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Prolonged thermal stress and high levels of solar irradiance can disrupt the coral-algal symbiosis and cause bleaching and lowered overall fitness that lead to the likely death of the cnidarian host. Adaptive bleaching and acclimatization of corals, which posits bleaching as an opportunity for the coral host to switch its currently susceptible endosymbionts to more stress-tolerant taxa, offers hope for survival of reefs amid rapidly warming oceans. In this study, we explored the diversity and distribution of coral-zooxanthellae associations in the context of geospatial patterns of sea surface temperature (SST) and thermal anomalies across the Philippine archipelago. Thermal clusters based on annual sea surface temperature means and each site’s frequency of exposure to heat stress were described using three-decade (1985–2018) remotely sensed data. Haphazard sampling of 628 coral fragments was conducted in 14 reef sites over 3 years (2015–2018). Using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and sequencing of the zooxanthellae ITS2 region, we characterized endosymbiont diversity within four reef-building coral families across archipelagic thermal regimes. Consistency in dominant Symbiodiniaceae taxon was observed in Acropora spp., Porites spp., and Heliopora coerulea. In contrast, the family Pocilloporidae (Pocillopora spp., Seriatopora spp., and Stylophora pistillata) exhibited biogeographic variability in zooxanthellae composition, concordant with inferred occurrences of sustained thermal stress. Multivariate analyses identify two broad Pocilloporidae clusters that correspond with mean SST ranges and frequency of exposure to bleaching-level thermal stress which are largely supported by ANOSIM. Differences in zooxanthellae assemblages may reflect host-specific responses to ecological or environmental gradients across biogeographic regions. Such patterns of variability provide insight and support for the adaptability and potential resilience of coral communities in geographically and oceanographically complex regions, especially amidst the increasing severity of global and local-scale stressors.

Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals in the Western Pacific Ocean. To determine the source of outbreaking COTS larvae and their dispersal routes across the Western Pacific, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS comprise two major clades, an East-Central Pacific clade (ECP-C) and a Pan-Pacific clade (PP-C). The ECP-C consists of COTS from French Polynesia (FP), Fiji, Vanuatu and the Great Barrier Reef (GBR), and does not appear prone to outbreaks. In contrast, the PP-C, which repeatedly spawns outbreaks, is a large clade comprising COTS from FP, Fiji, Vanuatu, GBR, Papua New Guinea, Vietnam, the Philippines, Japan, Micronesia, and the Marshall Islands. Given the nature of Pacific Ocean currents, the vast area encompassing FP, Fiji, Vanuatu, and the GBR likely supplies larvae for repeated outbreaks, exacerbated by anthropogenic environmental changes, such as eutrophication.

The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.

Connectivity of marine populations is shaped by complex interactions of biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications to the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genetics approach combining larval dispersal modeling and population genomic analysis based on RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly-dispersive mud crab, Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal, significant genetic differentiation was detected among eight Sulu Sea populations based on 1,655 single-nucleotide polymorphism (SNP) markers (FST = 0.0057, p = 0.001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p = 0.001). Oceanography influences genetic structure, as redundancy analysis (RDA) revealed significant contribution of asymmetric ocean currents to neutral genetic variation (R2adj = 0.133; p = 0.035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p = 0.001), significantly correlated with variability in mean sea surface temperatures during peak spawning months of S. olivacea (R2adj = 0.763; p = 0.041), suggesting putative signatures of selection and local adaptation of early life history stages to thermal clines. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly-dispersive marine species, and provides information useful for spatial management of the fishery resource.

Pocillopora acuta, formerly synonymized with P. damicornis, is an ecologically important reef-building coral that exhibits mixed reproductive modes, geographic variation in clonality, and conflicting reports of population genetic structure. Using 16 polymorphic microsatellite loci, this study examined clonality, genetic differentiation, and connectivity of genetically identified P. acuta (n = 428) in the Bolinao–Anda Reef Complex (BARC), Philippines, characterized by varying levels of wave exposure. Estimates of clonal richness indicate that the populations are largely derived from asexual reproduction, more likely via dispersal of ameiotic larvae. Clonal richness, population density, and mean colony size vary with wave exposure, suggesting the potential influence of local-scale disturbance on clonality, reproductive mode, and population structure. Populations in low-energy environments were characterized by greater colony density, larger colonies, and a greater proportion of clones compared to high-energy environments. Despite evidence for realized clonal dispersal of P. acuta extending up to 22 km, significant genetic differentiation among BARC populations reveals restricted gene flow at small spatial scales. Moreover, genetic differentiation is more pronounced when considering the spatial distribution of clones (FST including clones = 0.059; FST excluding clones = 0.028), suggesting that (1) asexually produced propagules are likely retained locally and across-site settlement is not as common; and (2) sexually derived propagules may have broader scales of dispersal. This study reexamines the population genetics of this often-problematic coral and underlines the importance of contextualizing site and species biology in designing or enhancing management towards the maintenance of functional genetic diversity and pathways of connectivity among populations.

The sandfishHolothuria scabrais a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performedde novotranscriptome assembly and characterization of fast- and slow-growing juvenileH. scabrafrom three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.HighlightsThe study explores the genomic basis of growth variation in juvenile sandfish by examining gene expression profiles of fast- and slow-growing early juvenile stages from three hatchery populations using RNA-seq.Sixty-six differentially regulated unigenes potentially related to growth variation are associated with several biological and molecular processes, including carbohydrate binding, extracellular matrix organization, fatty-acid metabolism, and metabolite and solute transport.A large number of potential microsatellite and growth category-associated SNP markers have been identified.

The sandfish, Holothuria (Metriatyla) scabra Jaeger, 1833 is a commercially-valuable tropical sea cucumber species which is overexploited throughout much of its distributional range, the Philippine archipelago included. The need for management interventions to sustain the fishery is recognized. However, the lack of knowledge on the genetic structure of natural populations needs to be addressed to guide management initiatives. The present study examined genetic diversity and spatial patterns of genetic structure of sandfish populations across the Philippine archipelago. Population genetic analysis using 11 microsatellite markers revealed weak yet significant regional genetic structure among 15 H. scabra populations across the Philippine archipelago (FST = 0.016; P 0.05). Peripheral locations exhibited limited gene flow (Philippine Sea, South China Sea, Sulu Sea and Celebes Sea; mean FST = 0.023, P

Extensive phenotypic plasticity generally confounds identification of the common reef-building coral Pocillopora damicornis. With the recognition of P. damicornis genetic lineages as taxonomic species, this study surveyed genetic lineages within P. damicornis sensu lato (Veron and Pichon in Scleractinia of Eastern Australia, Australian Institute of Marine Science, Australia, 1976) in the Philippines. Employing a PCR–RFLP assay of the mitochondrial control region and sequencing of the mitochondrial open reading frame for lineage identification, we examined 694 P. damicornis s.l. colonies from 16 locations across the Philippine archipelago to characterize Pocillopora species distribution in the region. Genetic identification reveals the occurrence of P. acuta and the absence of P. damicornis in the Philippines. This study highlights the need to revisit the distributional limits of this extensively studied species complex and the necessity of using genetic information for taxonomic identification where morphological identification is unreliable.

Population genetic structure of Sardinella lemuru in Philippine waters was examined using mitochondrial DNA markers, control region (CR) and cytochrome oxidase I (COI). The sampling effort was focused along the northern coast of Mindanao where the species was previously reported to have regionally structured stocks. Sequences from online databases were included to expand geographic coverage of the analyses. Phylogeographic and population genetic inferences revealed the presence of genetically structured sympatric haplogroups across the archipelago (CR: n = 493, K = 3, between-group genetic distance = 0.038 – 0.054, global Φ ST = 0 . 41 p = 159, K = 2, between-group genetic distance = 0.012, global Φ ST = 0 . 77 , p 0.001). In contrast, little to no genetic differentiation was inferred when samples were assigned based on geographic location (CR global Φ ST = 0 . 01 , p Φ ST = 0 . 001 , p > 0.05). These results suggest that (1) gene flow occurs across space, but is limited among sympatric haplogroups, (2) these sympatric haplogroups do not correspond to cryptic species, and (3) differences in mutation rates between the two markers may have led to a different number of haplogroups being recovered. High haplotype diversity (H CR = 0 . 99 ; H COI = 0 .798), low nucleotide diversity ( π CR = 0 . 041 ; π COI = 0 . 005 ), and significantly negative Fu’s F S values implied demographic expansion for all haplogroups. The mismatch distribution and Bayesian Skyline plot indicated that expansion occurred during the late Pleistocene. Based on our results, we hypothesize that the Philippines is a secondary contact zone for S. lemuru, and testing this requires that samples be obtained from the entire habitat range of the species along the Indo-West Pacific Region.

Molecular tools and analyses have played pivotal roles in uncovering the processes and patterns of biodiversity in the Indian and Pacific oceans. However, integrating genetic results into management and conservation objectives has been challenging, with few examples that show practical applicability. This review aims to address some of the perceived barriers to an enhanced approach that integrates molecular data into management and conservation goals, by reviewing papers relevant to both conservation and fisheries management in the Indo-Pacific region, particularly with respect to phylogeography, connectivity, and species identification, as well as stock delineation, restoration of depleted wild stocks, mislabeled marine resources and "molecular forensics." We also highlight case studies from each of these areas that illustrate how molecular analyses are relevant to conservation and management in the Indo- Pacific, spanning a variety of vertebrate and invertebrate species. We discuss the application of genetic data to the design and evaluation of the effectiveness of marine protected area networks, stock delineation, and restoration and the usage of exclusion tests and parentage analyses for fisheries management. We conclude that there is a distinct need for increasing public awareness and ownership of genetically unique lineages and, ultimately, the increased inclusion of genetic research into management policy and conservation. Finally, we make a case for the importance of clear and effective communication for promoting public awareness, public ownership, and for achieving conservation goals within the region.

Historical isolation during Pleistocene low sea level periods is thought to have contributed to divergence among marine basin populations across the Coral Triangle. In the Philippine archipelago, populations in the South China Sea, Sulu Sea-inland seas, and Philippine Sea-Celebes Sea basins might have been partially isolated. Meanwhile, present-day broadscale oceanographic circulation patterns suggest connectivity between these basins. To evaluate hypotheses regarding the influence of historical and contemporary factors on genetic structure, phylogeographic patterns based on mitochondrial control region sequences for a reef-associated fish, Siganus fuscescens, were analysed. Three distinct lineages were recovered. One lineage was identified as the morphologically similar species Siganus canaliculatus, while two lineages are monophyletic with S. fuscescens. Clade divergence and demographic expansion in S. fuscescens occurred during the Pleistocene. A strong signal of latitudinal structure was detected (Φ(CT) = 0.188), driven by marked differences in clade distribution: one clade is widely distributed (clade A), while a second clade (clade B) has a restricted northern distribution. Regional structure of clade A is consistent with the basin isolation hypothesis (Φ(CT) = 0.040) and suggests isolation of the South China Sea (Φ(CT) = 0.091). Fine-scale structure was observed in the South China Sea and south Philippine Sea, while Sulu Sea and inland seas were unstructured. Genetic structure across multiple spatial scales (archipelagic, regional, and fine-scale within basins) suggests the influence of vicariant barriers and contemporary limits to gene flow in S. fuscescens that may be influenced by oceanographic circulation, geographical distance between available habitats, and latitudinal temperature differences.

Tridacna crocea populations were sampled from 15 locations throughout the eastern Philippine seaboard and screened for allozyme variation at 7 polymorphic loci in order to examine the influence of the North Equatorial Current (NEC) bifurcation on population genetic structure. Signif- icant genetic differentiation among all populations was detected (FST = 0.065). Ordination methods and cluster analysis revealed 2 regional groups and a north-south spatial genetic structure broadly concordant with the bifurcation of the NEC into the Kuroshio and Mindanao current branches. Analysis of molecular variance (AMOVA) indicated greater partitioning of genetic variance among groups (FCT = 0.049) than among populations within groups (FSC = 0.029). An isolation-by-distance signal across the entire Philippine seaboard and marked geographical variation of allele frequencies between Kuroshio and Mindanao Current regions suggested that genetic differentiation is likely due to limited larval exchange and genetic drift. The Mindanao current populations are characterized by greater genetic diversity and differentiation (observed heterozygosity, HO = 0.298; FST = 0.056) than the Kuroshio populations (HO = 0.152; FST = 0.025), attributable to variable atmospheric and hydro- graphic regional conditions. Weaker connectivity among Mindanao current populations are attrib- uted to complex patterns of hydrographic circulation south of the NEC bifurcation, which may translate to greater entrainment potential, in turn influencing dispersal and recruitment of planktonic propagules at varying spatial and temporal scales. Fine-scale genetic differentiation was also detected within Kuroshio and Mindanao current populations, indicating the influence of small-scale temporal and spatial physical processes that affect larval dispersal and recruitment along the eastern Philippine seaboard.

Allozyme variation of 10 populations of Linckia laevigata at 8 polymorphic loci and 13 populations of Tridacna crocea at 6 polymorphic loci were analyzed to compare genetic variability and genetic affinities among reefs in Palawan, Philippines. Two to five populations were sampled from each of four regions: the shelf reefs in (1) northern Palawan and (2) southern Palawan and the offshore reefs in (3) the Kalayaan island group (KIG) in the South China Sea and (4) the Tubbataha shoals in the Sulu Sea. Heterozygosity was highest in populations of L. laevigata from the south shelf of Palawan and populations of T. crocea from the Tubbataha shoals of the Sulu Sea. The lowest heterozygosity estimates were from the reefs of the KIG in the South China Sea, for both species. Overall F ST values for both species were significant, with an estimated average number of effective migrants per generation (N EM) of 4.85 (~5 individuals) for L. laevigata and 3.54 (~4 individuals) for T. crocea. Within-region comparisons showed NEM ranging from 6.29 to 92.34 for L. laevigata and from 3.40 to 6.30 for T. crocea. The higher gene flow among L. laevigata populations relative to T. crocea is consistent with the greater dispersal potential of the former species. Finer scale genetic structuring was evident in T. crocea populations. For both species, the Tubbataha reefs in the Sulu Sea have higher genetic affinity with the populations from the southern shelf of Palawan, while the reefs in the KIG had higher affinity with the northern Palawan shelf reefs. The north and south shelf populations have the least genetic affinity. Genetic patchiness among reefs within regions suggests the importance of small-scale physical factors that affect recruitment success in structuring populations in small island and shoal reef systems in Palawan.

Molecular assays are described for the identification of six rabbitfish (Siganus) species. A multiplex PCR assay using primers targeting the mitochondrial cytochrome b region simultaneously identifies four species: Siganus canaliculatus, S. fuscescens, S. javus, and S. spinus. Subsequent RFLP assays of multiplex amplicons differentiate between S. virgatus and S. corallinus based on diagnostic fragments from the mitochondrial cytochrome oxidase I region. Assays were validated with known specimens demonstrating accuracy of the molecular identification. Applied to morphologically indistinguishable early developmental stages, these assays can facilitate studies on species-specific spatio-temporal patterns of larval dispersal and population connectivity to aid fishery management.

The mottled spinefoot, Siganus fuscescens, is an economically important rabbitfish species widely distributed in shallow waters throughout the Indo-Pacific. We describe methods for the identification of thirteen novel microsatellite markers for S. fuscescens using an enrichment protocol. The loci were screened in 126 individuals, revealing moderate to high levels of polymorphism with 5 to 28 alleles per locus and observed heterozygosity ranging from 0.111 to 0.921. No significant deviations from Hardy–Weinberg equilibrium were detected. These polymorphic microsatellites will be useful for studies of genetic diversity, population structure, and demographic connectivity of S. fuscescens.

The world is in the midst of a biodiversity crisis, threatening essential goods and services on which humanity depends. While there is an urgent need globally for biodiversity research, growing obstacles are severely limiting biodiversity research throughout the developing world, particularly in Southeast Asia. Facilities, funding, and expertise are often limited throughout this region, reducing the capacity for local biodiversity research. Although western scientists generally have more expertise and capacity, international research has sometimes been exploitative ``parachute science,'' creating a culture of suspicion and mistrust. These issues, combined with misplaced fears of biopiracy, have resulted in severe roadblocks to biodiversity research in the very countries that need it the most. Here, we present an overview of challenges to biodiversity research and case studies that provide productive models for advancing biodiversity research in developing countries. Key to success is integration of research and education, a model that fosters sustained collaboration by focusing on the process of conducting biodiversity research as well as research results. This model simultaneously expands biodiversity research capacity while building trust across national borders. It is critical that developing countries enact policies that protect their biodiversity capital without shutting down international and local biodiversity research that is essential to achieve the long-term sustainability of biodiversity, promoting food security and economic development.

The milkfish, Chanos chanos (Forsskal, 1775) is a pelagic, monotypic gonorhynchiform widely distributed in the tropical Indo-Pacific. This study evaluates temporal variability of milkfish samples from the Philippine archipelago, and spatial variability at two geographic scales based on restriction fragment length polymorphism (RFLP) analysis of a portion of the mitochondrial control region. High levels of genetic diversity characterize the milkfish control region (mean h=0.908, π=1.59%), with 74 haplotypes detected among the 367 fish analyzed. For temporal analysis of Philippine samples, milkfish were collected over 2 years from three sites (inter-annual variation), and sampled twice within a year during different seasons at four sites (intra-annual variation). No significant temporal variability was detected between or within years. Significant spatial differentiation among the Philippine samples was observed (F ST=0.006, P