The breeding biology of lemon sharks at a tropical nursery lagoon

Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.

Insights into the nuclear and mitochondrial genome of the Lemon shark Negaprion brevirostris using low-coverage sequencing: Genome size, repetitive elements, mitochondrial genome, and phylogenetic placement

The Lemon shark Negaprion brevirostris is an important species experiencing conservation issues that is in need of genomic resources. Herein, we conducted a genome survey sequencing in N. brevirostris and determined genome size, explored repetitive elements, assembled and annotated the 45S rRNA DNA operon, and assembled and described in detail the mitochondrial genome. Lastly, the phylogenetic position of N. brevirostris in the family Carcharhinidae was examined using translated protein coding genes. The estimated haploid genome size ranged between 2.29 and 2.58 Gbp using a k-mer analysis, which is slightly below the genome size estimated for other sharks belonging to the family Carcharhinidae. Using a k-mer analysis, approx. 64-71 % of the genome of N. brevirostris was composed of repetitive elements. A relatively large proportion of the 'repeatome' could not be annotated. Taking into account only annotated repetitive elements, Class I - Long Interspersed Nuclear Element (LINE) were the most abundant repetitive elements followed by Class I - Penelope and Satellite DNA. The nuclear ribosomal operon was fully assembled. The AT-rich complete mitochondrial genome was 16,703 bp long and encoded 13 protein coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Negaprion brevirostris is closely related to the genera Carcharhinus, Glyphis and Lamiopsis in the family Carcharinidae. This new genomic resources will aid with the development of conservation plans for this large coastal shark.

Individual residency behaviours and seasonal long-distance movements in acoustically tagged Caribbean reef sharks in the Cayman Islands

Understanding how reef-associated sharks use coastal waters through their ontogeny is important for their effective conservation and management. This study used the horizontal movements of acoustically tagged Caribbean reef sharks (Carcharhinus perezi) to examine their use of coastal space around the Cayman Islands between 2009 and 2019. A total of 39 (59.1%) tagged sharks (male = 22, female = 17, immature = 18, mature = 21) were detected on the islands wide network of acoustic receivers. The detection data were used to calculate values of Residency Index (RI), Site-Fidelity Index (SFI) and minimum linear displacement (MLD), as well as for network analysis of individual shark movements to test for differences between demographics, seasons, and diel periods. Sharks were detected for up to 1,598 days post-tagging and some individuals showed resident behaviour but the majority of tagged individuals appear to have been one-off or only occasional transient visitors to the area. Generally, individuals showed strong site-fidelity to different areas displaying linear home ranges of < 20 km. The evidence indicates that there was no pattern of diel behaviour. Tagged sharks generally showed increased movements within and between islands during the summer (April-September), which may be related to breeding activity. Some individuals even made occasional excursions across 110 km of open water > 2,000 m deep between Grand Cayman and Little Cayman. One mature female shark showed a displacement of 148.21 km, the greatest distance reported for this species. The data shows that the distances over which some sharks moved, greatly exceeded the extent of any one of the islands' marine protected areas indicating that this species may be more mobile and dispersive than previously thought. This study provides support for the blanket protection to all sharks throughout Cayman waters, which was incorporated within the National Conservation Act in 2015.

The biology and ecology of the basking shark: A review

Here we review the literature on the basking shark (Cetorhinus maximus, Gunnerus, 1765), well known as the second largest extant shark (and fish) species globally. Previous reviews were published by Kunzlik in 1988 and Sims in 2008, but in the last 15 years modern electronic and DNA sequencing technologies have resulted in considerable advances in our knowledge of the species' behaviour and ecology. Basking sharks are planktivores and under appropriate conditions spend prolonged periods at the ocean surface feeding on copepod prey that primarily make up their diet, the behaviour that gave rise to their common name. In general, they are migratory and move into higher latitude waters during the summer months, when loose surface-feeding aggregations may form at favoured sites, the best known of which at present occur at hotspots on the west coasts of Britain and Ireland. The species is found circumglobally in temperate waters, but they are also now known on occasion to migrate at depth between northern and southern hemispheres, as well as across oceans within the northern hemisphere. In the past basking shark were more abundant across much of their range, but, consequent on targeted fisheries and in some places intentional eradication, became everywhere scarce, with recent population recovery in the north-east Atlantic being the result of protective measures initiated in the 1990s. Despite their charismatic nature, some of their most fundamental biological processes including copulation, gestation and birth remain largely unknown, due to their migratory and often deep-water lifestyle. In contrast, the deployment of small-scale archival and satellite tags has revealed the details of both broadscale migratory movements and horizontal and vertical foraging behaviours. Recent genetic studies support evidence suggesting a degree of site fidelity in relation to seasonal feeding grounds, which likely explains why in the past local populations have collapsed following periods of intensive fishing. Other recent research using aerial drones and towed cameras has revealed within loose feeding aggregations elements of social behaviour that may have a courtship function as well as enhance feeding efficiency.

Genetic structure and relatedness of juvenile sicklefin lemon shark (Negaprion acutidens) at Dongsha Island

Negaprion acutidens (sicklefin lemon shark) is distributed in the Indo-Pacific and in close association with coral reefs. Under the protection of the Dongsha Atoll National Park, a small but well-established juvenile population of N. acutidens inhabiting coastal areas of Dongsha Island was recently observed to display site fidelity by using acoustic telemetry. This study was designed to reveal the fine scale genetic structure and relatedness within and among 5 juvenile shark cohorts inhabiting 3 sampling sites at Dongsha Island. A total 188 juveniles were caught and sampled between 2016 and 2017, and genotyped with twelve loci. They were assigned to 5 year cohorts (2013-2017) based on the body length and date they were caught, also assigned to 3 sites based on where they were caught. Among five cohorts, the percentage of unrelated pairs within a cohort is more than 62% in average, suggesting a potential high mortality during their early life stage. The results of Fst and assignment testing showed that there was no significant genetic structure between sites and cohorts indicating that there was no fine scale genetic structure, even though the juveniles possessed strong site fidelity. A small effective population size (Ne) was detected (Ne = 86.7) which indicates the presence of a potentially isolated and vulnerable population at Dongsha. These results provide the genetic diversity as a baseline for future management and conservation of N. acutidens in the South China Sea.

Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

Information on the spatial ecology of reef sharks is critical to understanding life-history patterns, yet gaps remain in our knowledge of how these species move and occupy space. Previous studies have focused on offshore reefs and atolls with little information available on the movement and space use of sharks utilising reef habitats closer to shore. Cross-shelf differences in physical and biological properties of reefs can alter regional ecosystem processes resulting in different movement patterns for resident sharks. Passive acoustic telemetry was used to examine residency, space use and depth use of 40 blacktip reef sharks, Carcharhinus melanopterus, on an inshore reef in Queensland, Australia, and assess temporal or biological influences. All sharks showed strong site-attachment to inshore reefs with residency highest among adult females. Sharks exhibited a sex-based, seasonal pattern in space use where males moved more, occupied more space and explored new areas during the reproductive season, while females utilised the same amount of space throughout the year, but shifted the location of the space used. A positive relationship was also observed between space use and size. There was evidence of seasonal site fidelity and long-distance movement with the coordinated, annual migration of two adult males to the study site during the mating season. Depth use was segregated with some small sharks occupying shallower depths than adults throughout the day and year, most likely as refuge from predation. Results highlight the importance of inshore reef habitats to blacktip reef sharks and provide evidence of connectivity with offshore reefs, at least for adult males.

Spotting the "small eyes": using photo-ID methodology to study a wild population of smalleye stingrays (Megatrygon microps) in southern Mozambique

Background

The smalleye stingray (Megatrygon microps) is a large and rare dasyatid ray, patchily distributed across the Indo-West Pacific. Free-swimming individuals have regularly been recorded in Southern Mozambican coastal waters utilizing different inshore environments. Distinctive features of the species include latitudinal rows of white spots on the dorsal surface of their pectoral disc.

Methods

This study aimed to determine if the natural spot patterns on M. microps are sufficiently unique and stable to use in photo-identification studies of wild populations. Research dive logs were combined with opportunistic photographs from local dive centers and recreational divers to create a photographic database from the Inhambane Province coastline.

Results

Seventy different individuals were identified over a 15-year period, all exhibiting uniquely identifiable patterns. Stingrays were easily identifiable over a period of six years with multiple re-sightings of the same individuals recorded. Analysis of encounters across the Inhambane coastline revealed that individual rays regularly use inshore reefs along a 350 km stretch of coastline. Fifteen stingrays were re-sighted during the study period, including one showing a 400 km return movement between Tofo Beach and the Bazaruto Archipelago, which is the longest distance traveled by a dasyatid ray on record. Several presumably pregnant females have also been recorded in the Bazaruto Archipelago National Park.

No apparent negative tagging effects after 13 years at liberty for lemon shark, Negaprion brevirostris implanted with acoustic transmitter

An intact and uncompromised internal acoustic transmitter was non-lethally recovered from a lemon shark Negaprion brevirostris, after 13 years at liberty. The shark, first tagged at an estimated age of 2 years old near South Bimini, Bahamas in 2004, was recaptured in 2017 with a total length of 264 cm. The tagged shark displayed typical growth rate, pregnancy, natal homing and pupping behaviour of other individuals in this population. This observation provides important evidence regarding the effects from long-term retention of implanted acoustic transmitters in a carcharhinid shark.

Variability in multiple paternity rates for grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini)

This study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini) opportunistically caught in Papua New Guinea (PNG). Litter size between species were significantly different with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 14 and 10 microsatellite loci respectively, we identified MP in 66% of grey reef sharks (4 out of 6 litters) and 100% MP in scalloped hammerheads (5 litters). We found high paternal skew (the uneven contribution of sires per litter) and a positive correlation between female adult size and litter size in scalloped hammerheads but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew may be linked with mating strategies and post-copulatory mechanisms. Multiple paternity is thought to benefit populations by enhancing genetic diversity therefore increasing the population’s genetic resilience to extrinsic pressures. The identification of MP in two shark species reported here, further elucidates the complex breeding strategies elasmobranchs undertake.

Three decades of longlining in Bimini, Bahamas, reveals long-term trends in lemon shark Negaprion brevirostris (Carcharhinidae) catch per unit effort

In Bimini, Bahamas, the consistent employment of longlines, beginning in 1982, provided a rare opportunity to explore population trends for large resident sharks. This study assessed three shallow water longline survey periods at this location; 1982-1989, 1992-2002 and 2003-2014, with the aim of determining trends in annual catch per unit effort (CPUE) for an IUCN listed near-threatened species, the lemon shark Negaprion brevirostris. A general additive model (GAM) was used to analyse the non-linear annual CPUE values over the entire 32-year research period. The GAM displayed high variability of annual CPUE, with a peak value of 0·026 N. brevirostris per hook day (hooks day(-1) ) in 2000. The temporal pattern of CPUE indicated an abundance trend with a complete cycle, from trough to trough, occurring over a period of approximately 18 years. The 1982-1989 survey period saw the highest proportion of mature individuals (19·8%) and the smallest average pre-caudal length (LPC ; 124·8 cm). The 1992-2002 survey period had the highest average annual CPUE (0·018 hooks day(-1) ), while the 2003-2014 research period saw largest average LPC size (134·8 cm) and the lowest average CPUE values (0·009 hooks day(-1) ) of the entire research period. The long-term trend identified in this study provides a baseline for future assessment.

Using genetic inference to re-evaluate the minimum longevity of the lemon shark Negaprion brevirostris

A combination of mark-recapture and genetic sampling was used to extend the minimum longevity of an elasmobranch species and the life span estimate of the lemon shark Negaprion brevirostris was increased conservatively from 20·2 to 37 years. This increase in longevity means higher vulnerability and a longer recovery time from exploitation.

Smells Like Home: The Role of Olfactory Cues in the Homing Behavior of Blacktip Sharks, Carcharhinus limbatus

Animal navigation in the marine environment is believed to be guided by different sensory cues over different spatial scales. Geomagnetic cues are thought to guide long-range navigation, while visual or olfactory cues allow animals to pinpoint precise locations, but the complete behavioral sequence is not yet understood. Terra Ceia Bay is a primary nursery area for blacktip sharks, Carcharhinus limbatus, on southwestern Florida's Gulf of Mexico coast. Young-of-the-year animals show strong fidelity to a specific home range in the northeastern end of the bay and rapidly return when displaced. Older juveniles demonstrate annual philopatry for the first few years, migrating as far south as the Florida Keys each fall, then returning to Terra Ceia Bay each spring. To examine the sensory cues used in homing, we captured neonate (<3 weeks old) blacktip sharks from within their home range, fitted them with acoustic tags, and translocated them to sites 8 km away in adjacent Tampa Bay and released them. Intact animals returned to their home range, within 34 h on average, and remained there. With olfaction blocked, fewer animals returned to their home range and they took longer to do so, 130 h on average. However, they did not remain there but instead moved throughout Terra Ceia Bay and in and out of Tampa Bay. Since sharks from both treatments returned at night in tannic and turbid water, vision is likely not playing a major role in navigation by these animals. The animals in this study also returned on incoming or slack tides, suggesting that sharks, like many other fish, may use selective tidal stream transport to conserve energy and aid navigation during migration. Collectively, these results suggest that while other cues, possibly geomagnetic and/or tidal information, might guide sharks over long distances, olfactory cues are required for recognizing their specific home range.

Bioaccumulation of organohalogenated compounds in sharks and rays from the southeastern USA

Organohalogenated compounds are widespread in the marine environment and can be a serious threat to organisms in all levels of aquatic food webs, including elasmobranch species. Information about the concentrations of POPs (persistent organic pollutants) and of MeO-PBDEs (methoxylated polybrominated diphenyl ethers) in elasmobranchs is scarce and potential toxic effects are poorly understood. The aims of the present study were therefore to investigate the occurrence of multiple POP classes (PCBs, PBDEs, DDXs, HCB, CHLs) and of MeO-PBDEs in various elasmobranch species from different trophic levels in estuarine and marine waters of the southeastern United States. Overall, levels and patterns of PCBs, PBDEs, DDXs, HCB, CHLs and of MeO-PBDEs varied according to the species, maturity stage, gender and habitat type. The lowest levels of POPs were found in Atlantic stingrays and the highest levels were found in bull sharks. As both species are respectively near the bottom and at top of the trophic web, with juvenile bull sharks frequently feeding on Atlantic stingrays, these findings further suggest a bioaccumulation and biomagnification process with trophic position. MeO-PBDEs were not detected in Atlantic stingrays, but were found in all shark species. HCB was not found in Atlantic stingrays, bonnetheads or lemon sharks, but was detected in the majority of bull sharks examined. Comparison with previous studies suggests that Atlantic stingrays may be experiencing toxic effects of PCBs and DDXs on their immune system. However, the effect of these compounds on the health of shark species remains unclear.

There and back again: a review of residency and return migrations in sharks, with implications for population structure and management

The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.

Modeling the population dynamics of lemon sharks

Background

Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population dynamics. In particular, factors such as age-structure, density-dependent feedbacks on reproduction, and demographic stochasticity are important for understanding population trends, but are often difficult to assess. Lemon sharks (Negaprion brevirostris) have a pelagic adult phase that makes them logistically difficult to study. However, juveniles use coastal nursery areas where their densities can be high.

Results

We use a stage-structured, Markov-chain stochastic model to describe lemon shark population dynamics from a 17-year longitudinal dataset at a coastal nursery area at Bimini, Bahamas. We found that the interaction between delayed breeding, density-dependence, and demographic stochasticity accounts for 33 to 49% of the variance in population size.

Conclusions

Demographic stochasticity contributed all random effects in this model, suggesting that the existence of unmodeled environmental factors may be driving the majority of interannual population fluctuations. In addition, we are able to use our model to estimate the natural mortality rate of older age classes of lemon sharks that are difficult to study. Further, we use our model to examine what effect the length of a time series plays on deciphering ecological patterns. We find that—even with a relatively long time series—our sampling still misses important rare events. Our approach can be used more broadly to infer population dynamics of other large vertebrates in which age structure and demographic stochasticity are important.

Reviewers

This article was reviewed by Yang Kuang, Christine Jacob, and Ollivier Hyrien.

Regional-scale migrations and habitat use of juvenile lemon sharks (Negaprion brevirostris) in the US South Atlantic

Resolving the geographic extent and timing of coastal shark migrations, as well as their environmental cues, is essential for refining shark management strategies in anticipation of increasing anthropogenic stressors to coastal ecosystems. We employed a regional-scale passive acoustic telemetry array encompassing 300 km of the east Florida coast to assess what factors influence site fidelity of juvenile lemon sharks (Negaprion brevirostris) to an exposed coastal nursery at Cape Canaveral, and to document the timing and rate of their seasonal migrations. Movements of 54 juvenile lemon sharks were monitored for three years with individuals tracked for up to 751 days. While most sharks demonstrated site fidelity to the Cape Canaveral region December through February under typical winter water temperatures, historically extreme declines in ocean temperature were accompanied by rapid and often temporary, southward displacements of up to 190 km along the Florida east coast. From late February through April each year, most sharks initiated a northward migration at speeds of up to 64 km day⁻¹ with several individuals then detected in compatible estuarine telemetry arrays in Georgia and South Carolina up to 472 km from release locations. Nineteen sharks returned for a second or even third consecutive winter, thus demonstrating strong seasonal philopatry to the Cape Canaveral region. The long distance movements and habitat associations of immature lemon sharks along the US southeast coast contrast sharply with the natal site fidelity observed in this species at other sites in the western Atlantic Ocean. These findings validate the existing multi-state management strategies now in place. Results also affirm the value of collaborative passive arrays for resolving seasonal movements and habitat preferences of migratory coastal shark species not easily studied with other tagging techniques.

Phylogeography and population structure of the red stingray, Dasyatis akajei inferred by mitochondrial control region

The red stingray Dasyatis akajei is distributed in both marine and freshwater, but little is known about its phylogeography and population structure. We sampled 107 individuals from one freshwater region and 6 coastal localities within the distribution range of D. akajei. Analyses of the first hypervariable region of mitochondrial DNA control region of 474 bp revealed only 17 polymorphism sites that defined 28 haplotypes, with no unique haplotype for the freshwater population. A high level of haplotype diversity and low nucleotide diversity were observed in both marine (h = 0.9393 ± 0.0104, π = 0.0069 ± 0.0040) and freshwater populations (h = 0.8333 ± 0.2224, π = 0.0084 ± 0.0063). Significant level of genetic structure was detected between four marine populations (TZ, WZ, ND and ZZ) via both hierarchical molecular variance analysis (AMOVA) and pairwise FST (with two exceptions), which is unusual for elasmobranchs detected previously over such short geographical distance. However, limited sampling suggested that the freshwater population was not particularly distinct (p > 0.05), but additional samples would be needed to confirm it. Demersal and slow-moving characters likely have contributed to the genetically heterogeneous population structure. The demographic history of D. akajei examined by mismatch distribution analyses, neutrality tests and Bayesian skyline analyses suggested a sudden population expansion dating to upper Pleistocene. The information on genetic diversity and genetic structure will have implications for the management of fisheries and conservation efforts.

Conservation of the critically endangered eastern Australian population of the grey nurse shark (Carcharias taurus) through cross-jurisdictional management of a network of marine-protected areas

Between 2001 and 2009, 26 marine-protected areas (MPA) were established on the east Australian seaboard, at least in part, to manage human interactions with a critically endangered population of grey nurse shark, Carcharias taurus. This network is spread across six MPA systems and includes all 19 sites outlined in the National Recovery Plan for C. taurus, though five sites remain open to some forms of fishing. The reserve network has complex cross-jurisdictional management, as the sharks occur in waters controlled by the Australian states of New South Wales (NSW) and Queensland, as well as by the Commonwealth (Federal) government. Jurisdiction is further complicated by fisheries and conservation departments both engaging in management activities within each state. This has resulted in protected area types that include IUCN category II equivalent zones in NSW, Queensland, and Commonwealth marine parks that either overlay or complement another large scaled network of protected sites called critical habitats. Across the network, seven and eight rule permutations for diving and fishing, respectively, are applied to this population of sharks. Besides sites identified by the recovery plan, additional sites have been protected as part of the general development of MPA networks. A case study at one of these sites, which historically was known to be occupied by C. taurus but had been abandoned, appears to shows re-establishment of an aggregation of juvenile and sub-adult sharks. Concurrent with the re-establishment of the aggregation, a local dive operator increased seasonal dive visitation rates at the site fourfold. As a precautionary measure, protection of abandoned sites, which includes nursery and gestating female habitats are options that may assist recovery of the east coast population of C. taurus.

Genetic network and breeding patterns of a sicklefin lemon shark (Negaprion acutidens) population in the Society Islands, French Polynesia

Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population's mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.

Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region

Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.

Microsatellite analyses of blacktip reef sharks (Carcharhinus melanopterus) in a fragmented environment show structured clusters

The population dynamics of shark species are generally poorly described because highly mobile marine life is challenging to investigate. Here we investigate the genetic population structure of the blacktip reef shark (Carcharhinus melanopterus) in French Polynesia. Five demes were sampled from five islands with different inter-island distances (50–1500 km). Whether dispersal occurs between islands frequently enough to prevent moderate genetic structure is unknown. We used 11 microsatellites loci from 165 individuals and a strong genetic structure was found among demes with both F-statistics and Bayesian approaches. This differentiation is correlated with the geographic distance between islands. It is likely that the genetic structure seen is the result of all or some combination of the following: low gene flow, time since divergence, small effective population sizes, and the standard issues with the extent to which mutation models actually fit reality. We suggest low levels of gene flow as at least a partial explanation of the level of genetic structure seen among the sampled blacktip demes. This explanation is consistent with the ecological traits of blacktip reef sharks, and that the suitable habitat for blacktips in French Polynesia is highly fragmented. Evidence for spatial genetic structure of the blacktip demes we studied highlights that similar species may have populations with as yet undetected or underestimated structure. Shark biology and the market for their fins make them highly vulnerable and many species are in rapid decline. Our results add weight to the case that total bans on shark fishing are a better conservation approach for sharks than marine protected area networks.

Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia

Conservation of top predators has been emphasized as essential in an ecosystem due to their role in trophic chain regulation. Optimizing conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity as these are essential to understanding the population dynamics. There have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses. However, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale like between islands remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Most females gave birth at their home island but some migrated to specific nursery areas outside the area they are attached to, sometimes going to another island 50 km away across deep ocean. Our analysis also revealed that females migrated to the same nursery for every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between populations. These results highlight the need to conserve coastal zones where female reef sharks seem to exhibit philopatry during the breeding season.

Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs

Application of modern molecular tools is expanding the understanding of elasmobranch reproductive ecology. High-resolution molecular markers provide information at scales ranging from the identification of reproductively isolated populations in sympatry (i.e. cryptic species) to the relationships among parents, offspring and siblings. This avenue of study has not only augmented the current understanding of the reproductive biology of elasmobranchs but has also provided novel insights that could not be obtained through experimental or observational techniques. Sharing of genetic polymorphisms across ocean basins indicates that for some species there may be gene flow on global scales. The presence, however, of morphologically similar but genetically distinct entities in sympatry suggests that reproductive isolation can occur with minimal morphological differentiation. This review discusses the recent findings in elasmobranch reproductive biology like philopatry, hybridization and polyandry while highlighting important molecular and analytical techniques. Furthermore, the review examines gaps in current knowledge and discusses how new technologies may be applied to further the understanding of elasmobranch reproductive ecology.

The use and abuse of photographic identification in sharks and rays

The use of photography to discriminate between individuals in a population using natural markings or aberrations is increasingly being utilized to support field research on elasmobranchs. This non-intrusive method has facilitated investigation of a wide variety of subjects including population composition, abundance estimates, residency and movement, demography and social behaviours. Here the first detailed review of photo-identification as a research technique for sharks and rays is provided, and its assumptions, current applications and potential highlighted. The limitations and practical considerations of photographic studies are also investigated with recommendations on initial survey design and ongoing data collection using current technology. Future directions are also explored with an emphasis on a move towards standardized approaches and automated recognition programmes to facilitate global collaborative work.

An analytical and hypothesis-driven approach to elasmobranch movement studies

The study of elasmobranch movements has increased steadily since the early 1970s. A great deal is now known about the horizontal and vertical movements of many elasmobranch species over multiple spatial and temporal scales. These studies illustrate that many species share certain behaviours such as diel shifts in habitat (both horizontal and vertical), continuous yo-yo bounce diving and in many cases, seasonal migrations. Hypothesis-driven studies explaining these behaviours or utilizing an eco-physiological predictive framework are, however, relatively rare. In this review, the descriptive and hypothesis-driven studies of elasmobranch movements are discussed, in addition to some of the analytical tools that can be used to generate or test predictions. There are many tools and analytical techniques available which are not currently being utilized for most studies of elasmobranch movements. With the constant improvement in technology and statistical techniques, the development of hypothesis-driven studies of elasmobranch movements should continue to increase.

Population structure and phylogeography of the short-tailed stingray, Dasyatis brevicaudata (Hutton 1875), in the Southern Hemisphere

There is accumulating evidence that the degree of vagility explains little of the extent of population subdivision found within elasmobranch species. Instead, patterns of gene flow in elasmobranchs appear more closely linked to the presence of dispersal barriers, either physical or biological. Here, we investigate the potential role of some of these isolating mechanisms in shaping the population structure of a member of the stingray family Dasyatidae (Dasyatis brevicaudata) at various scales (southern hemisphere vs. coastal New Zealand). Analyses of the mitochondrial DNA control region from 176 individuals revealed significant genetic structure between South Africa, Australia, and New Zealand populations (analysis of molecular variance [AMOVA], overall Ф(ST) = 0.67, P < 0.001), although New Zealand and Australia shared some haplotypes. Surprisingly, significant population differentiation was found among several coastal New Zealand locations (AMOVA, overall Ф(ST) = 0.05, P < 0.05). However, data did not support the genetic differentiation between individuals from an offshore breeding area and mainland individuals. Comparisons suggest that these stingrays exhibit similar levels of population differentiation as other coastal elasmobranchs, with high divergence across oceanic basins and lower differentiation along continuous coastal habitats. Differences in coastal population structuring in elasmobranch species studied to date may be attributed to species-specific preferences for coastal habitats, which may be linked to life history functions (e.g., feeding and pupping).

First analysis of multiple paternity in an oviparous shark, the small-spotted catshark (Scyliorhinus canicula L.)

Multiple paternity (MP) has been demonstrated in a variety of sharks, although its prevalence and the number of sires per litter vary considerably among species. To date, such analyses have focused on viviparous species that possess only part of the wide spectrum of reproductive strategies developed in elasmobranchs. We analyzed MP in an oviparous species, the small-spotted catshark (Scyliorhinus canicula). In total, 150 neonates originating from 13 different mothers were genotyped using 12 microsatellite loci. MP was commonplace, with progeny from 92% of females sired by multiple males. This result is consistent with the reproductive biology of the species, particularly its protracted breeding season and potential for long-term sperm storage. The significance of these findings is discussed in light of small-spotted catshark behavior, which suggests that the cost of avoiding mating attempts initiated by males may be high and is therefore supportive of convenience polyandry as an explanation for MP. Eggs were followed from the time they were laid to when they hatched, offering a rare opportunity to investigate juvenile development in more detail.

Frequency of multiple paternity in the spiny dogfish Squalus acanthias in the western north Atlantic

Multiple paternity (MP) has been shown to be widespread in elasmobranch fishes although its prevalence and the number of sires per litter vary considerably among species. In the squaloid shark Squalus acanthias, MP has been reported, but whether it is a common feature of the species' reproductive strategy is unknown. In this study, we determined the frequency of MP in 29 litters of S. acanthias sampled from the lower Chesapeake Bay and coastal Virginia waters, using 7 highly polymorphic nuclear DNA microsatellite loci. Only 5 litters (17% of the total) were genetically polyandrous, with at least 2 sires per litter. Litter size increased with female size but was similar between polyandrous and monandrous females.