Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south-eastern U.S.A. and Caribbean

Mitochondrial DNA patterns describe the evolutionary history of the bonnethead shark Sphyrna tiburo (Linneus 1758) complex in the western Atlantic Ocean

The apparent lack of physical barriers in the marine realm has created the conception that many groups have a constant gene flow. However, changes in ocean circulation patterns, glacial cycles, temperature, and salinity gradients are responsible for vicariant events in many fish species, including sharks. The bonnethead shark, Sphyrna tiburo, is an endangered small coastal shark species. Although considerable efforts have recently been undertaken, little remains known about the possible biogeographic scenario that can explain its actual distribution within the western Atlantic (WA). Here, we used 599 mitochondrial sequences to assess the phylogeographic structure and implement Bayesian phylogenetic analyses to obtain divergence times and reconstruct the ancestral geographic range. This allowed us to infer processes responsible for the diversification of S. tiburo into major divergent lineages. Our results indicated that S. tiburo in the WA represents three independent lineages, with Brazilian samples differentiated into a distinct genetic cluster. The posterior probability of ancestral range analysis indicated that the species likely originated in the northern region (Carolina Province and the southern Gulf of Mexico), where it colonized southward through the uplifting of the Central American Isthmus (CAI). The Northern and Caribbean genetic clusters appear to have arisen from the intensification of the Loop Current, which currently flows northward passing the Yucatan Peninsula, Gulf of Mexico, and east Florida. Following initial colonization, the Northeastern Brazil group differentiated from the Caribbean region due to the sediment and freshwater discharge of the Amazon-Orinoco Plume. Thus, the evolutionary history of the S. tiburo complex can be explained by a combination of dispersal and vicariance events that occurred over the last ~5 million years (MY). We established and confirmed the species and population limits, demonstrating that the Amazon-Orinoco Plume constitutes a significant dispersal barrier for coastal sharks. Finally, we discuss some recommendations for the conservation of the bonnethead shark.

Sphyrna alleni sp. nov., a new hammerhead shark (Carcharhiniformes, Sphyrnidae) from the Caribbean and the Southwest Atlantic

Hammerhead sharks (Family Sphyrnidae) comprise a monophyletic Miocene radiation of carcharhiniform sharks characterized by their laterally expanded and dorsoventrally compressed head ('cephalofoil'). The bonnethead shark (Sphyrna tiburo) is currently described as a single amphi-American hammerhead species composed of the subspecies Sphyrna tiburo tiburo in the Western Atlantic Ocean (WA) and S. tiburo vespertina in the Eastern Pacific Ocean (EP). Variation in mitochondrial DNA and cephalofoil shape suggest a species complex, with S. tiburo occurring in the U.S., Mexico, and Bahamas; S. aff. tiburo occurring from Belize to Brazil; and S. vespertina occurring in the EP. Morphometric, meristic, and genetic variation was used to resolve the bonnethead shark complex in the Western Atlantic. Twenty-three specimens (12 S. aff. tiburo from Belize and 11 S. tiburo from U.S.) were subject to sixty-one morphometric measurements and three meristic characters (counts of the number of precaudal vertebrae, lower and upper rows of functional teeth). An allometric formula was used to standardize any effect caused by differences in size of the individuals and data were analyzed with univariate and multivariate statistics. Sphyrna aff. tiburo and S. tiburo have non-overlapping vertebral counts (80-83 and 71-74 respectively) but no morphometric differences were detected. Although not captured in morphometric analysis, the cephalofoil of S. aff. tiburo has a more pointed anterior margin than S. tiburo that together with lobule shaped posterior margins gives the cephalofoil a distinctive shovel-shaped appearance. Concatenated mitochondrial sequences and 12 nuclear microsatellite markers clearly separated S. aff. tiburo and S. tiburo. We conclude that this complex comprises two species in the Western Atlantic, S. tiburo and S. alleni sp. nov., and we provide a description of the latter, which is distinguished by precaudal vertebral counts (80-83), a shovel-shaped cephalofoil with rounded posterior margins, and robust differences in mitochondrial and nuclear genetic markers. We suggest nuclear genetic and meristic examination of EP bonnetheads is needed to update the taxonomical status and redescribe S. vespertina.

Evidence for gene flow from the Gulf of Mexico to the Atlantic Ocean in bonnethead sharks (Sphyrna tiburo)

Gene flow is important for maintaining the genetic diversity required for adaptation to environmental disturbances, though gene flow may be limited by site fidelity in small coastal sharks. Bonnethead sharks (Sphyrna tiburo)-a small coastal hammerhead species-demonstrate site fidelity, as females are philopatric while males migrate to mediate gene flow. Consequently, bonnetheads demonstrate population divergence with distance, and Atlantic populations are genetically distinct from those of the Gulf of Mexico. Indeed, Florida forms a vicariant zone between these two bodies of water for many marine species, including some sharks. However, while bonnetheads are expected to have limited dispersal, the extent and rate of bonnethead migration remain uncertain. Thus, we aimed to determine their dispersal capacity by evaluating connectivity between disparate populations from the Gulf of Mexico and Atlantic Ocean. Using 10,733 SNPs derived from 2bRAD sequences, we evaluated genetic connectivity between Tampa Bay on the Gulf Coast of Florida and Biscayne Bay on the Atlantic coast of Florida. While standard analyses of genetic structure revealed slight but significant differentiation between Tampa Bay and Biscayne Bay populations, demographic history inference based on the site frequency spectrum favored a model without divergence. However, we also estimate that if population divergence occurred, it would have been recent (between 1500 and 4500 years ago), with continuous unidirectional gene flow from Tampa Bay to Biscayne Bay. Our findings support the hypothesis that bonnetheads can migrate over relatively large distances (>300 miles) to find mates. Together, these results provide optimism that under proper management, a small-bodied globally endangered shark can undergo long migrations to sustain genetic diversity.

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Phylogeography and population genetics of the cryptic bonnethead shark Sphyrna aff. tiburo in Brazil and the Caribbean inferred from mtDNA markers

Resolving the identity, phylogeny and distribution of cryptic species within species complexes is an essential precursor to management. The bonnethead shark, Sphyrna tiburo, is a small coastal shark distributed in the Western Atlantic from North Carolina (U.S.A.) to southern Brazil. Genetic analyses based on mitochondrial markers revealed that bonnethead sharks comprise a species complex with at least two lineages in the Northwestern Atlantic and the Caribbean (S. tiburo and Sphyrna aff. tiburo, respectively). The phylogeographic and phylogenetic analysis of two mitochondrial markers [control region (mtCR) and cytochrome oxidase I (COI)] showed that bonnethead sharks from southeastern Brazil correspond to S. aff. tiburo, extending the distribution of this cryptic species >5000 km. Bonnethead shark populations are only managed in the U.S.A. and in the 2000s were considered to be regionally extinct or collapsed in southeast Brazil. The results indicate that there is significant genetic differentiation between S. aff. tiburo from Brazil and other populations from the Caribbean (Φ_ST  = 0.9053, P < 0.000), which means that collapsed populations in the former are unlikely to be replenished from Caribbean immigration. The species identity of bonnethead sharks in the Southwest Atlantic and their relationship to North Atlantic and Caribbean populations still remains unresolved. Taxonomic revision and further sampling are required to reevaluate the status of the bonnethead shark complex through its distribution range.

Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico

This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.

Mitochondrial DNA genome evidence for the existence of a third divergent lineage in the western Atlantic Ocean for the bull shark (Carcharhinus leucas)

We report for the first time a highly divergent lineage in the Caribbean Sea for the bull shark (Carcharhinus leucas) based on the analysis of 51 mitochondrial DNA genomes of individuals collected in the western North Atlantic. When comparing the mtDNA control region obtained from the mitogenomes to sequences reported previously for Brazil, the Caribbean lineage remained highly divergent. These results support the existence of a discrete population in Central America due to a phylogeographic break separating the Caribbean Sea from the western North Atlantic, Gulf of Mexico and South America.

Delimiting cryptic species within the brown-banded bamboo shark, Chiloscyllium punctatum in the Indo-Australian region with mitochondrial DNA and genome-wide SNP approaches

Background

Delimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group.

Results

Both mtDNA and SNP analyses showed potential delimitation within C. punctatum from the Indo-Australian region and consisted of four operational taxonomic units (OTUs), i.e. those from Indo-Malay region, the west coast of Sumatra, Lesser Sunda region, and the Australian region. Each OTU can be interpreted differently depending on available supporting information, either based on biological, ecological or geographical data. We found that SNP data provided more robust results than mtDNA data in determining the boundary between population and cryptic species.

Conclusion

To split a cryptic species complex and erect new species based purely on the results of genetic analyses is not recommended. The designation of new species needs supportive diagnostic morphological characters that allow for species recognition, as an inability to recognise individuals in the field creates difficulties for future research, management for conservation and fisheries purposes. Moreover, we recommend that future studies use a comprehensive sampling regime that encompasses the full range of a species complex. This approach would increase the likelihood of identification of operational taxonomic units rather than resulting in an incorrect designation of new species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01852-3.

Using fisher-contributed secondary fins to fill critical shark-fisheries data gaps

Developing-world shark fisheries are typically not assessed or actively managed for sustainability; one fundamental obstacle is the lack of species and size-composition catch data. We tested and implemented a new and potentially widely applicable approach for collecting these data: mandatory submission of low-value secondary fins (anal fins) from landed sharks by fishers and use of the fins to reconstruct catch species and size. Visual and low-cost genetic identification were used to determine species composition, and linear regression was applied to total length and anal fin base length for catch-size reconstruction. We tested the feasibility of this approach in Belize, first in a local proof-of-concept study and then scaling it up to the national level for the 2017-2018 shark-fishing season (1,786 fins analyzed). Sixteen species occurred in this fishery. The most common were the Caribbean reef (Carcharhinus perezi), blacktip (C. limbatus), sharpnose (Atlantic [Rhizoprionodon terraenovae] and Caribbean [R. porosus] considered as a group), and bonnethead (Sphyrna cf. tiburo). Sharpnose and bonnethead sharks were landed primarily above size at maturity, whereas Caribbean reef and blacktip sharks were primarily landed below size at maturity. Our approach proved effective in obtaining critical data for managing the shark fishery, and we suggest the tools developed as part of this program could be exported to other nations in this region and applied almost immediately if there were means to communicate with fishers and incentivize them to provide anal fins. Outside the tropical Western Atlantic, we recommend further investigation of the feasibility of sampling of secondary fins, including considerations of time, effort, and cost of species identification from these fins, what secondary fin type to use, and the means with which to communicate with fishers and incentivize participation. This program could be a model for collecting urgently needed data for developing-world shark fisheries globally. Article impact statement: Shark fins collected from fishers yield data critical to shark fisheries management in developing nations.

Map-like use of Earth's magnetic field in sharks

Migration is common in marine animals,^1-5 and use of the map-like information of Earth's magnetic field appears to play an important role.^2,6-9 While sharks are iconic migrants^10-12 and well known for their sensitivity to electromagnetic fields,^13-20 whether this ability is used for navigation is unresolved.^14,17,21,22 We conducted magnetic displacement experiments on wild-caught bonnetheads (Sphyrna tiburo) and show that magnetic map cues can elicit homeward orientation. We further show that use of a magnetic map to derive positional information may help explain aspects of the genetic structure of bonnethead populations in the northwest Atlantic.^23-26 These results offer a compelling explanation for the puzzle of how migratory routes and population structure are maintained in marine environments, where few physical barriers limit movements of vagile species. VIDEO ABSTRACT.

Reproductive cycle and fecundity of the bonnethead Sphyrna tiburo L. from the northwest Atlantic Ocean

The present study examined temporal changes in plasma sex hormone concentrations and the morphology and histology of reproductive organs in mature northwest Atlantic (NWA) bonnetheads Sphyrna tiburo L. to characterize reproductive cycle, breeding periodicity and fertility in this still poorly studied population. Progressive increases in testis width, epididymis head width, plasma testosterone (T) concentrations, and occurrence of mature spermatozoa were observed in male S. tiburo from June to September, demonstrating that spermatogenesis occurs during the summer. Nonetheless, increases in maximum follicle diameter, oviducal gland width, plasma 17β-estradiol and T concentrations, and occurrence of vitellogenic follicles were not observed in mature females until between October and April, demonstrating non-synchronous patterns of gametogenesis in males and females. Fresh copulatory wounds were observed in females collected during late September along with histological evidence for sperm presence in the oviducal gland between September and April, confirming a 6- to 7 month period of female sperm storage. Ovulation occurred between mid-April and early May in concert with increases in female plasma progesterone concentrations. Gestation occurred during a 4.5- to 5 month period between May and early September, and 97% of mature females collected during this period were gravid, indicating a highly synchronized, annual reproductive periodicity. Brood size was significantly correlated with maternal size and ranged from 1 to 13 pups with a mean ± S.D. of 8.1 ± 2.2, which was significantly lower than reported in Gulf of Mexico (GOM) populations. The occurrence of non-fertile offspring was observed in 17% of broods with a range of 1-7 non-fertile eggs present in individual females. Thus, as previously reported in GOM S. tiburo, this unusual form of infertility also appears to be prevalent in the NWA population and requires further study. This study has demonstrated meaningful differences in reproductive biology of these populations, emphasizing the need for region-specific approaches for population management.

Conservation genetics of the bonnethead shark Sphyrna tiburo in Bocas del Toro, Panama: Preliminary evidence of a unique stock

The bonnethead shark, Sphyrna tiburo, is a small elasmobranch distributed in the Eastern Pacific from southern California to Ecuador, and along the Western Atlantic, with preferences for continental margins of North, Central and South America, the Gulf of Mexico, and the Caribbean. Recent studies have suggested that it could be under a process of cryptic speciation, with the possibility to find different species in similar geographic locations. Here we assessed the population structure and genetic diversity of this highly philopatric and non-dispersive species in the Bocas del Toro Archipelago, Panama. Fragments of the mitochondrial genes cytochrome oxidase I and control region, were used to test the genetic structure of adult and juvenile S. tiburo in this area, and were compared with other locations of the Western Atlantic and Belize. We found significant genetic differentiation between Caribbean bonnethead sharks from Bocas del Toro and Belize, when compared to bonnetheads from other locations of the Western Atlantic. These results also suggest that Bocas del Toro could constitute a different genetic population unit for this species, whereby bonnethead sharks in this area could belong to a unique stock. The information obtained in this study could improve our understanding of the population dynamics of the bonnethead shark throughout its distribution range, and may be used as a baseline for future conservation initiatives for coastal sharks in Central America, a poorly studied an often overlooked region for shark conservation and research.

Updated checklist of the extant Chondrichthyes within the Exclusive Economic Zone of Mexico

The checklist presented in this study includes the latest taxonomic and systematic modifications and updates (early 2018) for the Chondrichthyes that inhabit the Exclusive Economic Zone (EEZ) of Mexico. The list is based on a literature review of field-specific books, scientific publications and database information from collections and museums worldwide available online such as, the Ocean Biogeographic Information System (OBIS), Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL), iSpecies, FishBase and the National Biodiversity Information System (SNIB–CONABIO). Information was cross-referenced with digital taxonomic systems such as the Catalog of Fishes of the California Academy of Sciences, the World Register of Marine Species (WoRMS), and the Integrated Taxonomic Information System (ITIS). There is a total of two subclasses two divisions, 13 orders, 44 families, 84 genera, and 217 species that represent approximately 18% of all living and described species of chondrichthyans worldwide. For the Mexican Pacific and the Gulf of California, 92 species of chondrichthyans are listed compared to 94 species for the Gulf of Mexico and the Caribbean Sea. Additionally, 31 species listed occur on both coasts of Mexico. The species richness of the Mexican chondrichthyans will surely continue to increase, due to the exploration of deep-water fishing areas in the EEZ.

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise ΦST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (FST = 0.023-0.035), mtDNA exhibited more divergence (ΦST = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.