Pronounced Genetic Structure in a Highly Mobile Coral Reef Fish, Caesio cuning, in the Coral Triangle

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We evaluated the genetic population structure of C. cuning using a 382 bp segment of the mitochondrial control region amplified from over 620 fish sampled from 33 localities across the Philippines and Indonesia. Phylogeographic analysis showed that individuals sampled from sites in western Sumatra belong to a distinct Indian Ocean lineage, resulting in pronounced regional structure between western Sumatra and the rest of the Coral Triangle (φCT = 0.4796, p \u3c 0.004). We found additional significant population structure between central Southeast Asia and eastern Indonesia (φCT = 0.0450, p \u3c 0.001). These data in conjunction with spatial analyses indicate that there are 2 major lineages of C. cuning and at least 3 distinct management units across the region. The location of genetic breaks as well as the distribution of divergent haplotypes across our sampling range suggests that current oceanographic patterns could be contributing to observed patterns of structure

Pronounced Genetic Structure in a Highly Mobile Coral Reef Fish, Caesio Cuning, in the Coral Triangle

The redbelly yellowtail fusilier, Caesio cuning, has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of regional limits to connectivity across this region. However, these have focused almost exclusively on benthic reef dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no in depth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We evaluated the genetic population structure of C. cuning using a 382bp segment of the mitochondrial control region amplified from over 620 fish sampled from 33 localities across the Philippines and Indonesia. Phylogeographic analysis showed that individuals sampled from sites in western Sumatra belong to a distinct Indian-Ocean lineage, resulting in pronounced regional structure between western Sumatra and the rest of the Coral Triangle (ΦCT = 0.4796, p \u3c 0.0043). We measured additional significant population structure between central Southeast Asia and eastern Indonesia (ΦCT = 0.0450, 36 p \u3c 0.0002). These data in conjunction with spatial analyses indicate that there are two major lineages of C. cuning and at least three distinct management units across the region. The location of genetic breaks as well as the distribution of divergent haplotypes across our sampling range suggests that current oceanographic patterns could be contributing to observed patterns of structure

Concordant Phylogenetic Patterns Inferred from Mitochondrial and Microsatellite DNA in the Giant Clam Tridacna Crocea

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

Variability in Philippine <i>Coffea liberica</i> Provides Insights into Development Amidst a Changing Climate

The Philippines is one of only a few countries where Coffea liberica is commercially produced. Two infra-species, C. liberica liberica (also locally known as ‘liberica’) and C. liberica var dewevrei (also known as ‘excelsa’) comprise 1.1% and 5.7% of the national coffee production, respectively. These rare varieties are produced widely in the provinces of Batangas and Cavite mainly because of historical affinity, a local market, and more recently the renewed interest from importers. Aside from its unique flavor profile, renewed interest comes from the potential of the larger beans and deeper root systems of the species to thrive on a warming planet. In this paper, we present work that has been performed in evaluating bean morphology, chlorogenic acid, caffeine content and genetic variability of C. liberica varieties from different areas of the country. The initial efforts to predict areas for increased production were based on a maximum entropy model. Combining these data provides insights into development areas for increased production in the Philippines

High throughput RNA sequencing reveals temperature tolerance mechanisms in Scylla serrata

Abstract only.The effects of increasing temperature from global climate change threaten the sustainability and production of mud crabs from farms and wild populations in mangroves. Adaptation of mud crab populations to temperature stress is difficult to evaluate until now, with the emergence of RNA-Seq, a method which evaluates total mRNA expression under different conditions. In this study, 10 individuals each of S. serrata from Buguey, Cagayan were exposed to 26~&amp;rsquo;C and 32~&amp;rsquo;C for two weeks and the mRNA profiles were compared based on 186 million high quality pair-end reads which were aligned to a S. serrata reference transcriptome assembled de novo from 24,350 contigs with an average N50 of 1564 bp. Temperature related differences in gene expression were not significantly detected between the control and treatment groups and this was mostly due to the highly expressed genes such as the low and high molecular weight heat shock proteins. However, variations were greater among genes involved in the process of cell cycle regulation, the dissimilation processes such as oxidative phosphorylation, reproduction and transport across membranes. Greater differences were observed between immature or mature males and females

Population structure of Scylla serrata from microsatellite and mtDNA markers

Abstract only.Determination of the population structure and connectivity of natural populations of Scylla serrata are useful tools for decision making related to conservation and management efforts of this species. They provide important considerations as recovery and sustainability of the industry relies on the availability of hardy recruits that can replenish harvested resources from the system. In the case of marine domesticated species, admixture is expected due to commodity trade and exchanges. Current population structure of five wild populations of S. serrata from Pangasinan, Bataan, Cagayan, Quezon, and Panay was determined using five microsatellite markers, cross-amplified from Scylla paramamosain in a total of 259 samples. Mitochondrial 16S rDNA sequences of 25 representative individuals from the same locations were used to provide a comparison with original evolutionary patterns. Quality check of microsatellite data revealed no null alleles in the data set, with all loci and populations exhibiting Hardy-Weinberg Equilibrium. Pairwise FST analysis reveals FST values between 0.001-0.08432 with 9 out of the 16 possible comparisons considered significant. Phylogenetic analysis was performed on the 16S rDNA sequences, supported by bootstrap values. Both sets of data suggest 2 distinct groupings: the east coast populations of Cagayan and Quezon, the west coast populations of Pangasinan and Bataan, with admixture observed in the group from Panay. Additional data from 5 microsatellite markers specifically developed for S. serrata and the D-loop region will be added to the analysis. The results from both mitochondrial and microsatellite markers, revealing an East-West separation of S. serrata populations, suggest that current and evolutionary population patterns are matching. Aquaculture practices appear to have not yet significantly affected the population structure of this domesticated species, as initially speculated

Identification of a species diagnostic character for instar and juvenile mud crabs (Genus Scylla)

A species diagnostic character in instar and juvenile Scylla spp. allows for more focused use of resources in farms, enhanced research in wild populations and improved culture practices into preferred species. Species identification using molecular methods entails extraction of soft tissue that can be fatal to early developmental morphs. This prevents downstream applications that require live samples. In this study, a potential species diagnostic character from the frontal lobe spine shapes of 177 wild-caught Scylla crablets was generated. The species of the samples were identified using the molecular internal transcribed spacer 1 and 16S rDNA markers. Fourier transformation was employed on the images of their spines using the software SHAPE and the results underwent discriminant and principal component analyses. This method was able to assign 92.4% of Scylla serrata, 96.2% of S. olivacea and 90.1% of S. tranquebarica to the right species. The frontal lobe spine shapes of each species group were then traced and used as a means for species identification on 50 cultured and 100 wild-caught Scylla crablets through Resemble.js. This method was then able to assign 85.9% of the instars and 84.7% to the correct species, verified using molecular markers. Results of this study show great potential for the use of the frontal lobe spines as a morphological diagnostic character for instars and juveniles. Increased accuracy can be achieved by expanding the reference shape database and inclusion of more Scylla populations across the region. © 2018 Elsevier B.V

Heavy metal levels in mud crabs (Scylla spp.) from East Bataan Coast

Heavy metal levels (Pb and Cu) on adult mud crabs (Scylla spp.) from the East Bataan Coast were determined. Muscle tissue from each crab was processed through nitric acid digestion and analyzed using atomic absorption spectroscopy. The average concentrations in the samples were 3.37 × 10−3 and 1.01 mg/L—both within WHO acceptable limits. These were contrasted with the levels found in sediments from catch and grow-out sites (17.9, 14.5, 37.8, and 31.3 mg/L) and were found to be significantly lower in concentration. It takes 3–8 months before adult mud crabs can be harvested from grow-out ponds, and the data suggests that the organisms, even when constantly exposed to high levels of Pb and Cu, do not bio-accumulate toxic levels of these heavy metals. Mud crabs constitute a major economic natural resource in the Philippines and in the province of Bataan. Commanding high prices due to the quality of its meat, it is also a preferred culture product due to its impressive size, rapid growth rate, and high flesh content. Mud crab culture in Bataan is primarily driven by grow-out of captured juveniles in pen or pond cultures sourced from nearby bodies of water—making them vulnerable to prolonged exposure to pollutants. The East Bataan Coast shares its waters with the polluted Manila Bay, giving rise to the concern of the quality of seafood acquired from the area. © 2015, Springer-Verlag Berlin Heidelberg

Expressions of molt-inhibiting hormone (MIH) and extracellular signal-regulated kinase (ERK) during the molting stages of the giant mud crab, Scylla serrata

Survival and growth of mud crabs and any other crustaceans depend on molting. Molting is influenced by several hormones, two of which are Molt-Inhibiting Hormone {MIH} and a molt promoting hormone, the Extracellular Signal-regulated Kinase (ERK). Controlling and synchronizing the molting of the crabs would be a big boost to the mud crab industry, especially in the production of soft shell crabs. The best way to control molting would be to stock juvenile crabs of the same molting stage together. In this study, hormone expressions were analyzed using quantitative Real-Time Polymerase Chain Reaction (1RT-PCR). Molt stages of 36 juvenile S. serrata were established based on MIH and ERK expression levels that was analyzed using Principal Component Analysis (PCA). One group of six individuals had MIH value equal to zero and presumed to be in the PR stage. The rest of the crabs had values for MIH and were presumed to be in the PM-IM stage. The value of ERK for the PM-IM stage was higher at 24.79 than in the PR stage at 21.67. Based on the data gathered, morphological markers may now be identified to standardize hormone expression. This would be the first study concerning the comparison of hormones during molting.This research was supported by the Department of Science and Technology - Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development and the Southeast Asian Fisheries Development Center - Aquaculture Department, along with CDO Foodsphere, Inc. for providing the mud crabs

Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results: We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.This work was funded by the Department of Science and Technology Philippine Council for Agriculture and Aquatic Resources Research and Development (DOST-PCARRD) Mangrove Crab Program to De La Salle University-Manila through MCAL. AMSS was partially funded by University Research Coordination Office, De La Salle University-Manila. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript