In an effort to provide a framework for the accurate identification of elasmobranchs, driven in large part by the needs of parasitological studies, a comprehensive survey of DNA sequences derived from the mitochondrial NADH2 gene was conducted for elasmobranchs collected from around the world. Analysis was based on sequences derived from 4283 specimens representing an estimated 574 (of ∼1221) species (305 sharks, 269 batoids), each represented by 1 to 176 specimens, in 157 (of 193 described) elasmobranch genera in 56 (of 57 described) families of elasmobranchs (only Hypnidae was not represented). A total of 1921 (44.9%) of the samples were represented by vouchers and/or images available in an online host specimen database (http://elasmobranchs.tapewormdb.uconn.edu). A representative sequence for each of the 574 species identified in this survey, as well as an additional 11 sequences for problematic complexes, has been deposited in GenBank. Neighbor-joining analysis of the data revealed a substant...

A DNA Sequence–Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology

Abstract In an effort to provide a framework for the accurate identification of elasmobranchs, driven in large part by the needs of parasitological studies, a comprehensive survey of DNA sequences derived from the mitochondrial NADH2 gene was conducted for elasmobranchs collected from around the world. Analysis was based on sequences derived from 4283 specimens representing an estimated 574 (of ∼1221) species (305 sharks, 269 batoids), each represented by 1 to 176 specimens, in 157 (of 193 described) elasmobranch genera in 56 (of 57 described) families of elasmobranchs (only Hypnidae was not represented). A total of 1921 (44.9%) of the samples were represented by vouchers and/or images available in an online host specimen database (http://elasmobranchs.tapewormdb.uconn.edu). A representative sequence for each of the 574 species identified in this survey, as well as an additional 11 sequences for problematic complexes, has been deposited in GenBank. Neighbor-joining analysis of the data revealed a substantial amount of previously undocumented genetic diversity in elasmobranchs, suggesting 79 potentially new taxa (38 sharks, 41 batoids). Within-species p-distance variation in NADH2-percent sequence divergence ranged from 0 to 2.12 with a mean of 0.27; within-genus p-distance variation ranged from 0.03 to 27.01, with a mean of 10.16. These values are roughly consistent with estimates from prior studies based on barcode COI sequences for elasmobranchs and fishes. While biogeographic influences have likely shaped the diversification of the entire group, the traces left by older influences tend to be overprinted by newer ones. As a result, the most clearly interpretable influences are those associated with recently diverged taxa. Among closely related elasmobranchs, four regions appear to be of particular importance: (1) the Atlantic Ocean, (2) Arabian Sea, Persian Gulf, and Red Sea, (3) Southeast Asia, and (4) Australia. Each of these regions has a substantial proportion of taxa that are genetically distinct from their closest relatives in other regions. These results suggest that great care should be taken in establishing the identities of elasmobranch hosts in parasitological studies. Furthermore, it is likely that many existing host records require confirmation.

A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology. (Bulletin of the American Museum of Natural History, no. 367)

Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0974 +/- 0008) and nucleotide diversity (pi = 0011 +/- 0006) The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp) Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0107, P < 0001) principally between the Atlantic and Indo-Pacific populations In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish

Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus)

Here we present a review of how the study of the geographic distribution of genetic lineages (phylogeography) has helped identify management units, evolutionary significant units, cryptic species, and areas of endemism, and how this information can help efforts to achieve effective conservation of coral reefs. These studies have confirmed the major biogeographic barriers that were originally identified by tropical species distributions. Ancient separations, identified primarily with mtDNA sequence comparisons, became apparent between populations on each side of the barriers. The general lack of correlation between pelagic larval duration and genetic connectivity across barriers indicates that life history and ecology can be as influential as oceanography and geography in shaping evolutionary partitions within ocean basins. Hence, conservation strategies require a recognition of ecological hotspots, those areas where habitat heterogeneity promotes speciation, in addition to more traditional approaches based on biogeography. Finally, the emerging field of genomics will add a new dimension to phylogeography, allowing the study of genes that are pertinent to recent and ongoing differentiation, and ultimately providing higher resolution to detect evolutionary significant units that have diverged in an ecological time scale.

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Phylogeography and the conservation of coral reef fishes

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Large marine fishes typically have little population genetic structure. The exceptions are associated with sedentary behaviour, disjunct distributions, or reproductive philopatry. Scalloped hammerhead sharks (Sphyrna lewini) incorporate the contrasting traits of oceanic habitat (usually associated with high dispersal) and possible fidelity to nursery grounds (for reproductive females). To evaluate the expectations of these contrasting behaviours, we examined the global genetic structure of S. lewini based on collections (n = 271 individuals) from 20 nursery areas. A 548-bp fragment of mitochondrial DNA control region revealed 22 polymorphic sites, 24 haplotypes, and three lineages distinguished by 2.56–3.77% sequence divergence. Coalescence analyses based on a provisional molecular clock indicate an origin in the Indo-West Pacific with late Pleistocene radiations into the central Pacific (Hawaii) and eastern Pacific (Central America), as well as recent interchange between oceans via southern Africa. Population subdivisions are strong (overall ΦST = 0.749, P   10). We conclude that nursery populations linked by continuous coastline have high connectivity, but that oceanic dispersal by females is rare. Although we cannot rule out philopatry to natal nurseries, oceanic barriers appear to have a much stronger influence on the genetic architecture of this species and may indicate a mechanism for recent evolutionary radiations in the genus Sphyrna.

K. M. Duncan

Papers

Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini)