Multiple paternity in two populations of finetooth sharks (Carcharhinus isodon) with varying reproductive periodicity.

The mechanisms underlying polyandry and female mate choice in certain taxonomic groups remain widely debated. In elasmobranchs, several species have shown varying rates of polyandry based on genetic studies of multiple paternity (MP). We investigated MP in the finetooth shark, Carcharhinus isodon, in order to directly test the encounter rate hypothesis (ERH), which predicts that MP is a result of the frequency of encounters between mature conspecifics during the breeding season, and should therefore increase when more time is available for copulation and sperm storage. Female finetooth sharks in the northern Gulf of Mexico (GoM) have been found to reproduce with both annual periodicity and biennial periodicity, while finetooth sharks from the northwestern Atlantic Ocean have only been found to reproduce biennially, allowing us to compare mating opportunity to frequency of MP. Our results show high rates of MP with no significant difference in frequency between females in the GoM (83.0%) and Atlantic (88.2%, p = .8718) and varying but nonsignificant rates of MP between females in the GoM reproducing annually (93.0%) and biennially (76.6%, p = .2760). While the ERH is not supported by this study, it remains possible that reproductive periodicity and other physiological factors play a role in determining rates of MP in elasmobranchs, with potential benefits to individuals and populations.

Swimming against the flow-Environmental DNA can detect bull sharks (Carcharhinus leucas) across a dynamic deltaic interface.

Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly disparate systems. As upper trophic level predators, bull sharks (Carcharhinus leucas) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama, suggest that bull sharks extensively use the northern portions of the bay, an estuarine-freshwater interface known as the Mobile-Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 × 1 L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile-Tensaw Delta, and ten sites throughout the Mobile-Tombigbee and Tensaw-Alabama Rivers. Water samples were vacuum-filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species-specific primers and an internal probe to amplify a 237-base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less-urbanized, riverine habitats up to 120 km upriver during Alabama's dry summer season.

Genetic evidence supports a range extension for the Brazilian cownose ray Rhinoptera brasiliensis in the western North Atlantic.

We report 24 new records of the Brazilian cownose ray Rhinoptera brasiliensis outside its accepted geographic range. Sequencing of a 442-base pair portion of the mitochondrial NADH dehydrogenase subunit 2 gene for 282 Rhinoptera samples revealed eight records off the east coast of the USA and 16 from the eastern Gulf of Mexico. Both sexes of all life stages were documented in all seasons over multiple years in the Indian River and Lake Worth lagoons, Florida, indicating that their range extends further in the western North Atlantic than previously described.

Marine environmental DNA: Approaches, applications, and opportunities.

Environmental DNA (eDNA) is increasingly being used to document species distributions and habitat use in marine systems, with much of the recent effort focused on leveraging advances in next-generation DNA sequencing to assess and track biodiversity across taxonomic groups. Environmental DNA offers a number of important advantages over traditional survey techniques, including non-invasive sampling, sampling where traditional approaches are impractical or inefficient (e.g. deep oceans), reduced cost, and increased detection sensitivity. However, eDNA applications are currently limited because of an insufficient understanding of the influence of sample source, analytical approach, and marker type on eDNA detections. Because approaches vary considerably among eDNA studies, we present a summary of the current state of the field and emerging best practices. The impact of observed variation in rates of eDNA production, persistence, and transport are also discussed and future research needs are highlighted with the goal of expanding eDNA applications, including the development of statistical models to improve the predictability of eDNA detection and quantification.

Description of a new deep-water dogfish shark from Hawaii, with comments on the Squalusmitsukurii species complex in the West Pacific.

Dogfish sharks of the genus Squalus are small, deep-water sharks with a slow rate of molecular evolution that has led to their designation as a series of species complexes, with low between-species diversity relative to other taxa. The largest of these complexes is named for the Shortspine spurdog (Squalusmitsukurii Jordan & Snyder), a medium-sized dogfish shark common to warm upper slope and seamount habitats, with a putative circumglobal distribution that has come under investigation recently due to geographic variation in morphology and genetic diversity. The Hawaiian population of Squalusmitsukurii was examined using both morphological and molecular analyses, putting this group in an evolutionary context with animals from the type population in Japan and closely-related congeners. External morphology differs significantly between the Hawaiian and Japanese S.mitsukurii, especially in dorsal fin size and relative interdorsal length, and molecular analysis of 1,311 base pairs of the mitochondrial genes ND2 and COI show significant, species-level divergence on par with other taxonomic studies of this genus. The dogfish shark in Hawaii represents a new species in the genus, and the name Squalushawaiiensis, the Hawaiian spurdog, is designated after the type location.

Squalus clarkae sp. nov., a new dogfish shark from the Northwest Atlantic and Gulf of Mexico, with comments on the Squalus mitsukurii species complex.

Sharks of the genus Squalus have slow reproductive rates coupled with low genetic diversity, as is typical of deep-water sharks, making this group slow to rebound from depletion due to overfishing. The number of species within Squalus has been expanding recently due to increased attention on taxonomic revision, and a growing research focus on little-known deep-water sharks in general. Here we use genetics and morphology to describe a new species of dogfish shark, Squalus clarkae sp. nov. from the Gulf of Mexico (GoM) which replaces Squalus mitsukurii in this region, and place it in the context of congeners from the Atlantic and elsewhere. Previously, S. clarkae sp. nov. was considered a part of the Squalus mitsukurii species complex, a group of closely related but distinct species. We sequenced the mitochondrial cytochrome oxidase I and the NADH Dehydrogenase II gene of S. mitsukurii from the type location in Japan, S. clarkae sp. nov. from the GoM, as well as three closely related species (S. cubensis, S. blainville, and S. megalops) and S. cf. mitsukurii from Brazil. Squalus clarkae sp. nov. is genetically distinct from other species with significant statistical support (>98.6% bootstrap support/posterior probability), and 2.8% divergent from S. mitsukurii in the type location of Japan. Morphological estimates also revealed differences between S. clarkae sp. nov., S. mitsukurii, and other Atlantic Squalus species, with S. clarkae sp. nov. exhibiting a longer body, smaller interorbital space, shorter caudal fin, and a differently-proportioned first dorsal fin. In general, dogfish sharks in the Atlantic and GoM are characterized by similar but distinct morphology, significant genetic variation, and small species ranges.

Review of Current Conservation Genetic Analyses of Northeast Pacific Sharks.

Conservation genetics is an applied science that utilizes molecular tools to help solve problems in species conservation and management. It is an interdisciplinary specialty in which scientists apply the study of genetics in conjunction with traditional ecological fieldwork and other techniques to explore molecular variation, population boundaries, and evolutionary relationships with the goal of enabling resource managers to better protect biodiversity and identify unique populations. Several shark species in the northeast Pacific (NEP) have been studied using conservation genetics techniques, which are discussed here. The primary methods employed to study population genetics of sharks have historically been nuclear microsatellites and mitochondrial (mt) DNA. These markers have been used to assess genetic diversity, mating systems, parentage, relatedness, and genetically distinct populations to inform management decisions. Novel approaches in conservation genetics, including next-generation DNA and RNA sequencing, environmental DNA (eDNA), and epigenetics are just beginning to be applied to elasmobranch evolution, physiology, and ecology. Here, we review the methods and results of past studies, explore future directions for shark conservation genetics, and discuss the implications of molecular research and techniques for the long-term management of shark populations in the NEP.

Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini).

BACKGROUND: The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA) markers demonstrated strong genetic partitioning overall (global Φ(ST) = 0.749) and significant population separations across oceans and between discontinuous continental coastlines. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed the same global range with increased sample coverage (N = 403) and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST) = 0.035) over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST) = 0.749). Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. CONCLUSIONS/SIGNIFICANCE: These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

Is the Great Barracuda (Sphyraena barracuda) a reef fish or a pelagic fish? The phylogeographic perspective.

Current taxonomy indicates a single global species of the Great Barracuda (Sphyraena barracuda) despite differences in color and behavior between Atlantic and Pacific forms. To investigate these differences and qualify the dispersal characteristics of this unique coastal- pelagic teleost (bony fish), we conducted a global phylogeographic survey of 246 specimens from thirteen sampling locations using a 629-base pair fragment of mtDNA cytochrome b. Data indicate high overall gene flow in the Indo-Pacific over large distances (>16,500 km) bridging several biogeographic barriers. The West Atlantic population contains an mtDNA lineage that is divergent from the Indo-Pacific (d = 1.9%), while the East Atlantic (N = 23) has two mutations (d = 0.6%) apart from the Indo-Pacific. While we cannot rule out distinct evolutionary partitions among ocean basins based on behavior, coloration, and near-monophyly between Atlantic and Indo-Pacific subpopulations, more investigation is required before taxonomic status is revised. Overall, the pattern of high global dispersal and connectivity in S. barracuda more closely resembles those reported for large oceanic predators than reef-associated teleosts.

Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago.

Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.

New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini.

We isolated 15 microsatellite markers for the scalloped hammerhead shark, Sphyrna lewini. Loci were tested on 80 specimens of S. lewini from four Eastern Pacific samples. The number of alleles per locus ranged from 6 to 31 (mean = 14). Observed and expected levels of heterozygosity per locus ranged from 0.39 to 0.91 (mean = 0.70) and from 0.54 to 0.90 (mean = 0.76), respectively. No pairs of loci were in gametic disequilibrium after Bonferroni correction of α. One locus showed significantly lower heterozygosity than expected under Hardy-Weinberg proportions in two populations, possibly caused by null alleles.