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.

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.

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.

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

Here, we examined the genetic variability in the coral genus , in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named complex , 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.

Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology.

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.

Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites.

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).

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

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.

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.

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.

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.

Phylogeography of the common ragworm Hediste diversicolor (Polychaeta: Nereididae) reveals cryptic diversity and multiple colonization events across its distribution.

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.

Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae).

Here we report on 16 microsatellite loci designed for the damselfish Dascyllus aruanus. All loci were tested on 98 individuals and were polymorphic (seven to 35 alleles). Expected heterozygosity ranged from 0.

Genetic structuring of the temperate gorgonian coral (Corallium rubrum) across the western Mediterranean Sea revealed by microsatellites and nuclear sequences.

In the past decades, anthropogenic disturbance has increased in marine costal habitats, leading to dramatic shifts in population size structure of various marine species. In the temperate region, the gorgonian coral (Corallium rubrum) is one of the major disturbed species, mostly owing to the exploitation of its red skeleton for jewellery purposes. Red coral is a gonocoric species inhabiting subtidal rocky habitats in the Mediterranean and neighbouring Atlantic coasts.

Inferring gene flow in coral reef fishes from different molecular markers: which loci to trust?

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.

Microsatellite flanking region similarities among different loci within insect species.

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.

Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.

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.

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.

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.

Short-term impact of disturbance on genetic diversity and structure of Indonesian populations of the butterfly Drupadia theda in East Kalimantan.

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).

Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change.

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.

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

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.