Community Marine Monitoring Toolkit: A tool developed in the Pacific to inform community-based marine resource management.

In the Pacific region, community engagement, participation and empowerment are key to effective and sustainable marine resource management at the local level. With the prevalence of a local marine tenure systems and the widespread decline of coastal resources, communities need to be part of the solution to facilitate recovery. A novel marine monitoring toolkit was developed in Vanuatu with the participation of community resource monitors to inform local management actions. The Toolkit includes simplified versions of established monitoring methods for marine habitats and resources to achieve a balance between robust science and methods appropriate for communities. Key to its success is that it was developed in response to community needs using a participatory approach and implemented through a series of training workshops with local environmental leaders. Of particular note, the Toolkit includes a standardised process for communities to use monitoring results instantly, without the need for complex data analyses or external support. Using the Toolkit, communities are able to adapt their traditional management to address immediate and medium-term issues in their local marine environment. The observed benefits of the Toolkit include increased local awareness through community-led environmental outreach, increased ownership of and motivation for local monitoring and management, implementation of local management actions, expansion of traditional marine managed areas, and new local ecotourism initiatives to generate revenue to support environmental stewardship.

Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized fishery collapse in a large Sciaenid fish, Protonibea diacanthus.

As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localized declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine- and broad-scale population connectivity. This study examined the population structure of P. diacanthus across north-western Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100 s of km) to account for the restricted exchange among populations (stocks) and to prevent localized extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.

Challenges and Priorities in Shark and Ray Conservation.

Sharks, rays, and chimaeras (Class Chondrichthyes; herein 'sharks') are the earliest extant jawed vertebrates and exhibit some of the greatest functional diversity of all vertebrates. Ecologically, they influence energy transfer vertically through trophic levels and sometimes trophic cascades via direct consumption and predation risk. Through movements and migrations, they connect horizontally and temporally across habitats and ecosystems, integrating energy flows at large spatial scales and across time. This connectivity flows from ontogenetic growth in size and spatial movements, which in turn underpins their relatively low reproductive rates compared with other exploited ocean fishes. Sharks are also ecologically and demographically diverse and are taken in a wide variety of fisheries for multiple products (e.g. meat, fins, teeth, and gills). Consequently, a range of fisheries management measures are generally preferable to 'silver bullet' and 'one size fits all' conservation actions. Some species with extremely low annual reproductive output can easily become endangered and hence require strict protections to minimize mortality. Other, more prolific species can withstand fishing over the long term if catches are subject to effective catch limits throughout the species' range. We identify, based on the IUCN Red List status, 64 endangered species in particular need of new or stricter protections and 514 species in need of improvements to fisheries management. We designate priority countries for such actions, recognizing the widely differing fishing pressures and conservation capacity. We hope that this analysis assists efforts to ensure this group of ecologically important and evolutionarily distinct animals can support both ocean ecosystems and human activities in the future.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification.

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1-1.5 million raw reads per species, we successfully obtained 10-13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae).

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis.

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.

Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae).

The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self-seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self-recruitment rather than passive dispersal.