The Phylogeny of Rays and Skates (Chondrichthyes: Elasmobranchii) Based on Morphological Characters Revisited.

Elasmobranchii are relatively well-studied. However, numerous phylogenetic uncertainties about their relationships remain. Here, we revisit the phylogenetic evidence based on a detailed morphological re-evaluation of all the major extant batomorph clades (skates and rays), including several holomorphic fossil taxa from the Palaeozoic, Mesozoic and Cenozoic, and an extensive outgroup sampling, which includes sharks, chimaeras and several other fossil chondrichthyans. The parsimony and maximum-likelihood analyses found more resolved but contrasting topologies, with the Bayesian inference tree neither supporting nor disfavouring any of them. Overall, the analyses result in similar clade compositions and topologies, with the Jurassic batomorphs forming the sister clade to all the other batomorphs, whilst all the Cretaceous batomorphs are nested within the remaining main clades. The disparate arrangements recovered under the different criteria suggest that a detailed study of Jurassic taxa is of utmost importance to present a more consistent topology in the deeper nodes, as issues continue to be present when analysing those clades previously recognized only by molecular analyses (e.g., Rhinopristiformes and Torpediniformes). The consistent placement of fossil taxa within specific groups by the different phylogenetic criteria is promising and indicates that the inclusion of more fossil taxa in the present matrix will likely not cause loss of resolution, therefore suggesting that a strong phylogenetic signal can be recovered from fossil taxa

Hunting “Big Fish”: A marine environmental history of a contested fishery in the Bohol Sea

The Bohol Sea in the Philippines has a high biodiversity of large marine vertebrates. It is also one of the primary fishing grounds in the Central Visayas. This is a study of the history of interactions of the fishers of the Bohol Sea with the ‘big fishes’ living within it. These ‘big fishes’ are the large marine vertebrates, namely whales, dolphins, whale sharks and manta rays. It is the story of the changes in the Bohol Sea and how the communities who depended on it affected these changes. Similarly, it discusses how the Bohol Sea and the large marine vertebrates shaped the lives of the coastal peoples living around it. This study aims to determine the extent of the fisheries for whales, dolphins, whale sharks and manta rays in the Bohol Sea from the 19th century to recent times. It focuses on the fishing communities of southern Bohol, Camiguin and Southern Leyte in the Central Visayas, who are known to hunt these large marine vertebrates, and aims to describe the characteristics and trace the evolution of these fisheries. Through a multidisciplinary approach, this study uses a combination of ethnographic and historical research methods, together with biological data, from published and unpublished sources. The study aims to determine if the abundance and distribution of large marine vertebrates in the Bohol Sea changed in the long-term. It also examines how the fishing communities adapted to the ecological, socio-economic and political changes over time. From its beginnings in the late nineteenth century, the hunting of whales, dolphins, whale sharks and manta rays, in the different communities around the Bohol Sea underwent very similar and, for some, identical technological developments. These fishing technologies and patterns were adapted to the nature of their target species. By the late twentieth century, with increasing population, worsening economic conditions, and declining fish stocks in the country, the Bohol Sea fishing communities’ dependence on the fisheries for large marine vertebrates also increased. Likewise, fishery policies and legislative frameworks were also evolving with a more protectionist and conservationist stance. The implementation of fishery bans in the 1990s compelled most fishers to comply and adapt, however others resisted. Communities who lived in an environment endowed with more diverse and abundant resources proved to be more resilient. While those who heavily depended on the fishery and had little else to turn to have continued to hunt up to the present day. Despite continuing protests and public clamour for a total ban on hunting for all other species of rays in the Philippines, the ray fishery in the Bohol Sea continues. This study demonstrates how state efforts to conserve whales, dolphins, whale sharks and manta rays in the Philippines have been ineffective. This is primarily because of the lack of legitimacy of these fishery policies in the eyes of the communities. This study also highlights the importance of using multiple and non-traditional data sources in evaluating fisheries that are data deficient. The study shows how it is important to examine the historical context of ecological and social systems in order to understand the causes of contemporary resource management problems

Ecology of rays on tropical coral reefs

Rays are a diverse group of elasmobranchs in both their morphology and ecology. They are among the most threatened elasmobranchs according to the International Union for the Conservation of Nature (IUCN), however, little is known about their life history, behaviour or population status. To be able to improve management of declining ray populations, their distribution and ecology must be better understood. Coastal species are most at risk from anthropogenic effects, however, the extent of impacts on rays have not been widely documented. Rays serve important ecosystems functions including stabilizing food webs and acting as ecosystem engineers through bioturbation. As mesopredators, rays prey on a variety of primary consumers, while also being prey for apex predators. Because of the many linkages in food webs among apex predators to producers, food web stabilization by mesopredators prevents trophic cascades. Some rays also serve their ecosystems through bioturbation, the biological reworking of sediments. During the act of feeding, some rays create feeding pits which oxygenate sediments, provides habitat for small teleosts and crustaceans, and facilitates meiofaunal movement. While rays serve important roles in their ecosystems, there is little species-specific information available. The lack of research is partially due to the cryptic nature of rays, making them difficult to study, and partially due to the charismatic nature of their relatives the sharks, which have received much more attention. Therefore, more research is needed to address the deficits in our knowledge of ray ecology and distribution. Baited remote underwater video systems (BRUVS) are increasingly used to study fish communities, biomass, and animal behaviour. BRUVS entail deploying baited video cameras in the absence of human presence in order to survey fish and invertebrate populations. This methodology reduces human influence on the study species and encourages more natural behaviours than with human presence. Due to the popularity of BRUVS approaches, there are many analysis methods. MaxN, which refers to the maximum number of individuals observed of a species in a single frame of a video, is the most commonly used metric of relative abundance when analysing BRUVS data. Chapter 3 presents a novel metric for BRUVS analysis that involves identifying and counting distinct individuals (MaxIND) to quantify the accuracy of MaxN. Individual oriental bluespotted maskray (Neotrygon orientalis) and the bluespotted fantail ray (Taeniura lymma) were identified on BRUVS by spot patterns, tail characteristics, and sex at three sites in Malaysian Borneo. We demonstrated that MaxIND gave abundances that were 2.4 and 1.1 times higher than MaxN for N. orientalis and T. lymma, respectively. These differences between methods were consistent for each species between sites regardless of the presence of marine reserves. However, differences in abundance estimates from MaxN to MaxIND were apparent between species, indicating that correction factors need to be developed on a species basis to better estimate true abundance. While identifying individuals is time consuming, it provides improved accuracy and information about populations. We therefore recommend the use of MaxIND when rare and threatened species are present, in high density populations, and for behavioural analyses, where distinguishing features are present. Ecological sampling must yield consistent results in order to reliably quantify predator populations. BRUVS are increasingly being used to evaluate and monitor predator communities in marine ecosystems. Many BRUVS studies compare multiple coral reef sites sampled at a single point in time. As coral reef monitoring using BRUVS grows in its capacity to provide data relevant to sustainable management, marine protected area efficacy, and overall reef health, understanding repeatability of sampling results is vital. Chapter 4 examined the repeatability of BRUVS results for the elasmobranch community both within and between seasons (dry and wet) and years, and explored environmental factors affecting abundances at two sites in Bau Bau, Indonesia. A total of 1139 elasmobranchs (69% rays, 31% sharks) were observed on 956 BRUVS across six sampling events. Consistent results were found both in species composition and abundances within a season and across multiple years using the same sampling protocol (number and location of BRUVS). However, abundances of all sharks and rays were significantly higher in the wet season in both years. The elasmobranch community was significantly different between the two sites sampled in a consistent manner. The results demonstrated that while BRUVS are a consistent, reliable and repeatable method for surveying elasmobranchs, care must be taken in timing of sampling various regions to ensure accuracy when comparing multiple locations as season was an important factor in the results. Coral reef ecosystems are highly dynamic environments with complex trophic interactions and environmental drivers. Rays are important members of these systems, however, in areas like Southeast Asia they are often heavily fished. Their conservation is difficult, as many countries in which they are fished do not have the capacity for effective fisheries management. For chapter 5, BRUVS were deployed at 70 reefs in 11 countries across the Coral Triangle and Australasian regions to determine ray abundances and assemblage. In 3426 BRUVS deployments, 1069 ray individuals were observed. The three most abundance species / genera were maskrays (Neotrygon spp.), fantail rays (Taeniura spp.), and eagle rays (Generas: Aetobatus, Aetomylaeus, Myliobatus). Ray assemblage was relatively consistant across the study area, however, ray abundances varied greatly with only a single individual in Vietnam to a very high abundance of rays in Indonesia. The differences in abundances are likely a reflection of fishing pressure and fisheries management. In countries with low fishing pressure, communities were species rich in both rays and sharks. Countries with moderate fishing pressure began to lose species richness, especially of sharks, although abundances of rays remained similar. With high fishing pressure, only small productive species of rays were present, and these were abundant due to the lack of top predators (i.e. sharks). Finally, in countries with extremely high fishing pressure, even productive species were absent. In order to conserve rays and their ecosystem services, fisheries management must be addressed. In some cases this requires fisheries management implementation and in some cases may involve increased management efficacy. Additionally, habitat quality and characteristics also affect the ray community at finer scales than fishing pressure. Benthic relief was most important to all rays with some species preferring low relief areas and some preferring high relief (coral dominated) areas. Thus, in addition to fisheries management, habitat quality and conservation is also important for ray species. Sharks are decreasing in abundance in many coral reef habitats, but the ecosystem effects of this loss are poorly understood. Rays are a prevalent mesopredator in tropical coral reef ecosystems experiencing low fishing pressure that are preyed upon by top predators like sharks. Across Southeast Asia and the Western Pacific there are varying abundances of coral reef predators that consume rays. Studies have suggested reduced predator abundances leads to increases in mesopredator abundance (mesopredator release) and potentially trophic cascades. In this study, we examined the relationship between top predator abundance (sharks) and the abundance and behaviour of two genera of small benthic rays using BRUVS at 19 sites across six countries. Where predators were more abundant, the bluespotted maskray complex (Neotrygon spp.) and two species of fantail rays (Taeniura lymma and T. lessoni) were sighted less often, possibly because of lower abundances. However, small ray behaviour was significantly affected by predator abundance. Individuals of focal ray species visited BRUVS significantly fewer times at sites with higher predator abundances. Where predators were less abundant, rays spent significantly more time in the video frame, visited BRUVS more often, and were more likely to feed from bait bags. In addition to predator abundance, small ray presence was significantly influenced by relief and depth. Neotrygon spp. were more abundant on deeper, lower relief habitats, while Taeniura spp. were more prevalent in reef-associated shallow, high relief habitats. Overall, this chapter found that predator abundance had a significant effect on small benthic ray abundance and behaviour in the presence of BRUVS. The results demonstrate that changes in behaviour associated with the loss of predators may make the interpretation of phenomena like mesopredator release more challenging unless behavioural effects are taken into account. This thesis demonstrates the many uses of BRUVS as a tool for surveying ray abundances, behaviours, and assemblage. A variety of analysis techniques were used for BRUVS data, with results proving the effectiveness of this survey method. Using the newly described metric MaxIND, more accurate abundance estimates and behavioural analyses are able to be performed in a natural setting. As there is limited data about rays on coral reefs globally, this thesis provides basic information about ray assemblages and abundances across the Coral Triangle and Australasian regions. Countries within these regions have extremely variable fishing pressure and management capacity leading towards changes in ray populations. In order to conserve ray species, improved fisheries management and habitat preservation are needed

How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae)

Manta rays and their relatives of the family Myliobatidae have pectoral fins that have been modified for underwater flight, as well as a pair of fleshy projections at the anterior of the body called cephalic lobes, which are specialized for feeding. As a unique trait with a dedicated function, cephalic lobes offer an excellent opportunity to elucidate the processes by which diverse body plans and features evolve. To shed light on the morphological development and genetic underpinnings of cephalic lobes, we examined paired fin development in cownose rays, which represent the sister taxon to manta rays in the genus Mobula. We find that cephalic lobes develop as anterior pectoral fin domains and lack independent posterior patterning by 5\u27 HoxD genes and Shh, indicating that cephalic lobes are not independent appendages but rather are modified pectoral fin domains. In addition, by leveraging interspecies comparative transcriptomics and domain-specific RNA-sequencing, we identify shared expression of anterior patterning genes, including Alx1, Alx4, Pax9, Hoxa13, Hoxa2, and Hoxd4, in the pectoral fins of cownose ray (Rhinoptera bonasus) and little skate (Leucoraja erinacea), providing evidence supporting homology between the cephalic lobes of myliobatids and the anterior pectoral fins of skates. We also suggest candidate genes that may be involved in development of myliobatid-specific features, including Omd, which is likely associated with development of thick anterior pectoral fin radials of myliobatids, and Dkk1, which may inhibit tissue outgrowth at the posterior boundary of the developing cephalic lobes. Finally, we observe that cephalic lobes share a surprising number of developmental similarities with another paired fin modification: the claspers of male cartilaginous fishes, including enrichment of Hand2, Hoxa13, and androgen receptor. These results suggest that cephalic lobes may have evolved by co-opting developmental pathways that specify novel domains in paired fins. Taken together, these data on morphological development and comparative gene expression patterns illustrate how distinct body plans and seemingly novel features can arise via subtle changes to existing developmental pathways

Marine Fisheries Information Service No.152

Marine Fisheries Information Service, Technical and Extension Serie

Flower Garden Banks National Marine Sanctuary: A rapid assessment of coral, fish, and algae using the AGRRA Protocol

The Flower Garden Banks are topographic features on the edge of the continental shelf in the northwest Gulf of Mexico. These banks are approximately 175 km southeast of Galveston, Texas at 28° north latitude and support the northernmost coral reefs on the North American continental shelf. The East and West Flower Garden Banks (EFG and WFG) and Stetson Bank, a smaller sandstone bank approximately 110 km offshore, are managed and protected as the Flower Garden Banks National Marine Sanctuary (FGBNMS). As part of a region-wide initiative to assess coral reef condition, the benthic and fish communities of the EFG and WFG were assessed using the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol. The AGRRA survey was conducted during a week-long cruise in August 1999 that was jointly sponsored by the FGBNMS and the Reef Environmental Education Foundation (REEF). A total of 25 coral transects, 132 algal quadrats, 24 fish transects, and 26 Roving Diver (REEF) surveys were conducted. These surveys revealed reefs with high coral cover, dominated by large, healthy corals, little macroalgae, and healthy fish populations. The percent live coral cover was 53.9 and 48.8 at the WFG and EFG, respectively, and the average colony diameter was 93 and 81 cm. Fish diversity was lower than most Caribbean reefs, but large abundances and size of many species reflected the low fishing pressure on the banks. The benthic and fish assemblages at the EFG and WFG were similar. Due to its near pristine conditions, the FGB data will prove to be a valuable component in the AGRRA database and its resulting scale of reef condition for the region. (PDF contains 22 pages.

Marine megafauna interactions with small-scale fisheries in the southwestern Indian Ocean: a review of status and challenges for research and management

In developing regions, coastal communities are particularly dependent on small-scale fisheries for food security and income. However, information on the scale and impacts of small-scale fisheries on coastal marine ecosystems are frequently lacking. Large marine vertebrates (marine mammals, sea turtles and chondrichthyans) are often among the first species to experience declines due to fisheries. This paper reviews the interactions between small-scale fisheries and vulnerable marine megafauna in the southwestern Indian Ocean. We highlight an urgent need for proper documentation, monitoring and assessment at the regional level of small-scale fisheries and the megafauna affected by them to inform evidence-based fisheries management. Catch and landings data are generally of poor quality and resolution with compositional data, where available, mostly anecdotal or heavily biased towards easily identifiable species. There is also limited understanding of fisheries effort, most of which relies on metrics unsuitable for proper assessment. Management strategies (where they exist) are often created without strong evidence bases or understanding of the reliance of fishers on resources. Consequently, it is not possible to effectively assess the current status and ensure the sustainability of these species groups; with indications of overexploitation in several areas. To address these issues, a regionally collaborative approach between government and non-governmental organisations, independent researchers and institutions, and small-scale fisheries stakeholders is required. In combination with good governance practices, appropriate and effective, evidence-based management can be formulated to sustain these resources, the marine ecosystems they are intrinsically linked to and the livelihoods of coastal communities that are tied to them

Sharks in Crisis: A Call to Action for the Mediterranean

Humans and sharks have a relationship stretching back into ancient history. This is particularly clear in the Mediterranean, where sharks were traded and consumed more than 4,000 years ago in the Chalcolithic era and during the Bronze Age. Culturally they've been significant for thousands of years, and even appear in the schemes of the mythological Greek gods

Marine Fisheries Information Service No.129

Marine Fisheries Information Service, Technical and Extension Serie