The Coral Triangle is the global center of marine biodiversity; however, its coral reefs are critically threatened. Because of the bipartite life history of many marine species with sedentary adults and dispersive pelagic larvae, designing effective marine protected areas requires an understanding of patterns of larval dispersal and connectivity among geographically discrete populations. We used mtDNA sequence data to examine patterns of genetic connectivity in the boring giant clam (Tridacna crocea) in an effort to guide conservation efforts within the Coral Triangle. We collected an approximately 485 base pair fragment of mtDNA cytochrome c oxidase 1 (CO1) from 414 individuals at 26 sites across Indonesia. Genetic structure was strong between regions (phi(ST)=0.549, p < 0.00001) with 3 strongly supported clades: one restricted to western Sumatra, another distributed across central Indonesia, and a third limited to eastern Indonesia and Papua. Even within the single largest clade, small but significant genetic structure was documented (phi(ST)=0.069, p < 0.00001), which indicates limited gene flow within and among phylogeographic regions. Significant patterns of isolation by distance indicated an average dispersal distance of only 25-50 km, which is far below dispersal predictions of 406-708 km derived from estimates of passive dispersal over 10 days via surface currents. The strong regional genetic structure we found indicates potent limits to genetic and demographic connectivity for this species throughout the Coral Triangle and provides a regional context for conservation planning. The recovery of 3 distinct evolutionarily significant units within a well-studied taxonomic group suggests that biodiversity in this region may be significantly underestimated and that Tridacna taxa may be more endangered than currently recognized.

The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ∼18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.

The formation and persistence of modern coral reefs depends largely on organisms that host dinoflagellate algal symbionts of the genus Symbiodinium. There are important ecological and physiological differences among Symbiodinium types, and many host species are able to associate with multiple types, which may facilitate adaptation to local environmental change. Using denaturing gradient gel electrophoresis (DGGE) and sequencing of internal transcribed spacer-2 (ITS2) ribosomal DNA, we identified 11 Symbiodinium types belonging to clades A, C, and D in 250 host animals from 3 Tridacna species in eastern Indonesia. Individuals with multiple symbiont types were common: 42% of all clams had symbionts from multiple clades and 15% of all clams had multiple types from a single clade. T. crocea associated more often with clade C symbionts and less frequently with clade D symbionts. T. squamosa associated more frequently with clade D and less often with clade C symbionts. T. maxima did not preferentially associate with a particular Symbiodinium clade, but sample sizes were low. We used both satellite sea surface temperature and in situ recordings to characterize the thermal environment in the study area. Clams with clade C and D symbionts were located in areas with higher mean temperatures, while clams with clade A symbionts were in cooler areas. This is consistent with previous research indicating that clade C and D types may be more heat-tolerant than clade A. These results support the hypothesis that giant clams can associate with different symbiont types based on local environmental conditions. KEY WORDS: Symbiodinium · Tridacna spp. · Thermal tolerance · Climate change · Coral reef · IndonesiaResale or republication not permitted without written consent of the publisher

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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.