Global Genetic Connectivity and Diversity in a Shark of High Conservation Concern, the Oceanic Whitetip, Carcharhinus longimanus

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a nominally significant signal of matrilineal structure between the Indian and Pacific Ocean sharks was detected by AMOVA and pairwise tests of the ND4 gene only (pairwise ΦST = 0.051, P = 0.046; pairwise Jost’s D = 0.311, 95% CI = 0.020, 0.0614). Although significant inter-basin population structure was evident, it was associated with deep phylogeographic mixing of mitochondrial haplotypes and evidence of contemporary migration between the Western Atlantic and Indo-Pacific Oceans. I theorize that semi-permeable thermal barriers are responsible for the differentiation between the Western Atlantic and Indo-Pacific set in a framework of global phylogeographic mixing. Relatively low mtDNA genetic diversity (concatenated mtCR-ND4 nucleotide diversity π = 0.32% ± 0.17%) compared to other circumtropical elasmobranch species raises potential concern for the future genetic health of this species. Overall, significant population structure exists, at a minimum, between the Western Atlantic and Indo-Pacific Ocean, and effective management strategies must take this into consideration

Complete mitogenome sequences of smooth hammerhead sharks, Sphyrna zygaena, from the eastern and western Atlantic

We report the first mitogenome sequences of the circumglobally distributed, highly mobile, smooth hammerhead shark, Sphyrna zygaena, from the eastern and western Atlantic. Both genomes were 16,729 bp long with 13 protein-coding genes, two rRNAs, 22 tRNAs and a non-coding control region. The two Atlantic shark sequences differ from each other by 13 SNPs, and by 43 and 44 SNPs from the published mitogenome of an S. zygaena specimen from the eastern Pacific Ocean. The cross-Atlantic mitogenome sequences reported here provide a resource to assist with population genetics studies of this widely exploited species of conservation concern

Deep-sea hydrothermal vents as natural egg-case incubators at the Galapagos Rift

The discovery of deep-sea hydrothermal vents in 1977 challenged our views of ecosystem functioning and yet, the research conducted at these extreme and logistically challenging environments still continues to reveal unique biological processes. Here, we report for the first time, a unique behavior where the deep-sea skate, Bathyraja spinosissima, appears to be actively using the elevated temperature of a hydrothermal vent environment to naturally “incubate” developing egg-cases. We hypothesize that this behavior is directly targeted to accelerate embryo development time given that deep-sea skates have some of the longest egg incubation times reported for the animal kingdom. Similar egg incubating behavior, where eggs are incubated in volcanically heated nesting grounds, have been recorded in Cretaceous sauropod dinosaurs and the rare avian megapode. To our knowledge, this is the first time incubating behavior using a volcanic source is recorded for the marine environment

Topside Photography: 3rd Place

Photograph taken in Mossel Bay, South Africahttps://nsuworks.nova.edu/occ_shuttershark_2014/1015/thumbnail.jp

Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

<p>The oceanic whitetip shark, <em>Carcharhinus longimanus</em>, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with <em>F</em><sub>ST </sub>but not Φ<sub>ST</sub>) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (Φ<sub>ST</sub> = 0.051; F<sub>ST</sub> = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.</p><p>Funding provided by: Save Our Seas Foundation<br>Crossref Funder Registry ID: https://ror.org/00rvg5p23<br>Award Number: </p><p>Funding provided by: Shark Foundation/Hai Stiftung*<br>Crossref Funder Registry ID: <br>Award Number: </p><p>Funding provided by: Guy Harvey Foundation*<br>Crossref Funder Registry ID: <br>Award Number: </p><p>Oceanic whitetip shark samples were genotyped at 14 microsatellite loci including three loci from <em>Carcharhinus longimanus</em> (OCS_08, OCS_13, OCS_19) previously described by Mendes et al. (2015) and 11 loci isolated in other shark species that also cross-amplified in <em>C. longimanus</em> [Cl13, Cl15, Cl17 from <em>Carcharhinus leucas </em>(Pirog et al. 2015); Cli107 from Keeney and Heist (2003); Cpe141, Cpe334, Cpe352 from <em>Carcharhinus perezi</em> (Bernard et al. 2017); Pgla-02 from <em>Prionace glauca</em> (Fitzpatrick et al. 2011); Ct06 from <em>Carcharhinus tilstoni</em> (Ovenden et al. 2006); and A2ASY, CY92Z from <em>Prionace glauca</em> (Taguchi et al. 2013)]</p> <p>Electrophoresis of amplified microsatellite loci was performed on an Applied Biosystems 3130 Genetic Analyzer. Alleles were sized using GeneScan LIZ 600 size standard and scored using the software GeneMapper v.3.7 (Applied Biosystems Inc.).</p> <ul> <li>Bernard AM, Horn RL, Chapman DD, Feldheim KA, Garla RC, Brooks EJ, Gore MA, Shivji MS (2017) Genetic connectivity of a coral reef ecosystem predator: the population genetic structure and evolutionary history of the Caribbean reef shark (<em>Carcharhinus perezi</em>). J Biogeogr 44:2488-2500. <a href="https://doi.org/10.1111/jbi.13062">https://doi.org/10.1111/jbi.13062</a> </li> <li>Fitzpatrick S, Shivji MS, Chapman DD, Prodöhl PA (2011) Development and characterization of 10 polymorphic microsatellite loci for the blue shark, <em>Prionace glauca</em>, and their cross shark-species amplification. Conserv Genet Resour 3:523-527. <u><a href="https://doi.org/10.1007/s12686-011-9395-6">https://doi.org/10.1007/s12686-011-9395-6</a></u> </li> <li>Keeney DB, Heist EJ (2003) Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharks. Mol Ecol Notes 3:501-504. <u><a href="https://doi.org/10.1046/j.1471-8286.2003.00492.x">https://doi.org/10.1046/j.1471-8286.2003.00492.x</a></u> </li> <li>Mendes NJ, Cruz VP, Mendonça FF, Pardo BG, Coelho R, Ashikaga FY, Camargo SM, Martínez P, Oliveira C, Santos MN, Foresti F (2015) Microsatellite loci in the oceanic whitetip shark and cross-species amplification using pyrosequencing technology. Conserv Genet Resour 7:585-589. <u><a href="https://doi.org/10.1007/s12686-015-0435-5">https://doi.org/10.1007/s12686-015-0435-5</a></u> </li> <li>Ovenden JR, Street R, Broderick D (2006) New microsatellite loci for Carcharhinid sharks (<em>Carcharhinus tilstoni </em>and <em>C. sorrah</em>) and their cross-amplification in other shark species. Mol Ecol Notes 6:415-418. <u><a href="https://doi.org/10.1111/j.1471-8286.2005.01254.x">https://doi.org/10.1111/j.1471-8286.2005.01254.x</a></u> </li> <li>Pirog A, Blaison A, Jaquemet S, Soria M, Magalon H (2015) Isolation and characterization of 20 microsatellite markers from <em>Carcharhinus leucas</em> (bull shark) and cross-amplification in <em>Galeocerdo cuvier</em> (tiger shark), <em>Carcharhinus obscurus</em> (dusky shark), and <em>Carcharhinus plumbeus</em> (sandbar shark). Conserv Genet Resour 7:121-124. <u><a href="https://doi.org/10.1007/s12686-014-0308-3">https://doi.org/10.1007/s12686-014-0308-3</a></u> </li> <li>Taguchi M, Shigenobu Y, Ohkubo M, Yanagimoto T, Sugaya T, Nakamura Y, Saitoh K, Yokawa K (2013) Characterization of 12 polymorphic microsatellite DNA loci in the blue shark, <em>Prionace glauca</em>, isolated by next generation sequencing approach. Conserv Genet Resour 5:117-119. <u>https://doi.org/10.1007/s12686-012-9746-y</u> </li> </ul&gt

Population genomics of the overfished shortfin mako shark in the Atlantic Ocean

The shortfin mako shark (Isurus oxyrinchus) is a large, globally distributed, oceanic species of urgent management and conservation concern. It is a target of commercial and recreational fishers, caught in large numbers worldwide as bycatch by pelagic longline fishing vessels, and makes up a significant portion of the mostly unregulated international shark fin trade. The International Union for Conservation of Nature (IUCN) lists the shortfin mako as globally ‘Vulnerable’ to extinction due to population declines caused by heavy fishing pressure. Furthermore, very recent studies have shown that previous Atlantic-wide stock assessments for this species have dramatically underestimated fishing mortality, underscoring the urgent need for accurate population dynamics data to improve stock assessments for this shark. To date, very little is known about the population genetic structure of the shortfin mako in the Atlantic. The few previous assessments conducted on shortfin mako population genetic dynamics have relied on small sample sizes and low resolution genetic markers, resulting in an unclear view of the true population status of this species and thus hindering effective management and conservation decision making. Herein, we propose a high-resolution genomics approach to resolve the detailed population dynamics (population structure, genetic diversity, and evolutionary history) of shortfin mako sharks throughout Atlantic waters. All shark samples required for this project are already available in our lab. We will use two complementary genomics approaches to achieve our study goal: First, we will use next generation sequencing in association with a high-throughput genotyping protocol called Restriction site Associated DNA Sequencing (RAD-Seq) to survey the genetic variation distributed across the entire shortfin mako nuclear genome. The power of RAD-Seq is that this method is able to identify thousands of variable nucleotide markers in a single individual, and can specifically target and survey the same markers in all other individuals tested to elucidate population genetic relationships. Second, we will obtain and analyze complete mitochondrial genome sequences to acquire a high resolution view of the matrilineal population genetic connectivity of shortfin makos across the Atlantic. This combination of nuclear and mitochondrial genomics approaches will provide an unprecedented level of statistical power to identify even subtle population differences and resolve the true state of shortfin mako population dynamics. The results of this research will be of direct value to international fishery and environmental agencies charged with the Atlantic-wide management and conservation of this vulnerable shark species. This project will also provide two NSU students with training in conducting advanced-level population genomics research

The Complete Mitochondrial Genome of the Endangered Great Hammerhead Shark, Sphyrna mokarran

We present the first mitochondrial genome sequence of the great hammerhead shark, Sphyrna mokarran. This species is of considerable conservation concern throughout its global distribution, and currently listed as Endangered on the IUCN Red List. The mitochondrial genome is 16,719 bp in length with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The gene arrangement is congruent with other shark and most vertebrate species. This S. mokarran mitogenome provides a genomic resource for assisting with population studies and conservation efforts for this highly depleted species

Global-Scale Genetic Population Structure and Diversity in the Oceanic Whitetip Shark, Carcharhinus longimanus

The oceanic whitetip, Carcharhinus longimanus, is a circumtropical, pelagic shark of high conservation concern (IUCN Red List: Critically Endangered in the W North and W Central Atlantic and Vulnerable globally). We present an updated assessment of the global population structure, genetic diversity, and demographic history of this shark based on analysis of two mitochondrial genome regions (whole control region and partial NADH dehydrogenase subunit 4 (ND4) gene) and nine nuclear microsatellite loci. No population differentiation was detected between the north and south Atlantic. However, significant structure was consistently detected between the Western Atlantic and Indo-Pacific Oceans across both mitochondrial and nuclear markers. This population structure was coupled with deep geographic mitochondrial haplotype mixing and evidence of contemporary migration between the Western Atlantic and Indo-Pacific Oceans. We theorize that semi-permeable thermal barriers are responsible for the differentiation between the Western Atlantic and Indo-Pacific. Additionally, a signal of matrilineal structure between the Indian and the Pacific Oceans was detected with AMOVA and pairwise analyses of the ND4 gene (pairwise ΦST = 0.051, P = 0.046; pairwise Jost\u27s D = 0.311, 95% CI = 0.020, 0.061). Relatively low mtDNA genetic diversity (concatenated mtCR-ND4: π = 0.32% ± 0.17%) compared to other globally distributed elasmobranch species raises concern for the future genetic health of these populations. Overall, despite the global distribution and high mobility of C. longimanus, significant population structure exists between the Western Atlantic and Indo-Pacific Oceans, and effective management strategies must take this into consideration

The Genetic Connectivity of a Euryhaline Elasmobranch, the Atlantic Stingray (Dasyatis sabina)

Identifying the genetic connectivity of elasmobranchs inhabiting coastal waters remains an important global priority, as these species are particularly susceptible to human mediated impacts and declines given their close proximity to highly populated areas. The Atlantic stingray (Dasyatis sabina), a small, coastal species whose range spans the western North Atlantic (Florida to Chesapeake Bay) and Gulf of Mexico, is one of the few elasmobranchs capable of occupying both estuarine and freshwater habitats. Within Florida waters, a putative ‘resident’ population inhabits the freshwater St. Johns River System (SJRS); however, the extent of this population’s connectivity to the remainder of its distribution remains unknown. To examine the genetic connectivity of the Atlantic stingray across its southern US distribution, including the SJRS, a total of 312 individuals from 11 sampling locations were genotyped at nine species-specific microsatellite loci. Population- and individual-level analyses identified high levels of genetic population structure among collections, with coastal populations within the Gulf of Mexico showing high genetic structure (FST = 0.011 – 0.034; P \u3c0.05) and a signal of isolation by distance (R2 = 0.957; P = 0.041). Interestingly, individual-based analyses showed that freshwater SJRS animals were differentiated from other locations, suggesting that these individuals may truly represent a ‘resident’ freshwater population. The presence of high genetic population structure, coupled with what may be locally adapted populations, suggests that care must be taken to conserve this species, as the extinction of even a single population may result in the irreversible loss of genetic diversity and adaptive potential

Global Population Genomics of the Endangered Great Hammerhead Shark, Sphyrna mokarran

The great hammerhead shark, Sphyrna mokarran, is a circumglobal coastal-pelagic species of high conservation concern (IUCN Red List: Endangered). Our earlier analysis of mitochondrial control region sequences in globally distributed animals uncovered two highly genetically divergent matrilines in this species (Testerman et al. In prep.). Here we present findings of a genomic level assessment of global population dynamics of the great hammerhead shark based on analyses of nuclear single nucleotide polymorphisms (SNPs) and whole mitochondrial genome sequences (17,719 bp). Analysis of 2330 neutral SNP loci with Discriminant Analysis of Principal Components (DAPC) and the Bayesian clustering program STRUCTURE reveals three geographic meta-populations (Western Atlantic, North Indian Ocean, and Australia). Pairwise comparisons (FST, G’’ST, and Jost’s D) further reveals highly structured sub-populations within these regions including evidence of differentiation between Western Australia and Eastern Australia individuals, which was previously undetected. Analysis of molecular variance (AMOVA, FST) of whole mitochondrial genomes supports the three meta-populations, with a lesser degree but still significant level of sub-population structuring. A median joining haplotype network additionally supports the previously detected divergent matrilines, separated by an estimated 99 mutational steps. Preliminary demographic analyses support the hypothesis of an Indo-West Pacific origin followed by colonization of the Indian Ocean and subsequently the Atlantic