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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.

Tropical coral reefs are threatened by local-scale stressors that are exacerbated by global ocean warming and acidification from the post-industrial increase of atmospheric CO2 levels. Despite their observed decline in the past four decades, little is known on how Philippine coral reefs will respond to ocean warming and acidification. This study explored individual and synergistic effects of present-day (pH 8.0, 28°C) and near-future (pH 7.7, 32°C) scenarios of ocean temperature and pH on the adult Favites colemani, a common massive reef-building coral in Bolinao-Anda, Philippines. Changes in seawater temperature drive the physiological responses of F. colemani, whereas changes in pH create an additive effect on survival, growth, and photosynthetic efficiency. Under near-future scenarios, F. colemani showed sustained photosynthetic competency despite the decline in growth rate and zooxanthellae density. F. colemani exhibited specificity with the Cladocopium clade C3u. This coral experienced lower growth rates but survived projected near-future ocean warming and acidification scenarios. Its pH-thermal stress threshold is possibly a consequence of acclimation and adaptation to local environmental conditions and past bleaching events. This research highlights the importance of examining the susceptibility and resilience of Philippine corals to climate-driven stressors for future conservation and restoration efforts in the changing ocean.

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.

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.

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.

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