Molecular research on the systematically challenging smoothhound shark genus Mustelus: a synthesis of the past 30 years

The species-rich genus Mustelus (smoothhounds) of the shark family Triakidae is one of the most bio-economically important groups of elasmobranchs in the world’s oceans. Despite the commercial value of Mustelus, the systematics of the group remains largely unresolved and there is no global review or synthesis of knowledge about the conservation status and conservation genetics of smoothhounds across all oceanic regions. Here, we analysed published studies as well as grey literature to gain insight into the biogeographic, ecological and behavioural factors that shape genetic diversity in smoothhounds, and we identify critical knowledge gaps. From a series of molecular phylogenetic studies it can be inferred that the genus Mustelus is paraphyletic and that the aplacental species evolved secondarily from the placental species of the genus. The increasing availability of genetic data aids in disentangling systematic issues, such that more meaningful morphological characters can be chosen for use in practical field-identification keys for co-occurring smoothhounds. An integrative taxonomic approach to the genus Mustelus may offer the best chance of recording and protecting the biodiversity of these sharks. Furthermore, it is evident that different smoothhound species exhibit unique gene-flow patterns, suggesting varying rates within species and hence that species-level conservation approaches would be most appropriate. Molecular studies have advanced our understanding of smoothhound biology (including reproductive traits), ecology and evolution. While many knowledge gaps remain, a crucial lesson from this review is that, when doing assessments on a molecular level, it is important to place genetic results in a broader context, by assimilating biological and ecological data, if definitive conclusions are to be drawn.Keywords: conservation genetics, endemism, genetic identification, integrative taxonomy, literature review, molecular ecology, multiple paternity, population structure, systematics, Triakida

Molecular phylogeny of South African abalone, its origin and evolution as revealed by two genes

The marine family Haliotidae (Mollusca: Gastropoda) includes approximately 56 extant abalone species found worldwide. None of these species are globally distributed while four areas of endemism (temperate Australia, South Africa, New Zealand and North Pacific) have been recognized. Phylogenetic relationships of 18 abalone species including five South African species were reconstructed using a combined data set containing sequence data of the mitochondrial NADH-dehydrogenase subunit 1 (ND1) gene and the nuclear hemocyanin gene. The molecular topologies confirmed former findings of two major abalone lineages with Northern and Southern Pacific distribution within the Haliotidae family. The phylogeny revealed all five South African species as a monophyletic group with a sister relationship to the Australian endemics clade. It further suggested a relatively recent radiation of the South African species and places it within the same evolutionary context as the Mediterranean/Atlantic and Australasian clades. Molecular phylogeny also revealed a split within the South African group as well as further speciation within one of the two subclades. Possible place of origin for South African abalone are discussed and ecological specialization, e.g. differential adaptation to environmental conditions, is proposed as the most likely scenario describing divergence within the South African clade. © 2012 Copyright Taylor and Francis Group, LLC

Evidence for multiple paternity and confirmation of an Indo-Pacific origin of blacktip shark Carcharhinus limbatus occurring in South Africa

The blacktip shark Carcharhinus limbatus is a cosmopolitan species found in warm-temperate, subtropical and tropical waters around the world. The research here aimed to assess whether multiple paternity exists in South African C. limbatus and to confirm phylogeographic patterns previously observed within the species. A minimum and maximum frequency of 50% and 71% multiple paternity, respectively, were observed in 14 litters genotyped with five microsatellite markers. Based on the mitochondrial control region, relatively high nucleotide and haplotype diversity characterised the South African sampling population, and pairwise φST values indicated that it significantly differed from the populations of the Pacific and the western Atlantic oceans. The haplotype network showed thatthe South African samples were grouped closely with the Australian, Indo-Pacific and West African C. limbatus samples, which is suggestive of an Indo-Pacific origin for this population. This study is the first to report multiple paternity in this species. Furthermore, the results reveal that C. limbatus from South Africa is genetically diverse and phylogeographically distinct from most other C. limbatus populations.Keywords: elasmobranchs, genetic divergence, haplotypes, microsatellites, mitochondrial DNA, polyandry, phylogeographic analysi

Genomic resources for the spotted ragged-tooth shark Carcharias taurus

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.Keywords: genotype, grey nurse shark, Illumina next-generation sequencing, microsatellites, mitogenome, primer design, sand tiger shar

A population genetic analysis of abalone domestication events in South Africa: Implications for the management of the abalone resource

ArticleAbalone culture is South Africa's largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective breeding vs. ranching; whilst conserving the genetic integrity of wild populations remains a national imperative. The present study found no significant decrease in genetic diversity between wild and cultured populations as based on heterozygosity and allelic content of genomic- and EST-microsatellite loci. However, estimates for pairwise genotypic differentiation, F st, AMOVA and Factorial correspondence analysis suggest the genetic heterogeneity of cultured populations and their significant differentiation from the wild progenitor populations. As expected, the cultured population showed reduced effective population sizes, but relatedness remained low. It is postulated that both neutral and selective evolutionary forces are responsible for the observed patterns of genetic variability within and amongst populations. The implications of the results are discussed in terms of broad managerial objectives for the South African abalone and continued monitoring is advised. © 2012 Elsevier B.V

Application of DNA mini-barcoding reveals illegal trade in endangered shark products in southern Africa

In recent decades, a combination of increasing demand and economic globalisation has created a global market for elasmobranch products, especially the highly prized shark fins for Asian markets. Morphological species identification, as well as traditional cytochrome c oxidase subunit I (COI) barcoding of shark fins and other products, become challenging when in a processed state (such as dried or bleached shark fins). Here a mini-barcoding multiplex assay was applied to determine the species of origin in case studies from southern Africa involving confiscated shark fins in different states of processing. This highlights that the illegal shark fin trade in southern Africa to a large extent comprises threatened species. Matching of sequences of the confiscated fins against public databases revealed several threatened species, including the CITES-listed species Carcharodon carcharias, Carcharhinus longimanus, Isurus oxyrinchus, Rhynchobatus djiddensis and Sphyrna lewini. The findings highlight the need for improved trade monitoring, such as to eliminate illegal trade in shark fins, which can in part be achieved through more widespread genetic sampling of internationally traded products. However, a major limitation to DNA barcoding in general lies in the lack of curated voucher specimens available on public databases. To facilitate the application of molecular methods in a more comprehensive evaluation of elasmobranch trade regionally, a concerted effort to create reliable curated sequence data is recommended