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

Reefs at Risk: A Map-Based Indicator of Threats to the Worlds Coral Reefs

This report presents the first-ever detailed, map-based assessment of potential threats to coral reef ecosystems around the world. "Reefs at Risk" draws on 14 data sets (including maps of land cover, ports, settle-ments, and shipping lanes), information on 800 sites known to be degraded by people, and scientific expertise to model areas where reef degradation is predicted to occur, given existing human pressures on these areas. Results are an indicator of potential threat (risk), not a measure of actual condition. In some places, particularly where good management is practiced, reefs may be at risk but remain relatively healthy. In others, this indicator underestimates the degree to which reefs are threatened and degraded.Our results indicate that:Fifty-eight percent of the world's reefs are poten-tially threatened by human activity -- ranging from coastal development and destructive fishing practices to overexploitation of resources, marine pollution, and runoff from inland deforestation and farming.Coral reefs of Asia (Southeastern); the most species-rich on earth, are the most threatened of any region. More than 80 percent are at risk (undermedium and high potential threat), and over half are at high risk, primarily from coastal development and fishing-related pressures.Overexploitation and coastal development pose the greatest potential threat of the four risk categories considered in this study. Each, individually, affects a third of all reefs.The Pacific, which houses more reef area than any other region, is also the least threatened. About 60 percent of reefs here are at low risk.Outside of the Pacific, 70 percent of all reefs are at risk.At least 11 percent of the world's coral reefs contain high levels of reef fish biodiversity and are under high threat from human activities. These "hot spot" areas include almost all Philippine reefs, and coral communities off the coasts of Asia, the Comoros, and the Lesser Antilles in the Caribbean.Almost half a billion people -- 8 percent of the total global population -- live within 100 kilometers of a coral reef.Globally, more than 400 marine parks, sanctuaries, and reserves (marine protected areas) contain coral reefs. Most of these sites are very small -- more than 150 are under one square kilometer in size. At least 40 countries lack any marine protected areas for conserving their coral reef systems

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

Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa)

Use of universal primers designed from a public DNA database can accelerate characterization of mitochondrial (mt) genomes for targeted taxa by polymerase chain reaction (PCR) amplification and direct DNA sequencing. This approach can obtain large amounts of mt information for phylogenetic inferences at lower costs and in less time. In this study, 88 primers were designed from 13 published scleractinian mt genomes, and these were tested on Euphyllia ancora, Galaxea fascicularis, Fungiacyathus stephanus, Porites okinawensis, Goniopora columna, Tubastraea coccinea, Pavona venosa, Oulastrea crispata, and Polycyathus sp., representing 7 families of complex and robust corals. Seventy-four of the 88 primers (84.1%) successfully amplified completed mt genomes of these 9 corals. Several unique features were identified, including a group I intron insertion in the cytochrome oxidase subunit I (COI) genes of Por. okinawensis, Gon. columna, T. coccinea, and F. stephanus and an extended length of the 3'-end of the COI gene of E. ancora. Preliminary tests using a subset of primers successfully obtained the COI 3'-end of Euphyllia representatives, and the resulting species phylogeny is in agreement with corallite characters and tentacle shapes. The universal primers provided herein effectively decoded scleractinian mt genomes, and can be used to reveal different levels of molecular phylogenetic inferences in scleractinian corals

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