The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.

Abstract <p>Significant efforts have been made to describe the diversity of the sponge class Homoscleromorpha across various oceanic regions, yet the Tropical Eastern Atlantic remains largely unexplored. The insular nature and volcanic origin of the Cape Verde archipelago favour the presence of numerous submarine caves, which are recognized as favourite habitats for Homoscleromorpha. Prior to this study, three species had previously been reported from shallow-water habitats of Cape Verde: Plakina monolopha, Plakortis simplex, and Oscarella lobularis, and all three species had long been considered cosmopolitan. Our exploration of submarine caves has led to the discovery of four new species and one new genus, belonging to the Families Oscarellidae and Plakinidae: Oscarella antea sp. nov., Aspiculina malanoba gen. nov., sp. nov., Plakinastrella fauvelotae sp. nov., and Plakinastrella freitasi sp. nov. We have also examined the two Plakinidae reported in past studies, which in fact correspond to a fifth new species, here named Plakinastrella cachupa sp. nov. These descriptions have been conducted using an integrative approach, combining molecular investigation with accurate morphological analyses. Among the new taxa, two skeleton-less sponges could be described only after histological and cytological investigations, underscoring the need to generalize this type of approach for all Homoscleromorpha. Additionally, for three new Plakinastrella, we have used, for the first time, a mathematical method to analyse spicule size distributions in different classes. We believe that only detailed descriptions of phenotypes such as these can help to reveal the true diversity of Homoscleromorpha and their evolutionary history.</p>

ABSTRACT Coastal marine megafauna faces increasing threats from habitat degradation, climate change, and human activities, making conservation efforts crucial for their survival. The New Caledonian dugong population was reclassified as Endangered on the IUCN Red List in 2021, following research on its abundance and genetic diversity. With fewer than 800 individuals estimated between 2008 and 2012, urgent conservation measures are needed to prevent further decline. Modern genetic tools provide critical insights into spatial genetic differentiation and gene flow across New Caledonia's extensive lagoon habitats. In this study, we analyzed 66 skin samples from live and stranded dugongs collected between 2003 and 2023, using a multiscale genetic approach. We examined mitochondrial DNA control region sequences at the Indo‐Pacific level, 13 microsatellite loci to compare New Caledonian and Australian populations, and 2499 single nucleotide polymorphisms (SNPs) to assess fine‐scale structure within New Caledonia. Our findings confirm that the New Caledonian dugong population has extremely low genetic diversity and is highly differentiated from its Australian counterpart. The effective population size ( N e ) was critically low, ranging between 95 and 160 individuals, depending on the analytical approach. Within New Caledonia, we identified two genetically distinct clusters along the west coast, north and south of Bourail, a division consistent with previous satellite tracking studies showing no movement across this natural boundary. These findings highlight the urgency of conservation action and suggest that the population's isolation and low genetic diversity may warrant an upgrade to Critically Endangered status.

The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.

The skin microbiome plays a vital role in the health of marine mammals, serving as a protective barrier and interacting with the host’s immune system. There is limited knowledge about the skin microbiome of dugongs (Dugong dugon), a vulnerable species with declining groups due to anthropogenic threats. This study provides the first comprehensive analysis of the skin microbiome of free-ranging dugongs in New Caledonia using 16S rRNA gene sequencing. The results show that the dominant bacterial phyla on dugong skin are Pseudomonadota, Bacteroidota, and Campylobacterota. Within Bacteroidota, the genus Tenacibaculum - which includes known opportunistic pathogens - was notably the most relatively abundant. Among Pseudomonadota, Psychrobacter was the most dominant genus; although it may contribute to maintaining skin homeostasis, its overrepresentation has been associated with compromised health in other marine mammals. Additionally, the genera Arcobacter and Campylobacter, both belonging to Campylobacterota, include zoonotic species and may warrant future monitoring in dugong populations. Distinct variations were noted between sex, with females predominantly hosting Psychrobacter, while males had higher abundances of Kinneretia and Dasania. Our results align with emerging evidence that marine mammal skin microbiota are shaped by host-specific traits, environmental conditions, and geographic context. These findings provide a baseline for future research on the skin microbiome of dugongs and highlight potential indicators of health and disease in this species.

The susceptibility of species to habitat changes depends on which ecological drivers shape individual fitness components. To date, only a few studies have quantified fitness components such as the Lifetime Reproductive Success across multiple generations in wild marine species. Because of a long-term sampling effort, such information is available for the population of wild orange clownfish, Amphiprion percula, from Kimbe Island (Papua New Guinea). Previous work on the wild orange clownfish near Kimbe Island suggests that there is little adaptive potential and that variation in LRS is mainly driven by a breeder’s habitat. Whether the host anemone species, geographic location, density or depth contributed to LRS remains however unknown because they were combined into a unique variable. We tested whether it is the ecology or the spatial distribution of clownfish that shaped the individual variation of a local fitness component, which would affect the population self-recruitment process and ultimately the maintenance of this wild population. Our spatially explicit analysis disentangled the role of these factors. We found that the host anemone species had an impact on wild clownfish LRS independently from their spatial distribution. The spatial distribution nevertheless had an impact on its own, as reflected by the spatial autocorrelation of LRS. Depth and density of anemones did not show a significant impact. Our findings imply that this clownfish population is susceptible to modifications of the spatial distribution and local assembly of anemone species

The small giant clam, Tridacna maxima, is distributed from the Red Sea and East African coast to French Polynesia. Across this widespread Indo-Pacific range, T. maxima shows strong population structure, in agreement with its limited dispersal abilities. Peripheral populations may have smaller effective population sizes, increasing their vulnerability under any environmental changes. Understanding evolutionary processes at play in such regions located at the edges of T. maxima distribution is a prerequisite in the context of transfers and restocking programmes. In this study, giant clams were sampled from 14 atolls and islands within four archipelagos in the peripheral region of French Polynesia, in 2001–2002 and/or in 2012–2013, then genotyped at the COI gene and at nine microsatellite loci. Mitochondrial lineages of T. maxima from French Polynesia diverged from those sampled in Micronesia, Melanesia, the Coral Triangle and the Red Sea by 6.6– 7.3%. Within French Polynesia, significant genetic structure was found, indicating restricted gene flow, and it was stable through time. Most of the genetic variation at microsatellite loci was between archipelagos. The most differentiated archipelago was the most geographically isolated (the Austral Islands). The current patterns of genetic structuring of T. maxima in French Polynesia probably result from long-term genetic isolation with limited dispersal ability. In addition, these results underlined that sufficiently large populations of T. maxima have persisted in the Central Pacific during the last sea-level regression. 6. Strategies to optimize transfers and restocking programmes should be designed to preserve the genetic diversity and structure observed here, to avoid the risks

Facing an alarming continuing decline of wild sea cucumber resources, management strategies were developed over the past three decades to sustainably promote development, maintenance, or regeneration of wild sea cucumber fisheries. In New Caledonia (South Pacific), dedicated management efforts via restocking and sea ranching programs were implemented to cope with the overharvesting of the sandfish Holothuria scabra and the recent loss of known populations. In order to investigate genetic implications of a major H. scabra restocking program, we assessed the genetic diversity and structure of wild stocks and hatchery-produced sandfish and compared the genetic outcomes of consecutive spawning and juvenile production events. For this, 1358 sandfish collected at four sites along the northwestern coasts of New Caledonia, as well as during five different restocking events in the Tiabet Bay, were genotyped using nine polymorphic microsatellite markers. We found that wild H. scabra populations from the northwestern coast of New Caledonia likely belonged to one panmictic population with high level of gene flow observed along the study scale. Further, this panmictic population displayed an effective size of breeders large enough to ensure the feasibility of appropriate breeding programs for restocking. In contrast, hatchery-produced samples did suffer from an important reduction in the effective population size: the effective population size were so small that genetic drift was detectable over one generation, with the presence of inbred individuals, as well as more related dyads than in wild populations. All these results suggest that dedicated efforts in hatcheries are further needed to maintain genetic diversity of hatchery-produced individuals in order to unbalance any negative impact during this artificial selection.

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-byenvironment 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.

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 (N-e) 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 N-e 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 N-e 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 N-e observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary N-e, 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.

Sponges are important components of coral reefs with diverse ecological roles. They can be dominant in certain ecosystems of the western Indian Ocean (WIO) region, but their biodiversity remains poorly studied. Most of the knowledge from this region originates from studies conducted 50 years ago in the South Western (SW) region of Madagascar, near Toliara, prior to the degradation of coral reefs and associated ecosystems caused by large environmental disturbances. Here, a reference list is presented including all sponge species that were recorded at that time in different marine habitats of Toliara. This state-of-the-art work includes taxonomic updates. So far, the sponge fauna of Toliara accounts for 267 species, belonging to 3 classes, 23 orders and 68 families, a remarkable diversity when compared to other tropical locations. More than 50 % of the past taxonomic names needed to be updated and with this new baseline it will be possible to allow assessment of long-term changes in sponge biodiversity in relation to environmental stressor changes that have occurred in the SW of Madagascar during the last 50 years.

The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult-disperser species, and when distribution-wide sampling is difficult. Here, we developed a two-step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos, a reef-associated shark distributed across the tropical Indo-Pacific. In the first step, we developed a seascape genomic approach based on isolation-by-resistance models involving circuit theory applied to 515 shark samples, genotyped for 4991 nuclear single-nucleotide polymorphisms. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global-scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.

Although fish is an important source of nutrients, including some of the healthiest proteins, long-chain fatty acids, and essential selenium, species at the top of the food chain frequently contain large amounts of toxic mercury (Hg). The provisional tolerable weekly intake (PTWI) of Hg from fish consumption is calculated from the total concentration of Hg and assuming that all Hg is speciated as organic methylmercury (MeHg). Using high energy-resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy, we show that blue marlin (Makaira sp.), a common top predator consumed by humans, contains high concentrations of inorganic Hg(II) complexed as 57 ± 10% Hg-tetraselenolate [Hg(Sec)4] and 43 ± 10% tiemannite (HgSe). The stable Hg–Se chemical bond likely attenuates the bioavailability of Hg and counteracts some of its health hazards to consumers. Thus, monitoring the concentration of MeHg, rather than total Hg, in top predators such as marlin would provide a more robust measure of potential Hg exposure and may be sufficient for food safety controls. The bonding of Hg atoms to four selenocysteine (Sec) residues in the Hg(Sec)4 complex severely depletes the stock of bioavailable Se, and quantification shows that blue marlin is not a chief source of dietary Se essential to selenoenzyme synthesis and activity.

Abstract 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 F ST = 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.

Giant clams are conspicuous bivalves inhabiting Indo-Pacific reefs. Since Rosewater’s seminal paper in 1965, the number of giant clam species described or resurrected has exactly doubled. The increased number of species reported and accessibility to genetic material of rare or uncommon species therefore call for a reappraisal of the phylogenetic relationships within the Tridacninae subfamily. Here, we aim to reconstruct the evolutionary relationships among all 12 extant species by performing a comprehensive phylogenetic analysis of mitochondrial genome and nuclear 18S rRNA data from a combination of genome skimming, Sanger sequencing and previously published sequences. Comparing the mitogenomes among Tridacninae species, we report two new findings: (1) the T. crocea mitogenome length obtained here (18,266 bp) is shorter than previously known, and (2) the mitochondrial gene order in T. crocea and T. squamosa differs from the other species. Our phylogeny based on a concatenated 16-gene dataset (15 mitochondrial markers and nuclear 18S rRNA) reveals highly supported relationships within and between the three subgenera, Tridacna (Tridacna), Tridacna (Persikima) and Tridacna (Chametrachea). Overall, the inclusion of new molecular markers greatly improves the confidence and support for the subfamily’s phylogeny. The availability of this comprehensive phylogenetic dataset serves as the foremost baseline of Tridacninae relationships to support future studies examining giant clam systematics, ecology and conservation.

We used genetic markers, namely allozymes, to study the genetic structure (stock unit) and the sardine stocks movement along the Moroccan Atlantic coast and its relationship regarding the environmental features, especially upwelling. In this study, we have combined previous results obtained by analyzing eight samples collected during the spawning season (winter 2004) (chlaida et al.2008) and new data obtained by analyzing eight samples gathered during the feeding season (summer 2006). Therefore, we compiled 765 individuals from an earlier study and the 2006 summer sampling and compared seasons' results. In winter, a substantial heterogeneity (Fst =0.205) is described, with a significant genetic break in the Agadir Bay (latitude 30° 48' N) that cuts the coastal sardine populations in the Moroccan Atlantic into two stocks (north and south). In summer, the genetic structure showing two groups is maintained (Fst= 0.135). Still, the genetic break separating the two stocks arises southward, near Tarfaya (latitude 28°08'10" N), suggesting a spreading out towards the south of the northern stocks. This result seems to be related to the sardine movement along the Moroccan Atlantic coast regarding reproduction needs in winter and for trophic reasons in summer. The species' observed genetic break and seasonal activity along the Moroccan coast are expected to result from the Cape Ghir Hydrological barrier, impermeable in winter and semi-permeable in summer. This barrier comprises currents, gyres, and different mesoscale structures related to upwelling dominating in this zone.

The unique biodiversity in the Red Sea is the result of complex ecological and evolutionary processes driven by Pleistocene climatic change. Here we investigate the species diversity, phylogenetic relationships and phylogeographical patterns of giant clams in the Western Indian Ocean (WIO) and the Red Sea to explore scenarios of marine speciation in this under-studied region.

We addressed the evolutionary history of Tridacna giant clams by combining molecular phylogenies with the geographic distribution of lineages across the Indo-West Pacific, with a focus on the Western Indian Ocean (WIO). A giant clam initially identified as T. maxima was genetically distinct and identified as T. elongatissima, a long-forgotten species from Mozambique. Two nominal species endemic to the Mascarene basin, T. lorenzi and T. rosewateri were found to be a single and same, distinct species. Tridacna elongatissima turned out to be the sister species of T. squamosina, another recently resurrected species endemic to the Red Sea. The T. elongatissima-T. squamosina pair was itself sister to T. rosewateri, highlighting this part of the world as a hotspot of endemism for giant clams. With two unrelated lineages in the WIO, one of which was sister to a third lineage endemic to the Red Sea, lineage diversification patterns within the widespread T. maxima mirrored those of T. elongatissima, T. rosewateri and T. squamosina. The same geographic barriers and speciation processes may thus have acted repeatedly at different periods in the Pleistocene.

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.

Noah’s giant clam (Tridacna noae), recently resurrected from synonymy with T. maxima, occurs from Christmas Island to the Northern Line Islands and from the Ryukyu Islands to New Caledonia. We used mitochondrial and microsatellite markers to investigate the phylogeographic structure and demographic history of T. noae over most of its geographical range. Results from the two types of markers reveal a consistent population structure, partitioning T. noae into three distinct lineages: (1) eastern half of the Indo-Malay archipelago and Western Australia, (2) Melanesia and Micronesia, and (3) Central Polynesia. Demographic expansion initiated between 300,000 and 400,000 years ago was detected for each haplogroup. This pattern, which is congruent with other co-occurring Tridacna species, indicates a shared evolutionary history with expansion from past refuges following late-Pleistocene sea-level changes.

Ce journal illustre le déroulement de la mission DHEEP à bord du N.O. Marion Dufresne, aux îles Eparses en avril 2019. L'objectif de cette mission était de récolter le matériel biologique nécessaire à l'étude de l'histoire démographique de la faune marine récifale de l’ouest de l’océan Indien. Des récoltes de millépores, tridacnes, chitons, bernard l’hermite, ophiures, holothuries et poissons ont été faites sur les récifs des îles Europa, Juan de Nova, Glorieuses et Tromelin. Parmi les événements marquants de cette mission sont la collecte de spécimens de deux nouvelles espèces de poissons du genre Gymnocranius et l’échantillonnage de deux tridacnes rares en cours de révision taxonomique, Tridacna elongatissima et T. rosewateri.

The critically endangered coral species Acropora palmata used to dominate shallow Caribbean reefs but since the early 1980s, populations have dramatically declined. At the Caribbean scale, A. palmata is divided into two genetically divergent lineages and most of previous works investigating population connectivity among populations involved the western line-age (in Florida, the Bahamas, the Mesoamerican Reef System, and the Greater Antilles). Small scale genetic connectivity among A. palmata populations was globally found, possibly enhancing populations' recovery at the local scale. Yet, little is known regarding the genetic connectivity of populations of the eastern lineage, especially those of the Lesser Antilles, a fragmented archipelago located at the edge of the species distribution. Here, we filled this gap by investigating the genetic diversity, population structure and connectivity of A. palmata populations among 36 sampled sites from 11 islands of the Lesser Antilles using 14 hypervariable microsatellite loci. Globally, genetic diversity levels in A. palmata populations from the Lesser Antilles were lower compared to what was previously reported within the Wider Caribbean. The analysis of the genetic structure, crossed with spatial autocorrelation analysis, revealed an isolation-by-distance pattern at both reef and Lesser Antilles scales. A gene dispersal distance of less than a kilometer, and a northward gene flow direction, in agreement with ocean surface currents in the region were found. Altogether, our results suggest a restricted population connectivity and short distance dispersal of A. palmata larvae within the Lesser Antilles further limited by geographic distances among suitable habitat patches. Additionally, our results suggest that southernmost populations are potential sources of larvae for the most northerly islands and have a key role in reseeding A. palmata populations of the Lesser Antilles.

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 ey-douxi/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 specia-tion 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.

Giant clams, the largest living bivalves, play important ecological roles in coral reef ecosystems and provide a source of nutrition and income for coastal communities; however, all species are under threat and intervention is required. Here, we re-examine and update their taxonomy, distribution, abundance and conservation status as a contribution to the protection, rebuilding and management of declining populations. Since the first comprehensive review of the Tridacnidae by Rosewater (1965), the taxonomy and phylogeny of giant clams have evolved, with three new species descriptions and rediscoveries since 1982 represented by Tridacna squamosina (formerly known as T. costata), T. noae and T. lorenzi. Giant clams are distributed along shallow coasts and coral reefs from South Africa to the Pitcairn Islands (32 degrees E to 128 degrees W), and from southern Japan to Western Australia (24 degrees N to 1.5 degrees S), Geographic distribution of the 12 currently recognized species is not even across the 66 localities we review here, Tridacna maxima and T. squamosa are the most widespread, followed by the intermediate-range species, T. gigas, T. derasa, T. noae, T. crocea and Hippopus hippopus, and the restricted-range species, Tridacna lorenzi, T. mbalavuana, T. squamosina, T. rosewateri and Hippopus porcellanus. The larger species, Tridacna gigas and T, derasa are the most endangered, with >50% of wild populations either locally extinct or severely depleted, The smaller and boring species, such as T. maxima and T. crocea, remain relatively abundant despite ongoing fishing activities. Population density also varies across localities. Areas with the lowest densities generally correspond with evidence of high historical exploitation intensity, while areas with the highest densities tend to be within marine reserves, remote from human populations or have low historical fishing pressures. Exploitation continues to be the main threat and conservation challenge for giant clams. Harvesting for subsistence use or local sale remains an important artisanal fishery in many localities; however, increased commercial demand as well as advances in fishing, transport and storage practices, are in large part responsible for the ongoing loss of wild populations. Habitat loss and a suite of other anthropogenic stressors, including climate change, are potentially accelerating stock depletions. Despite these challenges, global efforts to protect giant clams have gained momentum. CITES Appendix II listings and IUCN conservation categories have raised awareness of the threats to giant clams and have contributed to stemming their decline, The continued development of mari-culture techniques may also help improve stock numbers and lend populations additional resilience. However, more effective implementation of conservation measures and enforcement of national and international regulations are needed. It is clear that active management is necessary to prevent the extinction of giant clam species as they continue to face threats associated with human behaviours.

Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis.

The scleractinian coral Pocillopora damicornis type β 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 β 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 β 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.

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.

Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. In this study, we assessed the diversity of the decapods involved in exosymbiotic assemblages for juvenile and adult Pocillopora damicornis types α and β on reefs of New Caledonia and Reunion Island. This approach revealed complex patterns of association at regional and local scales with a prevalence of assemblages involving crab-shrimp partnerships. Furthermore, the distinction of two lineages in the snapping shrimp Alpheus lottini complex, rarely recognized in ecological studies, reveals a key role for cryptic diversity in structuring communities of mutualists. The existence of partnerships between species that occurred more commonly than expected by chance suggests an increased advantage for the host or a better adaptation of associated species to local environmental conditions. The consideration of cryptic diversity helps to accurately describe the complexity of interaction webs for diverse systems such as coral reefs, as well as the functional roles of dominant associated species for the persistence of coral populations. Mutualistic interactions are diverse, widespread and central to the structure and function of both terrestrial and marine ecosystems 1-3. Tropical coral reefs, one of the most diverse ecosystem on Earth 4 , are particularly renowned for depending on complex networks of mutualistic relationships for their establishment and maintenance 3,5. The collection of partnerships of scleractinian corals with other organisms represents one of the most complex interactive networks, in which multiple endo-(in situ) and exo-(ex situ) mutualistic species promote the growth, survival and reproduction of the coral host, which in turn provides crucial food and shelter. While the association between corals and their endosymbiotic zooxanthellae is the best studied 5-7 , the importance of the partnerships between corals and larger epifaunal macro-invertebrates 8 , mostly represented by decapod crustaceans 8,9 is increasingly recognized. These understudied coral dwellers, also called exosymbionts, are either obligate or facultative (i.e., opportunistic) associates 10. Some obligate exosymbionts are well known for their key contribution to coral host survival, among the most notable being the crabs in the genus Trapezia and the snapping shrimp Alpheus lottini (Guérin Méneville 1829). These exosymbionts are both exclusively associated with pocilloporid corals 8,11,12 and provide various cleaning 11,13 , physiological 14 and defense services 12,15,16 to their host, such as the removal of sediments and the deter-rence of large corallivorous predators (e.g., Acanthaster planci).

Giant clam populations have been over-exploited throughout their range over the past decades for their meat and shells. Tridacna maxima, commonly known as the ‘small giant clam’, has remained relatively untargeted by fishers in areas where larger species occur (e.g. Tridacna squamosa), and high densities of the species are still observed on some isolated and enclosed reefs of the Central Pacific. However, it is unclear whether reported discrepancies in densities worldwide reflect differences in fishing pressure only or a combination of differences in exploitation levels and environmental forcing. We reviewed T. maxima surveys throughout its range to (i) identify patterns of density at global scale, site scale (e.g. island) and intrasite scale; (ii) discuss the influence of sampling method on density estimates; and (iii) identify the primary drivers of giant clam density along gradients of human pressure and natural forcing. We found 59 studies that reported density estimates for 172 sites across 26 countries in the Indo-Pacific and Red Sea. At intrasite scale, densities were strongly dependent on sampling protocols and surveyed habitats. At site scale, we found close links between T. maxima density and human population per reef area, suggesting that isolated reefs where exploitation only recently started may be more vulnerable to stock collapse in the future. Density patterns were also found to vary significantly depending on reef type (e.g. atoll, island, continental coastline). We discuss how natural processes and fishing pressure may control population dynamics and densities among sites, and make recommendations for future research.

Previously confused with the small giant clam Tridacna maxima, the recently-resurrected Noah’s giant clam, Tridacna noae has been reported from the Taiwanese and the Ryukyu archipelagoes. Our recent underwater observations now extend its distribution to Dongsha (northern South China Sea), Bunaken (Sulawesi Sea), Madang and Kavieng (Bismarck Sea), the Alor archipelago (Sawu Sea), Kosrae (Caroline Islands), New Caledonia, the Loyalty Islands and Vanuatu (Coral Sea), Viti-Levu (Fiji), Wallis Island, and Kiritimati (Northern Line Islands). Published mitochondrial DNA sequences retrieved from open-access databases also indicate its presence in eastern Negros (Philippines), in the Molucca Sea, at Ningaloo Reef (Western Australia), and in the Solomon Islands. Noah’s giant clam is thus a widely distributed Indo-West Pacific species. Wherever research has been done on small giant clams throughout T. noae’s range, the inadvertent confusion of T. noae with T. maxima might have led to overestimating actual T. maxima densities and to errors in estimating demographic parameters.

Since the 1980s, population densities of Acroporidae have dramatically declined in the Caribbean Sea. Quantitative censuses of Acroporidae provide information on the number of colonies (i.e. ramets), but not on the number of genetically distinct individuals (i.e. genets). In this context, the aim of our study was to provide an overview of the genetic status of Acropora populations in Guadeloupe by examining the genotypic richness of Acropora palmata and Acropora cervicornis. Using 14 microsatellite loci, we found extremely low genotypic richness for both species from Caye-à-Dupont reef (i.e. 0.125 for A. palmata and nearly zero for A. cervicornis). Because genetic diversity contributes to the ability of organisms to evolve and adapt to new environmental conditions, our results are alarming in the context of ongoing global warming as long periods of clonal growth without sexual recruitment may lead to the extinction of these populations.

A new giant clam species, Tridacna ningaloo Penny & Willan, 2014 has been described from Ningaloo Reef, Western Australia. Meanwhile, it has been suggested that Noah's giant clam, Tridacna noae (Röding, 1798), previously resurrected from synonymy with T. maxima (Röding, 1798), is an invalid name. We assessed the validity of resurrecting T. noae and designating a neotype for it against the rules of zoological nomenclature and found no flaw in these acts. We then compared the genetic and morphological characters used in the respective diagnoses of T. noae and the newly-described Tridacna ningaloo. No difference was apparent between T. ningaloo and T. noae except, possibly, in mantle ornamentation patterns. In particular, the holotype of T. ningaloo possesses a mitochondrial DNA haplotype identical to T. noae. Thus, the hypothesis that T. ningaloo is a species distinct from T. noae was not supported by clear morphological evidence and it was contradicted by the available genetic evidence. Tridacna ningaloo should be regarded as a junior synonym of T. noae.

Centropyge bispinosa is one of the most frequently coral reef fish exported through the aquarium trade. We developed fifteen microsatellite markers to evaluate possible distinct breeding stocks throughout its Indo-Pacific distribution range. Number of alleles varied from 2 to 50 per locus, observed and expected heterozygosities ranged from 0.486 to 0.953 and 0.482 to 0.974 respectively. Significant deviations from HWE were detected in two loci. Cross-amplifications were tested in four congener species: C. loriculus, C. bicolor, C. flavissima and C. vroliki. The 15 new microsatellite loci will be helpful tools for the identification of breeding units, connectivity studies, as well as phylogenetic relationships among pygmy angelfishes.

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.

The giant clam Tridacna noae was first described by Röding in 1798, distinguishing it from other species based on the characteristic spacing of the scales on the ribs of the shell. In 1947, McLean described it as very similar in general appearance to T. maxima. So much so that, over the years, it lost its recognition as a distinct species and came to be identified as a “maxima” clam.

Fifteen polymorphic microsatellite markers were developed for Hippopus hippopus in order to assess the effectiveness of population replenishment within marine protected areas in New Caledonia. Number of alleles varied from 2 to 11 per locus, observed and expected heterozygosities ranged from 0.300 to 0.866 and 0.495 to 0.858 respectively. Significant deviations from HWE were detected in two loci. Cross-amplifications were tested in four other species of Tridacnidae.

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Human-made structures are increasingly built in marine coastal habitats for a variety of purposes. Offshore oil and gas production platforms are among the largest examples. Yet, biological effects of these increasing density artificial substrata are under evaluated. The objective of our study is to investigate the possible role of offshore platforms in modifying the genetic composition of populations of natural rocky shores species. The serpulid Pomatoceros triqueter was used as a model, and genetic variation was assessed using a 419 bp fragment of the mtDNA COI gene in samples collected on eleven offshore gas platforms, on one coastal buoy on the sandy shore and in four sites located on natural rocky shores in the Adriatic Sea. Deep phylogenetic lineages were uncovered over all samples. Nucleotide diversity and mean number of pairwise differences among haplotypes were significantly smaller in offshore platform samples compared to rocky shores samples. No significant genetic structure was observed over all samples. We found direct evidence of lower genetic diversity on platforms confirming that, although artificial structures attract and support species typical of hard bottoms, they are not analogues of natural rocky habitats.

Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.

Until recently, our ability to implement and assess spatial marine management approaches has been limited by a lack of information regarding processes that bind marine ecosystems, including habitat locations, larval and adult movement, trophic interactions, and fisher behavior. However, recent advances in habitat-mapping technologies, genetics, marine microchemistry, animal tracking and numerical modeling have greatly enhanced our knowledge of these processes. Although these advances have yet to be fully integrated into management decisions, they have the potential to revolutionize spatial marine management. Nevertheless, this revolution will require advances in our ability to share and integrate data into models of marine ecosystems.

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.

Human-made structures are increasingly found in marine coastal habitats. The aim of the present study was to explore whether urban coastal structures can affect the genetic variation of hard-bottom species. We conducted a population genetic analysis on the limpet Patella caerulea sampled in both natural and artificial habitats along the Adriatic coast. Five microsatellite loci were used to test for differences in genetic diversity and structure among samples. Three microsatellite loci showed strong Hardy-Weinberg disequilibrium likely linked with the presence of null alleles. Genetic diversity was significantly higher in natural habitat than in artificial habitat. A weak but significant differentiation over all limpet samples was observed, but not related to the type of habitat. While the exact causes of the differences in genetic diversity deserve further investigation, these results clearly point that the expansion of urban structures can lead to genetic diversity loss at regional scales.

Previous studies on the common ragworm Hediste diversicolor (Polychaeta: Nereididae) revealed a marked genetic fragmentation across its distribution and the occurrence of sibling taxa in the Baltic Sea. These results suggested that the phylogeographic patterns of H. diversicolor could reflect interactions between cryptic differentiation and multiple colonization events. This study aims to describe the large-scale genetic structuring of H. diversicolor and to trace the phylogeographic origins of the genetic types described in the Baltic Sea. Samples of H. diversicolor (2 < n < 28) were collected at 16 locations across the NE Atlantic coasts of Europe and Morocco and in the Mediterranean, Black and Caspian Seas and sequenced at two mitochondrial gene fragments (COI and cytb, 345 and 290 bp, respectively). Bayesian analyses revealed deep phylogeographic splits yielding three main clades corresponding to populations (i) from the NE Atlantic coasts (from Germany to Morocco) and from part of the Western Mediterranean, (ii) from the Mediterranean Sea, and (iii) from the Black and Caspian Seas. These clades are further divided in well-supported subclades including populations from different regions of NE Atlantic and Mediterranean (i.e. Portugal/Morocco, Western Mediterranean, Adriatic Sea). The Baltic Sea comprises three sympatric lineages sharing a common evolutionary history with populations from NE Atlantic, Western Mediterranean and Black/Caspian Seas, respectively. Hence, the current patterns of genetic structuring of H. diversicolor appear as the result of allopatric isolation, multiple colonization events and possible adaptation to local environmental conditions.

In previous studies, members of the three-spot damselfish species complex composed by four nominal species: Dascyllus albisella Gill, D. auripinnis Randall and Randall, D. strasburgi Klausewitz, and D. trimaculatus (Ruppell) were sampled from the Indian Ocean, the Pacific Rim (Japan to Wallis Island), French Polynesia, Hawaii, and Marquesas. Analyses of the control region of the mitochondrial DNA (D-loop) revealed five different clades: 3 of which correspond to the Pacific Rim (D. trimaculatus and D. auripinnis), Hawaii (D. albisella) and Marquesas (D. strasburgi) and the remaining two clades, Indian Ocean and French Polynesia (D. trimaculatus). We developed microsatellite primers to determine if clades uncovered by the mitochondrial analyses were consistent with nuclear data. Color morphs, species boundaries and incipient speciation in the three-spot damselfish complex are discussed

Allelic richness is one of the most basic measures of genetic diversity. Its calculation is, however, still problematic because estimates depend on sample size. This paper describes an r library that calculates mean allelic richness with confidence bounds for a range of sample sizes. It takes a file in GENEPOP format as input, or alternatively a binary data matrix with columns representing different individuals and rows representing different alleles. The output is tabular as well as graphical. Unlike existing tools, ARES does extrapolate beyond the sample size and provides confidence bounds for these predictions.

Contrasting results are usually reported in the literature regarding the factors influencing observed structuring of genetic variability. The goals of this study were, for five coral reef fishes in French Polynesia, (1) to infer the theoretical variance of single locus F(ST) estimates expected under neutrality in order to exclude outlier loci before inferring gene flow and (2) to test thereafter whether species laying pelagic eggs effectively disperse more than species laying benthic eggs in this system. For this purpose, a total of 952 individuals from five species belonging to two families (Chaetodontidae and Pomacentridae) were screened among populations sampled within a 60-600 km spatial range for intron length polymorphism at 11 loci in order to illuminate contrasting results previously published on allozymes and mitochondrial DNA (mtDNA) control region polymorphisms. Statistically speaking, among the five species, four loci (three allozymes and one intron) were identified as outliers and discarded before interpretation of genetic differentiation in terms of effective dispersal. Biologically speaking, our results suggest that the observed genetic structure is not significantly related to the reproductive strategy of coral reef fish in the island system we analysed and that observed random genetic differentiation accommodates Wright's island model in all five species surveyed. Overall, our study emphasizes how cautious one has to be when trying to interpret present-day genetic structure in terms of gene flow while using a limited number of loci and/or different sets of loci.

Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences

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 seminatural 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.

Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.

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 Oscillationinduced 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.

We investigated the short-term impact of disturbance on genetic diversity and structure of the tropical butterfly Drupadia theda Felder (Lepidoptera: Lycaenidae). Populations were sampled from five landscapes in East Kalimantan (Borneo, Indonesia) which were differentially disturbed by selective logging and the 1997/1998 El Niño Southern Oscillation (ENSO)-induced drought and fires. Sampling occurred before (in 1997) and after the forest fires (in 1998, 1999, 2000, and 2004). Drupadia theda populations underwent serious population size reductions following the 1997/1998 ENSO event. For a total of 208 individuals, we sequenced a 509-bp segment of mtDNA containing the control region plus the 5' end of the 12S rDNA gene. Haplotype diversity in D. theda populations ranged from 0.468 to 0.953. Just after the 1997/1998 ENSO event, number of recorded individuals and genetic diversity were very low in D. theda populations sampled in the two severely burned areas and in a small pristine forest fragment that was surrounded by burned forest and thereby affected by drought. Interestingly, higher levels of genetic diversity were observed in logged forest compared to proximate pristine forest. After 1998, the genetic composition within the three ENSO-disturbed areas diverged. In the twice-burned forest, the genetic diversity in 1999 already approached pre-fire levels, while it remained nearly unchanged in proximate onceburned forest. Our data suggest that the 1997/1998 ENSO-induced drought and fires caused massive reductions in the genetic diversity of D. theda and that population recoveries were linked to their geographical position relative to patches of unburned forest (and thus to source populations).

Sagitta elegans and S. setosa are the two dominant chaetognaths in the NorthEast (NE) Atlantic. They are closely related and have a similar ecology and life history, but differ in distributional ranges. Sagitta setosa is a typical neritic species occurring exclusively above shelf regions, whereas S. elegans is a more oceanic species with a widespread distribution. We hypothesised that neritic species, because of smaller and more fragmented populations, would have been more vulnerable to population bottlenecks resulting from range contractions during Pleistocene glaciations than oceanic species. To test this hypothesis we compared mitochondrial Cytochrome Oxidase II DNA sequences of S. elegans and S. setosa from sampling locations across the NE Atlantic. Both species displayed very high levels of genetic diversity with unique haplotypes for every sequenced individual and an approximately three times higher level of nucleotide diversity in S. elegans (0.061) compared to S. setosa (0.021). Sagitta setosa mitochondrial DNA (mtDNA) haplotypes produced a star-like phylogeny and a uni-modal mismatch distribution indicative of a bottleneck followed by population expansion. In contrast, S. elegans had a deeper mtDNA phylogeny and a multi-modal mismatch distribution as would be expected from a more stable population. Neutrality tests indicated that assumptions of the standard neutral model were violated for both species and results from the McDonald-Kreitman test suggested that selection played a role in the evolution of their mitochondrial DNA. Congruent with these results, both species had much smaller effective population sizes estimated from genetic data when compared to census population sizes estimated from abundance data, with a factor of $10 8-10 9 difference. Assuming that selective effects are comparable for the two species, we conclude that the difference in genetic signature can only be explained by contrasting demographic histories. Our data are consistent with the hypothesis that in the NE Atlantic, the neritic S. setosa has been more severely affected by population bottlenecks resulting from Pleistocene range shifts than the more oceanic S. elegans.

Little is known about the effect of El Niño Southern Oscillation-induced fires on the genetic diversity of tropical rainforest species. Here, I report on the isolation and characterization of 10 microsatellite loci, five loci each, for two lycaenid butterfly species in East Kalimantan, Indonesia, namely Drupadia theda and Arhopala epimuta , which will be used to specifically study the impact of disturbance on genetic diversity. Microsatellite enrichment was carried out using streptavidin-coated magnetic beads. Positive colonies were identified with the three-primer polymerase chain reaction (PIMA). Cross-species amplifications conducted both within and between genera were successful in 16 out of 20 tests.

This study investigated the influence of reproductive strategy (benthic or pelagic eggs) and habitat preferences (lagoon or outer slope) on both diversity and genetic differentiation using a set of populations of seven coral reef fish species over different geographic scales within French Polynesia. We hypothesized that a Holocene sea-level decrease contributed to severe reduction of population size for species inhabiting lagoons and a subsequent decrease of genetic diversity. Conversely, we proposed that species inhabiting stable environments, such as the outer slope, should demonstrate higher genetic diversity but also more structured populations because they have potentially reached a migration-genetic drift equilibrium. Sequences of the 5Ј end of the mitochondrial DNA (mtDNA) control region were compared among populations sampled in five isolated islands within two archipelagos of French Polynesia. For all the species, no significant divergences among populations were found. Significant differences in mtDNA diversity between lagoonal and outer-slope species were demonstrated both for haplotype diversity and sequence divergence but none were found between species with different egg types. Pairwise mismatch distributions suggested rapid population growth for all the seven species involved in this study, but they revealed different distributions, depending on the habitat preference of the species. Although several scenarios can explain the observed patterns, the hypothesis of population size reduction events relative to Holocene sea-level regression and its consequence on French Polynesia coral reefs is the most parsimonious. Outer-slope species have undergone a probable weak and/or old bottleneck (outer reefs persisted during low sea level, leading to reef area reductions), whereas lagoonal species suffered a strong and/ or recent bottleneck since Holocene sea-level regression resulted in the drying out of all the atolls that are maximum 70 meters deep. Since present sea level was reached between 5000 and 6000 years ago, different demographic events (bottlenecks or founder events) have lead to the actual populations of lagoons in French Polynesia.

We used exon-primed, intron-crossing polymerase chain reaction (EPIC-PCR) amplification to assay variation in nuclear loci in some teleost fishes (Carangidae, Centropomidae, Chaetodontidae, Clupeidae, Holocentridae, Moronidae, Mullidae, Pomacentridae, Scombridae, Siganidae). We designed primers in the conserved regions flanking splice sites of consecutive exons of different genes, allowing the amplification of 17 putative introns. Among the satisfactory amplified systems, 14 showed length polymorphism with 2-14 alleles.

Determining the origin of genetic structure is of wide interest because of its use in stock discrimination in marine organisms. Schematically, genetic differentiation can result from historical patterns maintained over geological time or from present-day isolation attributable to biological characteristics of the species. We used a comparative approach to population genetic analysis based on allozyme polymorphism to determine the impact of reproductive strategy (i.e. biological origin) and habitat (i.e. historical origin) on the genetic structure of individuals sampled from five isolated islands in French Polynesia. Eight species of coral reef fishes from two families (Chaetodontidae and Pomacentridae) were selected to test the impact of sea-level change (historical origin) and reproductive strategy (biological origin) on genetic structure. Seven of the eight study species showed significant divergence in allelic frequencies computed over all sites. For these seven species, multilocus F st values ranged from 0.0114 to 0.0287. None of the eight species showed a significant relationship between genetic divergence and geographical distance between sites. Significant divergence (difference in allozyme frequencies) between some pairs of sites occurred but was unrelated to distances between them. These results suggest that the genetic structure of coral reef fish in French Polynesia is likely to be driven according to an island model in which migrations between populations are rare and random in space and time. Overall, none of the species showed congruent genetic structures between sites sampled. Genetic structure of the eight species did not appear significantly related either to reproductive strategy or habitat preference. Genetic diversity (heterozygosity) was significantly correlated with these two factors, with species laying benthic eggs and/or inhabiting lagoons showing significantly higher multilocus heterozygosity than species laying pelagic eggs and/or living on the outer reef slope. Overall, the absence of differences according to habitat and/or reproductive strategy did not provide any conclusive pattern regarding the origin of the genetic structure, but the limited divergence in allelic frequencies suggests recent differentiations.

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F ST ϭ 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F ST) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.