Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea.

For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.

Genomic insights into the historical and contemporary demographics of the grey reef shark.

Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.

Highly restricted dispersal in habitat-forming seaweed may impede natural recovery of disturbed populations.

Cystoseira sensu lato (Class Phaeophyceae, Order Fucales, Family Sargassaceae) forests play a central role in marine Mediterranean ecosystems. Over the last decades, Cystoseira s.l. suffered from a severe loss as a result of multiple anthropogenic stressors. In particular, Gongolaria barbata has faced multiple human-induced threats, and, despite its ecological importance in structuring rocky communities and hosting a large number of species, the natural recovery of G. barbata depleted populations is uncertain. Here, we used nine microsatellite loci specifically developed for G. barbata to assess the genetic diversity of this species and its genetic connectivity among fifteen sites located in the Ionian, the Adriatic and the Black Seas. In line with strong and significant heterozygosity deficiencies across loci, likely explained by Wahlund effect, high genetic structure was observed among the three seas (ENA corrected FST = 0.355, IC = [0.283, 0.440]), with an estimated dispersal distance per generation smaller than 600 m, both in the Adriatic and Black Sea. This strong genetic structure likely results from restricted gene flow driven by geographic distances and limited dispersal abilities, along with genetic drift within isolated populations. The presence of genetically disconnected populations at small spatial scales (< 10 km) has important implications for the identification of relevant conservation and management measures for G. barbata: each population should be considered as separated evolutionary units with dedicated conservation efforts.

New microsatellite DNA markers to resolve population structure of the convict surgeonfish, Acanthurus triostegus, and cross-species amplifications on thirteen other Acanthuridae.

Microsatellites are widely used to investigate connectivity and parentage in marine organisms. Despite surgeonfish (Acanthuridae) being dominant members of most reef fish assemblages and having an ecological key role in coral reef ecosystems, there is limited information describing the scale at which populations are connected and very few microsatellite markers have been screened. Here, we developed fourteen microsatellite markers for the convict surgeonfish Acanthurus triostegus with the aim to infer its genetic connectivity throughout its distribution range. Genetic diversity and variability was tested over 152 fishes sampled from four locations across the Indo-Pacific: Mayotte (Western Indian Ocean), Papua New Guinea and New Caledonia (Southwestern Pacific Ocean), and Moorea (French Polynesia). Over all locations, the number of alleles per locus varied from 5 to 24 per locus, and expected heterozygosities ranged from 0.468 to 0.941. Significant deviations from Hardy-Weinberg equilibrium were detected for two loci in two to three locations and were attributed to the presence of null alleles. These markers revealed for the first time a strong and significant distinctiveness between Indian Ocean and Pacific Ocean A. triostegus populations. We further conducted cross-species amplification tests in 13 Pacific congener species to investigate the possible use of these microsatellites in other Acanthuridae species. The phylogenetic placement of A. triostegus branching off from the clade containing nearly all Acanthurus + Ctenochaetus species likely explain the rather good transferability of these microsatellite markers towards other Acanthuridae species. This suggests that this fourteen new microsatellite loci will be helpful tools not only for inferring population structure of various surgeonfish but also to clarify systematic relationships among Acanthuridae.

From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals.

Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.

Considering reefscape configuration and composition in biophysical models advance seascape genetics.

Previous seascape genetics studies have emphasized the role of ocean currents and geographic distances to explain the genetic structure of marine species, but the role of benthic habitat has been more rarely considered. Here, we compared the population genetic structure observed in West Pacific giant clam populations against model simulations that accounted habitat composition and configuration, geographical distance, and oceanic currents. Dispersal determined by geographical distance provided a modelled genetic structure in better agreement with the observations than dispersal by oceanic currents, possibly due to insufficient spatial resolution of available oceanographic and coastal circulation models. Considering both habitat composition and configuration significantly improved the match between simulated and observed genetic structures. This study emphasizes the importance of a reefscape genetics approach to population ecology, evolution and conservation in the sea.

Superclone Expansion, Long-Distance Clonal Dispersal and Local Genetic Structuring in the Coral Pocillopora damicornis Type ß in Reunion Island, South Western Indian Ocean.

The scleractinian coral Pocillopora damicornis type ß is known to present a mixed reproduction mode: through sexual reproduction, new genotypes are created, while asexual reproduction insures their propagation. In order to investigate the relative proportion of each reproduction mode in P. damicornis type ß populations from Reunion Island, Indian Ocean, clonal propagation along the west coast was assessed through four sampling sites with increasing geographical distance between sites. Coral colonies were sampled either exhaustively, randomly or haphazardly within each site, and genotypic diversity was assessed using 13 microsatellite loci over a total of 510 P. damicornis type ß determined a posteriori from their mtDNA haplotype (a 840 bp sequenced fragment of the Open Reading Frame). Overall, 47% of all the sampled colonies presented the same multi-locus genotype (MLG), a superclone, suggesting that asexual propagation is extremely important in Reunion Island. Within each site, numerous MLGs were shared by several colonies, suggesting local clonal propagation through fragmentation. Moreover, some of these MLGs were found to be shared among several sites located 40 km apart. While asexual reproduction by fragmentation seems unlikely over long distances, our results suggest a production of parthenogenetic larvae. Despite shared MLGs, two differentiated clusters were enclosed among populations of the west coast of Reunion Island, revealing the necessity to set up appropriate managing strategies at a local scale.

Endangered New Caledonian endemic mushroom coral Cantharellus noumeae in turbid, metal-rich, natural and artificial environments.

Since its description in 1984, little attention has been paid to the New Caledonian endemic mushroom coral Cantharellus noumeae (Fungiidae), an IUCN Red-listed, endangered coral species. Our study presents the first ever quantitative assessment conducted on C. noumeae populations for two contrasting sites in the same turbid bay. Sites differed by their substrates of artificial or natural origins. Metal concentrations of superficial sediment were measured. C. noumeae was found in high densities in metal-rich and turbid environments at both locations, reaching up to 288 individuals per 50m(2). It was 3.5 times more abundant on natural rock than on artificial substrates. Recruitment was also higher proportionally on rock (47% vs 7-14%). The composition of the associated coral communities included 30-37 species occurring in low densities. Our findings clarify the environmental niche of this species and its colonization potential, in order to eventually better characterize its conservation status.

Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.).

Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus.

Genetic relatedness in groups of the humbug damselfish Dascyllus aruanus: small, similar-sized individuals may be close kin.

Kin selection plays an important role in the evolution of social behaviour in terrestrial systems. The extent to which kin selection influences the evolution of social behaviour in marine systems is largely unexplored. Generally, it is considered that kin selection is irrelevant in marine systems, because it is assumed that the dispersing larval phase of marine organisms will break up kin associations. Here, we challenge this assumption and investigate the opportunity for kin selection in a coral reef fish: the humbug damselfish Dascyllus aruanus. This fish lives in groups composed of a large male and a number of smaller females and nonbreeders. We use 10 polymorphic microsatellite loci to assess the relatedness of 265 individuals from 35 groups. The mean coefficient of relatedness among group members is 0.01 +/- 0.04, suggesting that individuals are not associated with close relatives. However, the distribution of pairwise relatedness of individuals within groups has an overabundance of positive values, and indicates that there might be 35 pairs of close relatives within groups. Further analyses reveal that close relatives likely are similar in size and small in size, suggesting that they might have recruited together. We conclude that it is possible for kin selection to operate in D. aruanus, but kin recognition will be a prerequisite for such selection. This study reveals that individuals can be associated with close relatives, and there is a hidden potential for kin selection, during certain parts of the life cycle of coral reef fishes.

Parallel responses of species and genetic diversity to El Niño Southern Oscillation-induced environmental destruction.

Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to suggest a novel macro-ecological pattern termed the species-genetic diversity correlation. We tested whether this prediction holds for areas affected by recent habitat disturbance using butterfly communities in east Kalimantan, Indonesia. Here, we show that both strong spatial and temporal correlations exist between species and allelic richness across rainforest habitats affected by El Niño Southern Oscillation-induced disturbance. Coupled with evidence that changes in species richness are a direct result of local extirpation and lower recruitment, these data suggest that forces governing variation at the two levels operate over parallel and short timescales, with implications for biodiversity recovery following disturbance. Remnant communities may be doubly affected, with reductions in species richness being associated with reductions in genetic diversity within remnant species.

Short-term impact of 1997/1998 ENSO-induced disturbance on abundance and genetic variation in a tropical butterfly.

In order to assess the short-term impact of habitat loss after disturbance, we studied Arhopala epimuta (Lepidoptera: Lycaenidae) populations in 5 landscapes in Borneo that were differentially affected by the 1997/1998 El Niño Southern Oscillation-induced drought and fire. Sampling was conducted before (1997) and after (1998 and 2000) disturbance. This study combined demographic and genetic data inferred from the analysis of 5 microsatellite loci and mitochondrial DNA (mtDNA) control region sequences. Over all 5 landscapes, a total of 313 A. epimuta were sampled over the 3-year survey. Butterfly abundance varied greatly both spatially and temporally (within disturbed landscapes). After the disturbance, a 4-fold population expansion was observed in a small unburned isolate, whereas population extinction was observed in one of the severely burned areas. The analysis of mtDNA sequences in a subsample of 106 A. epimuta revealed no significant spatial or temporal genetic structure. The analysis of 5 microsatellite loci revealed high frequencies of null alleles. Genetic evidence of recent change in population size was found in all 3 unburned landscapes using microsatellites. Congruent to mtDNA, microsatellites failed to detect significant genetic structure according to sampling year or landscapes. Our results suggest that, for mobile species within recently fragmented habitat, habitat loss after disturbance may lead to local population extinction but may augment genetic diversity in remnant local populations because of increased gene flow.