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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.

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.

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