Andrea M. Bernard

DNA barcoding of billfishes.

DNA barcoding is a method promising fast and accurate identification of animal species based on the sequencing of the mitochondrial c oxidase subunit (COI) gene. In this study, we explore the prospects for DNA barcoding in one particular fish group, the billfishes (suborder Xiphioidei—swordfish, marlins, spearfishes, and sailfish). We sequenced the mitochondrial COI gene from 296 individuals from the 10 currently recognized species of billfishes, and combined these data with a further 57 sequences from previously published projects. We also sequenced the rhodopsin gene from a subset of 72 individuals to allow comparison of mitochondrial results against a nuclear marker. Five of the 10 species are readily distinguishable by COI barcodes. Of the rest, the striped marlin (Kajikia audax) and white marlin (K. albida) show highly similar sequences and are not unambiguously distinguishable by barcodes alone, likewise are the three spearfishes Tetrapturus angustirostris, T. belone, and T. pfluegeri. We discuss the taxonomic status of these species groups in light of our and other data, molecular and morphological.

The behavioural and genetic mating system of the sand tiger shark, Carcharias taurus, an intrauterine cannibal

Sand tiger sharks (Carcharias taurus) have an unusual mode of reproduction, whereby the first embryos in each of the paired uteri to reach a certain size (‘hatchlings’) consume all of their smaller siblings during gestation (‘embryonic cannibalism’ or EC). If females commonly mate with multiple males (‘behavioural polyandry’) then litters could initially have multiple sires. It is possible, however, that EC could exclude of all but one of these sires from producing offspring thus influencing the species genetic mating system (‘genetic monogamy’). Here, we use microsatellite DNA profiling of mothers and their litters (n = 15, from two to nine embryos per litter) to quantify the frequency of behavioural and genetic polyandry in this system. We conservatively estimate that nine of the females we examined (60%) were behaviourally polyandrous. The genetic mating system was characterized by assessing sibling relationships between hatchlings and revealed only 40 per cent genetic polyandry (i.e. hatchlings were full siblings in 60% of litters). The discrepancy stemmed from three females that were initially fertilized by multiple males but only produced hatchlings with one of them. This reveals that males can be excluded even after fertilizing ova and that some instances of genetic monogamy in this population arise from the reduction in litter size by EC. More research is needed on how cryptic post-copulatory and post-zygotic processes contribute to determining paternity and bridging the behavioural and genetic mating systems of viviparous species.

DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern

Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or – in two cases – to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories ‘Endangered’ and ‘Vulnerable’, raising further concerns about the impacts of this trade on the sustainability of these low productivity species.

The Complete Mitochondrial Genome of the Basking Shark Cetorhinus maximus (Chondrichthyes, Cetorhinidae)

Abstract The basking shark (Cetorhinus maximus) is the world’s second largest fish and the subject of strong conservation concern. Minimal genetic assessment exists for this globally distributed but regionally endangered species. We describe the complete mitochondrial genome sequence of C. maximus, obtained via polymerase chain reaction-based Sanger sequencing. The total length of the mitogenome is 16,670 bp and consists of 2 rRNAs, 22 tRNAs and 13 protein-coding genes. The base composition has an A + T bias (63.6%), as is often seen in other sharks. Gene order is equivalent to that found in most vertebrates.

Comparative population genetics and evolutionary history of two commonly misidentified billfishes of management and conservation concern

BackgroundMisidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the roundscale spearfish, utilizing nuclear microsatellite and mitochondrial DNA sequence markers. Furthermore, we re-evaluated existing white marlin mitochondrial genetic data and present our findings in a comparative context to the roundscale spearfish.ResultsMicrosatellite and mitochondrial (control region) DNA markers provided mixed evidence for roundscale spearfish population differentiation between the western north and south Atlantic regions, depending on marker-statistical analysis combination used. Mitochondrial DNA analyses provided strong signals of historical population growth for both white marlin and roundscale spearfish, but higher genetic diversity and effective female population size (1.5-1.9X) for white marlin.ConclusionsThe equivocal indications of roundscale spearfish population structure, combined with a smaller effective female population size compared to the white marlin, already a species of concern, suggests that a species-specific and precautionary management strategy recognizing two management units is prudent for this newly validated billfish.

Development and characterization of 11 novel microsatellite loci for the roundscale spearfish Tetrapturus georgii and their cross-species amplification among other istiophorid species.

Eleven novel polymorphic microsatellite loci were developed and characterized for the recently validated roundscale spearfish Tetrapturus georgii. Characterization of these markers, based on 35 roundscale spearfish from the western North Atlantic, revealed two to 21 alleles per locus with an average expected heterozygosity (H(E) ) of 0·09-0·94, and all loci conformed to Hardy-Weinberg expectations. Cross-amplification of these 11 loci against all other eight known istiophorid species indicates promising prospects for the utility of these markers for istiophorids in general.

Development and characterization of fifteen novel microsatellite loci for the Nassau grouper (Epinephelus striatus) and their utility for cross-amplification on a suite of closely related species

The Nassau grouper (Epinephelus striatus), a severely overexploited and endangered coral reef fish in the Western Atlantic, is in urgent need of conservation and management measures. We report the development and characterization of 15 polymorphic, mostly tetranucleotide microsatellite loci based on 40 Nassau grouper samples collected from two Caribbean spawning aggregations. The number of alleles per locus and expected heterozygosities ranged from 4 to 19 and 0.40 to 0.92, respectively. We also demonstrate the cross-amplification utility of these microsatellites for genetic studies of five other grouper species of conservation interest.

Forecasting Lionfish Sources and Sinks in the Atlantic: Are Gulf of Mexico Reef Fisheries at Risk?

AbstractInvasive lionfish (Pterois volitans/miles complex) now permeate the entire tropical western Atlantic, Caribbean Sea, and Gulf of Mexico, but lionfish abundance has been measured only in select locations in the field. Despite its rapid range expansion, a comprehensive meta-population analysis of lionfish ‘sources’ and ‘sinks’ and consequentially the invader’s potential abundance and impacts on economically important, sympatric reef fishes have not been assessed. These data are urgently needed to spatially direct control efforts and to plan for and perhaps mitigate lionfish-caused damage. Here, we use a biophysical computer model to: (1) forecast larval lionfish sources and sinks that are also delineated as low to high lionfish ‘density zones’ throughout their invaded range, and (2) assess the potential vulnerability of five grouper and snapper species—Epinephelus morio, Mycteroperca microlepis, Epinephelus flavolimbatus, Lutjanus campechanus, and Rhomboplites aurorubens—to lionfish within these density zones in the Gulf of Mexico. Our results suggest that the west Florida shelf and nearshore waters of Texas, USA, and Guyana, South America, function both as lionfish sources and sinks and should be a high priority for targeted lionfish control. Furthermore, of the five groupers and snappers studied, the high fishery value E. morio (red grouper) is the Gulf of Mexico species most at risk from lionfish. Lacking a comprehensive lionfish control policy, these risk exposure data inform managers where removals should be focused and demonstrate the risk to five sympatric native groupers and snappers in the Gulf of Mexico that may be susceptible to dense lionfish aggregations, should control efforts fail.

A DNA tool for the identification of heavily exploited Atlantic billfishes

Due to the morphological similarities among species, the International Commission for the Conservation of the Atlantic Tunas has recommended the use of diagnostic molecular tools to allow for robust species-level identifications of the billfishes. In this study, a protocol for the molecular identification of all six Atlantic billfishes was developed utilizing a PCR–RFLP approach, targeting the mitochondrial gene cytochrome c oxidase subunit 1. A survey of 28 restriction endonucleases identified two enzymes (TaqI and HaeIII) that produced species-specific banding patterns sufficient to distinguish species. The protocol was validated against billfishes captured across their Atlantic distributions.