Evidence for extensive population structure in the white-spotted eagle ray within the Indo-Pacific inferred from mitochondrial gene sequences

Rays in the Shadows: Batoid Diversity, Occurrence, and Conservation Status in Fiji

Over recent decades, elasmobranchs (sharks, rays, and skates) have been increasingly recognized among the world's most threatened marine wildlife, leading to heightened scientific attention. However, batoids (rays and skates) are relatively understudied, especially in Large Ocean States of the Pacific. This synthesis compiles insights on batoid diversity and occurrence in Fiji's waters by integrating a literature review, participatory science programs such as the Great Fiji Shark Count (GFSC) Initiative, Projects Abroad Fiji (PA), Manta Project Fiji (MPF), and iNaturalist, along with environmental DNA. Nineteen batoid species from seven families were identified: 19 species from the literature, 12 from participatory science programs, and six from eDNA analysis. Notably, this study provides the first photographic evidence for the bentfin devil ray (Mobula thurstoni, Lloyd, 1908) in Fiji. GFSC data indicated the highest species diversity in the Western Division, with spotted eagle rays (Aetobatus ocellatus, Kuhl, 1823) and maskrays (Neotrygon sp.) being observed most. In-person interviews conducted by PA provided information on the occurrence of wedgefishes and potentially sawfishes. MPF records and iNaturalist uploads were dominated by reef manta rays (M. alfredi, Krefft, 1868), while the pink whipray (Pateobatis fai, Jordan and Seale, 1906) yielded the most DNA sequences. Overall, 68.4% of the species face an elevated extinction risk based on the International Union for the Conservation of Nature Red List criteria. Although caution is warranted with older literature-based records for the giant guitarfish (Glaucostegus typus, Anonymous [Bennett], 1830), giant stingaree (Plesiobatis daviesi, Wallace, 1967), and the lack of sawfish verification, this synthesis highlights the effectiveness of a combined methodological approach in establishing a reference point for the diversity and occurrence of this understudied taxon in Fiji.

Reproductive biology of the whitespotted eagle ray Aetobatus narinari (Myliobatiformes) captured in the coast of Paraíba and Pernambuco, Brazil

The present study analysed aspects of reproductive biology based on macroscopic and microscopic structures of whitespotted eagle ray Aetobatus narinari captured by artisanal fishing off the coast of Paraíba and Pernambuco (7° 30' S, 34° 49' W; 7° 47' S, 34° 51' W), northeast Brazil. Of the 71 individuals in the sample, 55% were female (disc width - W_D : 532-1698 mm) and 45% were male (W_D : 442-1410 mm). The body size at which 50% of the individuals are mature (W_D50 ) for males was 1155.8 mm; the clasper length varied between 24 and 184 mm. The W_D50 for females was 1293.9 mm; the diameter of the largest vitellogenic follicle varied between 11 and 31 mm; and only the left ovary and uterus were functional. The microanatomy of the reproductive tract of males and females agrees with that of other elasmobranch species. In males, the highest hepato-somatic index (I_H ) average and gonado-somatic index (I_G ) average occurred in the third bimester of the year, whereas in females the highest values (average I_H and I_G , respectively) were in the second bimester of the year. Based on the information on reproduction of A. narinari from this study, it will be possible to contribute to the correct management and protection of this species.

Site affinity of whitespotted eagle rays Aetobatus narinari assessed using photographic identification

Photographic identification was used to track the movements of the whitespotted eagle ray Aetobatus narinari around South Caicos, Turks and Caicos Islands. A total of 165 individuals were identified, aided by the computer program I³ S Spot. The sex ratio across all study sites in 2015 was not significantly different from 1:1 (χ²  = 2·8, P > 0·05). 33·9% of all individual rays were resighted at least once and the maximum number of days between the first and last sighting was 1640 (median 165, interquartile range, IQR = 698). Sightings of individuals occurred at locations differing from the original sighting location 24·6% of the time (0·7-20 km away). The entire population around South Caicos has yet to be sampled and these rays exhibited site affinity during the study period; they are either resident to South Caicos or are using the area for parts of the year before making movements elsewhere and then returning. Given these results, A. narinari is suited to local-scale management and conservation efforts.

Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo-Malay Archipelago: inferences from a mitochondrial and microsatellite loci

To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo-Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker-derived results. Both marker systems detected a strong overall genetic structure (ΦST = 0.096, P < 0.0001; mean D est = 0.17; F ST = 0.015, P < 0.0001) and best supported regional groupings (ΦCT = 0.199 P < 0.0001; F CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker-specific results have important implications for conservation efforts concerning this and similar species.

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.

Identification of rays through DNA barcoding: an application for ecologists

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.