Kinship genomics approach to study mating systems in a depleted sea turtle rookery

Knowledge of demographic processes and life history strategies is necessary for the conservation and management of endangered sea turtle populations, but it is difficult to ascertain because of the limited accessibility to marine environments that sea turtles use during the different stages of their life cycle. In such cases, molecular genetics and genomic approaches are useful to assess mating systems and operational sex ratios (OSR), which ultimately influence demography. This pilot study used genome-wide single nucleotide polymorphism (SNP) genetic markers for exploring kinship and mating systems in sea turtles where major obstacles prevent a comprehensive assessment in the wild. We sampled 217 young hawksbill turtles (Eretmochelys imbricata) of unknown parentage that had originally been collected locally from seven nests and were being temporarily kept in captivity by Treasure Island Ltd as part of its captive rearing conservation project at Bounty and Treasure Islands, Fiji, in the South Pacific. The raw dataset comprised 13,573 SNPs, of which we retained 639 SNPs for parentage and relatedness analyses. Our findings from seven different pairs of parents suggest a 1:1 male:female OSR and demonstrate that genome-wide SNP genotyping approaches can be used to infer OSR. Knowledge of OSR can help evaluate the magnitude of the impact of warming temperatures and consequent feminisation in sea turtles. Our approach can complement or substitute field observation of breeding males and nesting females when logistical or budgetary constraints prevent observation of OSR in wild sea turtle populations. This approach allows inference of OSR. Protection of beaches with a higher number of pairs of parents should be prioritised to increase genetic resilience. Conservation actions in rookeries with a female-skewed OSR should be prioritised to address population declines in the long run

Trace metal content in sediment cores and seagrass biomass from a tropical southwest Pacific Island

A unique feature of seagrass among other ecosystem services is to have high phytoremediation potential that is a cost-effective plant-based approach and environmentally friendly solution for metal contamination in coastal areas. The goal of this study was to assess the phytoremediation prospective of seagrass for Cu, Fe, Mn and Zn in Fiji Islands. Heavy metal content was measured in sediments and tissues of the seagrasses Halophila ovalis, Halodule pinifolia and Halodule uninervis to test for local-scale differences. The local study shows that metal concentration in sediment and seagrass tissue was significantly variable, regardless of species and sediment type. Sedimentary concentration of Cu, Fe, Mn and Zn obtained in the present study seemed to be lower than that of previous studies. The results support that H. ovalis is a good bioindicator species since it accumulated up to 5-fold more of these metals compared to the Halodule species

Genome-wide comparisons reveal evidence for a species complex in the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae)

Evolutionary relationships in the black-lip pearl oyster Pinctada margaritifera which is highly valued for pearl production remain poorly understood. This species possesses an 18,000 km Indo-Pacific natural distribution, and its current description includes six subspecies defined exclusively on morphological characters. To evaluate its taxonomic identity using molecular data, 14 populations in both the Indian and Pacific Oceans (n = 69), and the congeneric taxa P. maxima and P. mazatlanica (n = 29 and n = 10, respectively) were sampled. Phylogenomic reconstruction was carried out using both 8,308 genome-wide SNPs and 10,000 dominant loci (DArTseq PAVs). Reconstructions using neighbour-joining (Nei’s 1972 distances), maximum likelihood and Bayesian approaches all indicate that the taxonomy of P. margaritifera is quite complex, with distinct evolutionary significant units (ESUs) identified within Tanzanian and Iranian populations. Contrastingly, phylogenies generated for Pacific Ocean oysters resolved a large monophyletic clade, suggesting little support for two current morphological subspecies classifications. Furthermore, P. mazatlanica formed a basal clade closest to French Polynesian P. margaritifera, suggesting it may be conspecific. Collectively, these findings provide evidence that P. margaritifera comprises a species complex, perhaps as a result of population fragmentation and increased divergence at range limits

An assessment of the aquaculture potential of indigenous freshwater food fish of Fiji, Papua New Guinea, Vanuatu, Solomon Islands, Samoa and Tonga as alternatives to farming of tilapia

An important driver behind introductions for aquaculture of alien fish species into Pacific Island Countries and Territories (PICTs) is a lack of knowledge about domestication suitability and specific culture requirements of indigenous taxa. Introductions may be appropriate in some circumstances, but in other circumstances, the associated risks may outweigh the benefits, so greater understanding of indigenous species' aquaculture potential is important. This review summarises literature for indigenous freshwater food fish species from Papua New Guinea, Fiji, Vanuatu, the Solomon Islands, Samoa and Tonga, and evaluates their aquaculture potential for food security and/or small-scale livelihoods. A species selection criteria incorporating economic, social, biological and environmental spheres was used to score 62 candidate species. Tilapia (Oreochromis mossambicus and O. niloticus) now established in PICTs were evaluated for comparison. Results show that 13 species belonging to the families Mugilidae (Mullets), Terapontidae (Grunters), Kuhliidae (Flagtails) and Scatophagidae (Scats) have the highest culture potential according to selection criteria. These feed at a relatively low trophic level (are herbivores/detritivores), have comparatively fast growth rates and overall possess characteristics most amenable for small-scale, inland aquaculture. The four top-ranked candidates are all mountain mullets Cestraeus spp., followed by Nile tilapia (Oreochromis niloticus). Lower ranked candidates include three other mullets (Planiliza melinoptera, P. subviridis and Mugil cephalus) and rock flagtail Kuhlia rupestris. Importantly, many species remain data deficient in aspects of their reproductive biology or culture performance. Species profiles and ranked priority species by country are provided with logistical, technological and environmental assessments of country capacities to culture each species

Leech breach: a first record of the invasive freshwater leech Helobdella europaea (Hirudinea: Glossiphoniidae) in Fiji

Context. The freshwater flat leech Helobdella europaea Kutschera, 1987 is a small annelid indigenous to South America. This invasive species feeds on the haemolymph of host aquatic invertebrates, with occurrences reported from Europe, USA, Taiwan, North Africa, Hawai‘i, Australia and New Zealand. A large number of individuals were discovered in the Ba River catchment, Fiji, during a 2015–2020 freshwater biodiversity survey, raising concerns of potential impacts on endemic Fijian aquatic invertebrate fauna and ecosystem integrity. Aims. To facilitate assessments of its spread and ethology, this study employed morphological and phylogenetic analyses for verification of taxonomic identity. Methods. Phylogenetic trees were constructed using a 658 bp fragment of the mitochondrial DNA cox1 (COI) gene. The first complete mitochondrial genome sequence of H. europaea was also determined using selective multiple displacement amplification and Oxford Nanopore Technology to provide a reference for future comparative analyses and source tracking of spread to other regions. Key results. Morphological and COI analyses identified all Fijian leech specimens collected (n = 16) as H. europaea, reporting the first occurrence of this species on a south-west Pacific Island. The complete mitochondrial genome was sequenced. Conclusions. Confirmation of its presence in Fiji is a national biosecurity concern and will guide the Biosecurity Authority of Fiji and national agencies in further ecosystem assessment and response strategies. Implications. With the complete mitochondrial genome of H. europaea now available, transmission pathway traceability is possible in other regions where this species may be detected

Sandfish generations: loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Hatcheries are indispensable for seed production of many commercial aquaculture species. However, for mass-spawning species in particular, they can be capricious environments where genetic diversity among progeny may be lost due to small effective broodstock population sizes, variable parental contributions and differential family survival. Understanding the genetic impacts of hatchery production is therefore important for addressing these problems and optimising propagation methods. We used 6051 genome-wide Single Nucleotide Polymorphisms (SNPs) to analyse genetic diversity, parental contributions and offspring kinship during a commercial-scale hatchery production run of sandfish (Holothuria scabra), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were highly skewed, with up to 26% of the parent pool contributing and kinship analyses determined that just two parents sired between 44.4 and 67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD = 1121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13–16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. As many sandfish broodstock remain wild-sourced, maintenance of healthy wild populations as reservoirs of genetic diversity is important, along with selection for spawning of genetically diverse individuals which are as distantly-related as possible

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmars.2024.1396016/full#supplementary-materialThe sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean Fst=0.016), with greater separation evident between geographically distant sites (Fst range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Australian Centre for International Agriculture Research (ACIAR) project FIS/2016/122: “Increasing technical skills supporting community-based sea cucumber production in Vietnam and the Philippines”. Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development of the Department of Science and Technology (DOST-PCAARRD: Project Numbers QSR-MR-CUC.02.01 and QSR-MR-CUC.02.02)

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

Sandfish (Holothuria scabra) DArTseq genotype

Genetic structure, population connectivity and taxonomic identity of the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae), across its Indo-Pacific distribution

The black-lip pearl oyster Pinctada margaritifera (L.) is a bivalve mollusc highly valued for cultured pearl and pearlshell production throughout its extensive Indo-Pacific natural distribution, where it makes substantial contributions to local economies and supports coastal community livelihoods. Despite its commercial importance, substantial knowledge gaps exist for this species, particularly regarding genetic structure and population connectivity at both local and regional scales, as well as its taxonomic identity. This information is required for the development of sustainable fishery management strategies, as well as responsible aquaculture practices, to ensure the persistence of healthy wild populations, and continued commercial production. The overarching goal of the research undertaken for this thesis was to investigate the stock structure, connectivity and taxonomy of P. margaritifera, to inform fishery management and aquaculture practices across the extent of its Indo-Pacific distribution, with a particular focus on the Fiji Islands. Specifically, over four separate investigations, I develop novel genomewide single nucleotide polymorphism (SNP) markers for this species, and use them to investigate population genetic structure, diversity, connectivity and local adaptation of Fijian oysters, as well as for populations sampled from across the broader ~18,000 km species distribution. I also compare estimates of population connectivity derived from genomic analyses with an independent hydrodynamic particle dispersal model, to corroborate patterns of larval transport between study sites. Finally, I utilise phylogenomic analyses to assess the evolutionary relationships of the black-lip pearl oyster across its natural distribution, and also to ascertain its taxonomic identity among other members of the family Pteriidae. The first investigation developed 5,243 novel genome-wide SNP markers for P. margaritifera, and tested their utility by assessing population structure, genetic diversity, as well as detecting regions of the genome underlying functional differences among populations. It involved 156 Fijian oysters sampled from three wild, and one hatchery produced population. Shallow but significant genetic structure was revealed among all wild populations (average pairwise Fₛₜ = 0.046), with clear evidence of a genetic bottleneck in the hatchery population (Nₑ(LD) = 6.1), compared to wild populations (Nₑ(LD) >192.5). Fₛₜ outlier detection to differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species, revealed 42-62 highly differentiated SNPs (p<0.02), while casecontrol association discovered up to 152 SNPs (p<0.001). Database searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This investigation demonstrated the utility of genome-wide SNP data for assessment of genetic structure and diversity in P. margaritifera, with transferability to other highly-dispersive marine taxa for their conservation and management. The second investigation utilised 4,123 genome-wide SNPs, together with an independent hydrodynamic particle dispersal model to assess genetic structure, diversity, local adaptation and population connectivity at 6 farm and 5 wild Fijian sites. Weak fine-scale patterns of population structure indicative of broad-scale admixture were observed among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (hatchery oysters cf. all other populations Fₛₜ=0.085–0.102). This hatchery-produced population had also experienced a bottleneck (Nₑ(LD)=5.1; 95% C.I.=[5.1-5.3]); compared to infinite Nₑ(LD) estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale admixture by surface ocean currents, correlating well with finescale patterns of population structure discovered. Fₛₜ outlier tests failed to detect genetic signatures supportive of selection, with only 2-5 directional outlier SNPs identified (average Fₛₜ=0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicated the existence of a single genetic stock of P. margaritifera in the Fiji Islands for management purposes. The combined use of independent high resolution genomic and oceanographic data as demonstrated here is a novel approach that can be applied to other broadcast spawning taxa. The third investigation examined the microevolutionary forces influencing genetic structure, connectivity and adaptive variation across the ~18,000 km Indo-Pacific distribution of P. margaritifera. Concordance with a theoretical population model known as the Core- Periphery Hypothesis (CPH), was used as a framework for this assessment. The CPH predicts that genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. Analyses utilising 9,624 genome-wide SNPs and 580 oysters sampled from 14 sites, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (Fₛₜ=0.253-0.418, p<0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (Fₛₜ=0.001-0.109, p<0.001). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively, while evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; Fₛₜ=0.101-0.437, FDR=0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations. These findings have revealed that population organisation in this species is highly complex and far more elaborate than generalised CPH predictions, with structuring being produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. The fourth and final investigation examined evolutionary relationships and the taxonomic identity of P. margaritifera. This study was required as the current species classification is not supported by molecular data, and includes a total of six subspecies that are described exclusively using morphological characters. Here, 69 oysters were sampled from 14 populations in both the Indian and Pacific Oceans. Samples were also collected from the congeneric taxa P. maxima and P. mazatlanica (n=29 and n=10, respectively), and phylogenetic reconstruction carried out using both 8,308 genome-wide SNPs and 10,000 dominant loci. Reconstructions using neighbour-joining (Nei's 1972 unbiased distances), maximum likelihood and Bayesian approaches all indicate that the taxonomy of P. margaritifera is more complex than previously indicated, with distinct evolutionary significant units (ESUs) identified within Tanzanian and Iranian populations, correlating with type localities for two Indian Ocean morphological subspecies descriptions. Contrastingly, phylogenies generated for Pacific Ocean P. margaritifera resolved a large monophyletic clade, suggesting little support for two of three morphological subspecies classifications reported from this ocean basin. Furthermore, P. mazatlanica specimens all formed a basal clade closest to French Polynesian P. margaritifera, suggesting it may not constitute a separate species. Collectively, these findings provide evidence to support a suggestion by previous studies that P. margaritifera comprises a species complex; however, further investigation involving finer-scale sampling with higher sample densities is required to resolve regional ESU boundaries. Collectively, this thesis presents the most comprehensive evaluation of genetic structure, population connectivity and evolutionary relationships for P. margaritifera to date. The data generated have permitted fundamental insights into the stock and taxonomic structure of this species, which are invaluable for its sustainable fishery management and aquaculture, with extension to other taxa possessing similar biological attributes

Discovery of an important aggregation area for endangered scalloped hammerhead sharks, Sphyrna lewini, in the Rewa River estuary, Fiji Islands

The scalloped hammerhead shark, Sphyrna lewini, is endangered throughout its global distribution. Management and protection of this species is challenging in many locations because of limited scientific data and the vulnerable life-history traits of the species. Our study investigated anecdotal evidence that the Rewa River estuary in Fiji serves as an important nursery area for this shark. Research findings indicated that the average length of both males (60.6 ± 6.78 cm, n ¼ 31) and females (60.4 ± 6.85 cm, n ¼ 51) was well within published size limits of juvenile S. lewini studied in other locations (range ¼ 38.0–89.5 cm). On the basis of published reference points for umbilical scar status we postulate that the first captured juveniles were born in January of the study year. Stomach content analysis found the following prey items: Decapoda (represented by prawns and shrimps), Stomatopoda, anguilliformes and osteichthyes. Decapods were the most numerous prey item by both count (59.17% of total prey items) and weight (60.25% of total weight). Our study provides strong support that the Rewa River estuary is an important aggregation area for S. lewini in Fiji