[Show abstract][Hide abstract] ABSTRACT: Sharks are apex predators and keystone species that have a profound influence on the ecology and food-web dynamics of coral reefs and epipelagic marine ecosystems. However, sharks are being heavily overfished compromising the health of the world’s reefs and pelagic environments. Although Indonesia is the world’s largest and most diverse coral reef ecosystem, information on the exploitation of sharks in this region is scarce. Results of DNA barcoding of shark fin revealed two alarming findings: (1) a rarity of reef sharks that should dominate Indonesia’s coastal ecosystems, and (2) a fishery that targets endangered sharks. The diversity and number of threatened species recovered in this study highlights the urgent need for improved regulation and control of Indonesia’s shark fishery.
Fisheries Research 04/2015; 164(April 2015):130-134. · 1.84 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We assessed the taxonomic diversity, geographic distributions, life history, ecology and fisheries of tarpons, ladyfishes and bonefishes (members of the subdivision Elopomorpha), which share many life history and habitat use characteristics that make them vulnerable to environmental and anthropogenic stresses in coastal environments. This assessment of Red List status for the International Union for the Conservation of Nature reveals three species considered near threatened or vulnerable, three species of least concern, and 11 data-deficient species. Although the taxonomy of tarpons appears stable, it is less so for ladyfishes and bonefishes. In aggregate, these species are distributed circumtropically and foray into temperate zones. Although they spawn in marine habitats, larvae of many species disperse into estuarine habitats, which are declining in area or degrading in quality. Several species support high-value recreational fisheries, or culturally important small-scale commercial and artisanal fisheries. Nonetheless, no formal stock assessment exists for any species, so improved data collection, information sharing and assessment techniques should facilitate socio-economic development of individual fisheries. Catch-and-release recreational fisheries that promote conservation of tarpon and bonefishes in some regions are promising models to improve the conservation status of these fishes elsewhere, as well as the economic development of these fishing communities. Most tarpons, ladyfishes and bonefishes likely face significant challenges from anthropogenically mediated habitat loss and alteration, and several are vulnerable to both habitat degradation and overfishing. Broader protection and enhancements to fisheries habitat in all regions will benefit these as well as many other coastal fishery species.
Fish and Fisheries 06/2014; 15(2). · 8.76 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The IUCN, in collaboration with the Harte Research Institute (HRI), is conducting Red List Assessment workshops with panels of marine species experts to review and assess the conservation status of all marine vertebrates, selected plants and invertebrates of the Gulf. Results from these workshops will provide comprehensive data on the distribution, life history, habitat requirements, and other ancillary information to augment HRI’s BioGoMx database. The initiative will identify current knowledge gaps, help inform decision makers, enable development of more effective conservation priorities and programs. It will also support major recovery and restoration efforts funded via the RESTORE Act and other investments made in response to the Deepwater Horizon blowout. Developing spatial modeling capacity protocols with species distribution maps and creating an ‘Expert Directory’ will improve disaster preparedness and identify needs for species-specific conservation action in the face of immediate threats to marine biodiversity within the region.
[Show abstract][Hide abstract] ABSTRACT: The rapid expansion of human activities threatens ocean-wide biodiversity. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally distributed lineage of 1,041 chondrichthyan fishes-sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world's ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery. DOI: http://dx.doi.org/10.7554/eLife.00590.001.
[Show abstract][Hide abstract] ABSTRACT: In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ("unplugged") approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches. perspective OA Open access content FastTrack ➲ publication
[Show abstract][Hide abstract] ABSTRACT: In recent decades, many marine populations have experienced major declines in abundance, but we still know little about where management interventions may help protect the highest levels of marine biodiversity. We used modeled spatial distribution data for nearly 12,500 species to quantify global patterns of species richness and two measures of endemism. By combining these data with spatial information on cumulative human impacts, we identified priority areas where marine biodiversity is most and least impacted by human activities, both within Exclusive Economic Zones (EEZs) and Areas Beyond National Jurisdiction (ABNJ). Our analyses highlighted places that are both accepted priorities for marine conservation like the Coral Triangle, as well as less well-known locations in the southwest Indian Ocean, western Pacific Ocean, Arctic and Antarctic Oceans, and within semi-enclosed seas like the Mediterranean and Baltic Seas. Within highly impacted priority areas, climate and fishing were the biggest stressors. Although new priorities may arise as we continue to improve marine species range datasets, results from this work are an essential first step in guiding limited resources to regions where investment could best sustain marine biodiversity.
PLoS ONE 01/2014; 9(1):e82898. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.
PLoS ONE 01/2014; 9(1):e84719. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Coral Triangle is a hotspot for marine species diversity as well as for intraspecific genetic diversity. Here, we used nuclear RAG2 and mitochondrial D-Loop genes to identify deep genetic divergence among Dascyllus aruanus (Linnaeus, 1758) populations across relatively short scales within the Coral Triangle. Mitochondrial clades different by >20 mutational steps were completely isolated from one another across the distance between Java and the Lesser Sunda Islands, and also showed frequency differences in the eastern and western Philippines. Evidence for population structure in the Sulu Sea and at the Lesser Sunda Islands was also identified. Our results suggest that the Sulu Sea Throughflow, Bohol Sea Throughflow, Indonesian Throughflow, signatures of extinction events from Pleistocene land barriers, and other past and present forces may be potential factors leading to lineage divergence of D. aruanus, and that these hypotheses should be tested in further studies.
[Show abstract][Hide abstract] ABSTRACT: We identify the sister species of the world's only freshwater sardinella, Sardinella tawilis (Herre, 1927) of Taal Lake, Philippines as the morphologically-similar marine Taiwanese sardinella Sardinella hualiensis (Chu and Tsai, 1958). Evidence of incomplete lineage sorting and a species tree derived from three mitochondrial genes and one nuclear gene indicate that S. tawilis diverged from S. hualiensis in the late Pleistocene. Neutrality tests, mismatch distribution analysis, sequence diversity indices, and species tree analysis indicate populations of both species have long been stable and that the divergence between these two lineages occurred prior to the putative 18th century formation of Taal Lake.
[Show abstract][Hide abstract] ABSTRACT: Marine habitats are in decline worldwide, precipitating a strong interest in marine conservation. The use of biogeographic data to designate ecoregions has had significant impacts on terrestrial conservation efforts. However, classification of marine environments into ecoregions has only become available in the last several years, based on biogeographic data supplemented by geomorphology, ocean currents, and water temperatures. Here we use a comparative phylogeographic approach to test for concordant phylogeographic patterns in three closely related species of Tridacna giant clams across the Coral Triangle, the most biodiverse marine region in the world and one of the most threatened. Data from a 450 base pair fragment of mitochondrial cytochrome-c oxidase subunit one DNA from 1739 giant clams across Indonesia and the Philippines show strong concordance between phylogeographic patterns in three species of giant clams as well as evidence for potentially undescribed species within the genus. Phylogeographic patterns correspond broadly to marine ecoregions proposed by Spalding et al. (2007), indicating that processes contributing to biogeographic boundaries likely also limit genetic connectivity across this region. These data can assist with designing more effective networks of marine protected areas by ensuring that unique biogeographic and phylogeographic regions are represented in regional conservation planning.
[Show abstract][Hide abstract] ABSTRACT: The boring giant clam, Tridacna crocea Lamarck, 1819, is a CITES-listed bivalve that is declining due to overharvest and environmental degradation. Previous molecular studies in the Coral Triangle using mitochondrial DNA indicated the presence of deep phylogenetic divergence and strong phylogeographic structure across this region, suggesting the possibility of multiple cryptic species. In the present study, we compare data from non-recombining mitochondrial (mtDNA; cytochrome oxidase subunit 1, COI) and eight microsatellite loci to better understand patterns of genetic structure and species boundaries in T. crocea populations across Indonesia and the Philippines. Microsatellite loci and mtDNA data from 618 individuals representing 27 populations revealed highly concordant phylogeographic patterns and identified three genetically distinct regions: (1) Western Indonesia, (2) Philippines and Central Indonesia, and (3) Eastern Indonesia. Both marker types also showed evidence of isolation by distance. These results build on previous studies and confirm the presence of only three genetic partitions and the genetic isolation of Western Indonesia and Eastern Indonesia. However, individual admixture analyses based on microsatellite data show that the mtDNA clade that defines a phylogeographic province spanning the Philippines and Central Indonesia is a mixture of unique genetic clusters from the Philippines/Central Indonesia and Eastern Indonesia. The admixture of nuclear loci from individuals with regionally distinct mtDNA genomes suggests that despite deep genetic divisions, the three mitochondrial lineages are likely not distinct species and that some populations in Central Indonesia may be a sink for genetic diversity accumulated from populations to the north and east. While microsatellite data refined our understanding of the biology and evolutionary history of T. crocea, the broad concordance between these markers highlights the continued utility of mtDNA, particularly in developing biodiversity-rich countries where resources to support biodiversity science are limited.