species of Hypanus (Rafinesque, 1818), a recently resurrected genus of marine stingrays comprising eight species, five of which occur in the western Atlantic. The species with the widest distribution, Hypanus americanus (Hildebrand and Schroeder, 1928), from the northeastern coast of the United States to southeastern Brazil, was demonstrated to be paraphyletic based on protein-coding mitochondrial genome analyses. This data set also indicates that the genetic distance between the new species Hypanus berthalutzae sp. nov. and its three closely related species (H. americanus, H. longus and H. rudis) varies from 0.82% to 3.14%. In addition, Bayesian Analysis of Population Similarity using the mitochondrial gene mt-nd2 supports the separation of H. berthalutzae sp. nov. (southwestern Atlantic) from its sister species H. rudis (eastern Atlantic). Similarly, morphological and morphometric analyses corroborated four morphotypes within the H. americanus species group and indicated the ventral caudal fold height and length and interspiracular and interorbital lengths as useful measurements to distinguish among them. Claspers of adult males also exhibit morphological differences among species. The ENM agreed with molecular and morphological analyses and delimits the distribution of H. berthalutzae sp. nov. to shallow areas close to shore along the Brazilian coast, from the mouth of the Amazon River to São Paulo State, including the northeastern oceanic islands, suggesting that the great outflow of fresh water and sediments and the Mid-Atlantic Ridge might act as barriers. The integration of these data to describe a new species provides information relevant to their conservation status, because all species of the H. americanus species group are under the "data-deficient" status.

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.

'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market

Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

Long-read sequence capture of the haemoglobin gene clusters across codfish species

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.

An In Silico Comparison of Protocols for Dated Phylogenomics

In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker. We then compare these data sets in terms of both phylogenetic resolution and ability to consistently and precisely estimate clade ages using fossil-calibrated molecular-clock models. Furthermore, we were also able to directly compare these results to previously published data sets from Sanger-sequenced nuclear exons and mitochondrial genomes under the same analytical conditions. Our results show-although with the exception of the mitochondrial genome data set and the smallest ddRADseq data set-that for uncontroversial nodes all data classes performed equally well, that is they recovered the same well supported topology. However, for one difficult-to-resolve node comprising a rapid diversification, we report well supported but conflicting topologies among the marker classes consistent with the mismodeling of gene tree heterogeneity as demonstrated by species tree analyses of single nucleotide polymorphisms. Likewise, clade age estimates showed consistent discrepancies between data sets under strict and relaxed clock models; for recent nodes, clade ages estimated by nuclear exon data sets were younger than those of the UCE, RADseq and mitochondrial data, but vice versa for the deepest nodes in the primate phylogeny. This observation is explained by temporal differences in phylogenetic informativeness (PI), with the data sets with strong PI peaks toward the present underestimating the deepest node ages. Finally, we conclude by emphasizing that while huge numbers of loci are probably not required for uncontroversial phylogenetic questions-for which practical considerations such as ease of data generation, sharing, and aggregating, therefore become increasingly important-accurately modeling heterogeneous data remains as relevant as ever for the more recalcitrant problems.

A rare contemporary record of the Critically Endangered Ganges shark Glyphis gangeticus

The first record of the Ganges shark Glyphis gangeticus from anywhere in its range in over a decade is reported from the Arabian Sea. One female specimen was recorded at Sassoon Docks in Mumbai, India in February 2016, measuring 266 cm total length. In light of the Critically Endangered status of this species and its rarity, urgent management actions are needed to determine population size and trends in abundance in combination with fisher education and awareness campaigns.

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

Currently one small, native population of the culturally and ecologically important Lahontan cutthroat trout (Oncorhynchus clarkii henshawi, LCT, Federally listed) remains in the Truckee River watershed of northwestern Nevada and northeastern California. The majority of populations in this watershed were extirpated in the 1940s due to invasive species, overharvest, anthropogenic water consumption and changing precipitation regimes. In 1977, a population of cutthroat trout discovered in the Pilot Peak Mountains in the Bonneville basin of Utah, was putatively identified as the extirpated LCT lacustrine lineage native to Pyramid Lake in the Truckee River basin based on morphological and meristic characters. Our phylogenetic and Bayesian genotype clustering analyses of museum specimens collected from the large lakes (1872-1913) and contemporary samples collected from populations throughout the extant range provide evidence in support of a genetically distinct Truckee River basin origin for this population. Analysis of museum samples alone identified three distinct genotype clusters and historical connectivity among water bodies within the Truckee River basin. Baseline data from museum collections indicate that the extant Pilot Peak strain represents a remnant of the extirpated lacustrine lineage. Given the limitations on high-quality data when working with a sparse number of preserved museum samples, we acknowledge that, in the end, this may be a more complicated story. However, the paucity of remnant populations in the Truckee River watershed, in combination with data on the distribution of morphological, meristic and genetic data for Lahontan cutthroat trout, suggests that recovery strategies, particularly in the large lacustrine habitats should consider this lineage as an important part of the genetic legacy of this species.

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.

Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

Population genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ~1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported an Nm value ~40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.

Annotated checklist of the living sharks, batoids and chimaeras (Chondrichthyes) of the world, with a focus on biogeographical diversity

An annotated checklist of the chondrichthyan fishes (sharks, batoids and chimaeras) of the world is presented. As of 7 November 2015, the number of species totals 1188, comprising 16 orders, 61 families and 199 genera. The checklist includes nine orders, 34 families, 105 genera and 509 species of sharks; six orders, 24 families, 88 genera and 630 species of batoids (skates and rays); one order, three families, six genera and 49 species of holocephalans (chimaeras). The most speciose shark orders are the Carcharhiniformes with 284 species, followed by the Squaliformes with 119. The most species-rich batoid orders are the Rajiformes with 285 species and the Myliobatiformes with 210. This checklist represents the first global checklist of chondrichthyans to include information on maximum size, geographic and depth distributions, as well as comments on taxonomically problematic species and recent and regularly overlooked synonymizations. Furthermore, a detailed analysis of the biogeographical diversity of the species across 10 major areas of occurrence is given, including updated figures for previously published hotspots of chondrichthyan biodiversity, providing the detailed numbers of chondrichthyan species per major area, and revealing centres of distribution for several taxa.