Interspecific, spatial and temporal variability of self-recruitment in anemonefishes

Gene flow throughout the evolutionary history of a colour polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sedentary adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterize the species' population structure, demographic history and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Interestingly, colour patterns differed noticeably among the Indonesian populations and the two populations at the extreme of the sampling distribution (i.e. Maldives and New Caledonia), which exhibited more comparable colour patterns despite their geographic and genetic distances. Our study emphasizes how whole-genome studies can uncover the intricate evolutionary past of wide-ranging species with diverse phenotypes, shedding light on the complex nature of the species concept paradigm.

Genetic population subdivision of the blue swimming crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: Implication to sustainable fishery

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodities with an export value for Indonesia and an increasing global market demand, annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, even when it is important to inform stock unit management and sustainable use. This study aimed to determine the genetic diversity and differentiation of blue swimming crabs across Indonesian populations in different Fishery Management Area (FMA), and their spatial genetic connectivity, as well as to deliver implications for sustainable fishery. A total of 297 individuals were collected and amplified using cytochrome oxidase I mitochondrial DNA. This study has showed the highest values for haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fisheries management areas (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia, likely have several stock units, and preferably different fisheries management plans and actions across the region thoroughly and simultaneously. This would be effective for management and their sustainable conservation.

Travel with your kin ship! Insights from genetic sibship among settlers of a coral damselfish

Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behavior and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment event of Dascyllus abudafur in the Red Sea (N = 168 settlers). We analyzed the genetic composition of the larvae and assessed whether kinship among these was significantly different from random as evidence for cohesive dispersal during the larval phase. We used Monte Carlo simulations of similar-sized recruitment cohorts to compare the expected kinship composition relative to our empirical data. The high number of siblings within the empirical cohort strongly suggests cohesive dispersal among larvae. This work highlights the utility of kinship analysis as a means of inferring dynamics during the pelagic larval phase.

Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on D_A distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.

Seascape and life-history traits do not predict self-recruitment in a coral reef fish

The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4-0.5% at 0.15 km(2)) and the lagoon scale (0.6-0.8% at approx. 700 km(2)). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.

Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo-Malay Archipelago: inferences from a mitochondrial and microsatellite loci

To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo-Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker-derived results. Both marker systems detected a strong overall genetic structure (ΦST = 0.096, P < 0.0001; mean D est = 0.17; F ST = 0.015, P < 0.0001) and best supported regional groupings (ΦCT = 0.199 P < 0.0001; F CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker-specific results have important implications for conservation efforts concerning this and similar species.