Search

In addressing human reasoning biases, "easy-fix" attentional focus interventions have shown that we can prompt reasoners to align responses with logico-mathematical principles. The current study aimed to test the impact of such interventions on both intuitive and deliberate responses on base-rate items. Using a two-response paradigm, participants provided initial intuitive responses under time constraints and cognitive load, followed by deliberate responses. During the intervention, we used attentional focus manipulations with base-rate items that aimed to redirect participants' attention toward the "logical" base-rate cue (i.e., the logical intervention) or toward the "heuristic" descriptive cue (i.e., the heuristic intervention). The results indicate that the logical intervention led to improved alignment with logico-mathematical principles in both intuitive and deliberate responses, albeit with a modest effect size. Conversely, the heuristic intervention had no discernible impact on accuracy. This indicates that our attentional focus manipulation is more effective at getting reasoners to respect rather than to override base-rates., (© 2024. The Psychonomic Society, Inc.)

Previous studies have shown that, in samples of non-Western observers, susceptibility to the Ebbinghaus illusion is stronger in urban than rural dwellers. While such relationship between illusion strength and urbanicity has often been ascribed to external factors (such as the visual impact of the environment), the present study explored the possibility that it is instead mediated by general cognitive ability, an internal factor. We recruited a sample of remote Namibians who varied in their level of urbanicity, and measured their susceptibility to the Ebbinghaus illusion, their levels of education and literacy, and their general cognitive ability. The results showed that urbanicity was related to Ebbinghaus susceptibility, and that general cognitive ability, literacy and education did not mediate this effect, which is reassuring with regard to the findings of previous studies that did not control for these variables. However, we found robust relationships between urbanicity, on the one hand, and cognitive ability, education and literacy, on the other, which advocates for careful consideration of the impact of the latter variables in studies about the cognitive effects of urban environments., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The blue shark, Prionace glauca, is the most abundant pelagic shark in the open ocean but its vulnerability remains poorly understood while being one of the most fecund sharks. In the Mediterranean Sea, the blue shark is listed as Critically Endangered (CR) by the International Union for Conservation of Nature. The species is facing a strong decline due to fishing, and scientific data regarding its genetic structure and vulnerability are still lacking. Here, we investigated the genetic diversity, demographic history, and population structure of the blue shark within the Mediterranean Sea, from samples of the Gulf of Lion and Malta, using sequences of the mtDNA control region and 22 microsatellite markers. We also compared our mitochondrial data to previous studies to examine the Atlantic-Mediterranean population structure. We assessed the blue shark's genetic vulnerability in the Mediterranean basin by modelling its effective population size. Our results showed a genetic differentiation between the Atlantic and the Mediterranean basins, with limited gene flow between the two areas, and distinct demographic histories making the Mediterranean population an independent management unit. Within the Mediterranean Sea, no sign of population structure was detected, suggesting a single population across the Western and Central parts of the sea. The estimated effective population size was low and highlighted the high vulnerability of the Mediterranean blue shark population, as the estimated size we calculated might not be sufficient to ensure the long-term persistence of the population. Our data also provide additional evidence that the Gulf of Lion area acts as a nursery for P. glauca, where protection is essential for the conservation strategy of the species in the Mediterranean., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dolfo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The effect of family socioeconomic status (SES) on academic achievement in literacy and numeracy has been extensively studied with educational inequalities already witnessed in preschoolers. This is presumably explained by the effect of family SES on cognitive and socioemotional abilities associated with academic achievement. Metacognition which refers to knowledge and regulation skills involving reflexivity about one's own cognitive processes is one of these abilities. However, most of the studies investigating the association between metacognition and academic achievement have focused on school-aged students and studies with younger students are only emerging. Meanwhile, the association between family SES and metacognition abilities has surprisingly received little attention regardless of participants' age. The aim of this study was to explore the associations between family SES, metacognition, language and mathematical abilities in preschoolers aged 5 to 6. We provide the first evidence that the effect of family SES on preschoolers' language and mathematical abilities is mediated by the effect of family SES on their metacognitive abilities. The implications for future research, education and policies aiming at reducing educational inequalities are discussed., (© 2024. The Author(s).)

Recent debiasing studies have shown that a short, plain-English explanation of the correct solution strategy can improve reasoning performance. However, these studies have predominantly focused on English-speaking populations, who were tested with problem contents designed for an English-speaking test environment. Here we explore whether the key findings of previous debiasing studies can be extended to native French speakers living in continental Europe (France). We ran a training session with a battery of three reasoning tasks (i.e., base-rate neglect, conjunction fallacy, and bat-and-ball) on 147 native French speakers. We used a two-response paradigm in which participants first gave an initial intuitive response, under time pressure and cognitive load, and then gave a final response after deliberation. Results showed a clear training effect, as early as the initial (intuitive) stage. Immediately after training, most participants solved the problems correctly, without the need for a deliberation process. The findings confirm that the intuitive debiasing training effect extends to native French speakers., Competing Interests: The authors have no competing interests to declare., (Copyright: © 2024 The Author(s).)

Human reasoning has been shown to be biased in a variety of situations. While most studies have focused on samples of WEIRD participants (from Western Educated Industrialized Rich and Democratic societies), the sparse non-WEIRD data on the topic suggest an even stronger propensity for biased reasoning. This could be explained by a competence issue (people lack the ability to integrate logical knowledge into their reasoning) or a performance issue (people possess the logical knowledge but do not know it is relevant). We addressed this question using a debiasing paradigm with the base-rate task on a sample of non-industrialized people, the Himba of Namibia. After a short training, most participants were debiased, lending credence to the performance account. Debiasing was however to some extent boosted by schooling and living environment suggesting that competence also plays a role (in that more acquired knowledge allows for a higher training benefit). Results imply that debias interventions can be successfully employed to boost sound reasoning around the world., Competing Interests: Declaration of Competing Interest The authors report no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ω cf ) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ω cf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus., (© 2023. The Author(s).)

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change., (© 2023. The Author(s).)

Data plots are widely used in science, journalism and politics, since they efficiently allow to depict a large amount of information. Graphicacy, the ability to understand graphs, has thus become a fundamental cultural skill comparable to literacy or numeracy. Here, we introduce a measure of intuitive graphicacy that assesses the perceptual ability to detect a trend in noisy scatterplots ("does this graph go up or down?"). In 3943 educated participants, responses vary as a sigmoid function of the t-value that a statistician would compute to detect a significant trend. We find a minimum level of core intuitive graphicacy even in unschooled participants living in remote Namibian villages (N = 87) and 6-year-old 1st-graders who never read a graph (N = 27). The sigmoid slope that we propose as a proxy of intuitive graphicacy increases with education and tightly correlates with statistical and mathematical knowledge, showing that experience contributes to refining graphical intuitions. Our tool, publicly available online, allows to quickly evaluate and formally quantify a perceptual building block of graphicacy., (© 2023. The Author(s).)

Heat waves are causing declines in coral reefs globally. Coral thermal responses depend on multiple, interacting drivers, such as past thermal exposure, endosymbiont community composition, and host genotype. This makes the understanding of their relative roles in adaptive and/or plastic responses crucial for anticipating impacts of future warming. Here, we extracted DNA and RNA from 102 Pocillopora colonies collected from 32 sites on 11 islands across the Pacific Ocean to characterize host-photosymbiont fidelity and to investigate patterns of gene expression across a historical thermal gradient. We report high host-photosymbiont fidelity and show that coral and microalgal gene expression respond to different drivers. Differences in photosymbiotic association had only weak impacts on host gene expression, which was more strongly correlated with the historical thermal environment, whereas, photosymbiont gene expression was largely determined by microalgal lineage. Overall, our results reveal a three-tiered strategy of thermal acclimatization in Pocillopora underpinned by host-photosymbiont specificity, host transcriptomic plasticity, and differential photosymbiotic association under extreme warming., (© 2023. The Author(s).)

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene., (© 2023. The Author(s).)

Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health., (© 2023. The Author(s).)

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions., (© 2022. The Author(s).)

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease., (© 2023. The Author(s).)

Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species., Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience., Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience., (© 2023. The Author(s).)

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems., (© 2023. The Author(s).)

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level., (© 2023. The Author(s).)

Background: The green sea turtle, Chelonia mydas, is a migratory species with a strong natal homing behavior leading to a complex population structure worldwide. The species has suffered severe declines in local populations; it is therefore crucial to understand its population dynamics and genetic structure to adopt appropriate management policies. Here, we describe the development of 25 new microsatellite markers specific to C. mydas and suitable for these analyses., Methods and Results: They were tested on 107 specimens from French Polynesia. An average allelic diversity of 8 alleles per locus was reported and observed heterozygosity ranged from 0.187 to 0.860. Ten loci were significantly deviant from the Hardy-Weinberg equilibrium, and 16 loci showed a moderate to high level of linkage disequilibrium (4-22%). The overall F is was positive (0.034, p-value < 0.001), and sibship analysis revealed 12 half- or full-sibling dyads, suggesting possible inbreeding in this population. Cross-amplification tests were performed on two other marine turtle species, Caretta caretta and Eretmochelys imbricata. All loci successfully amplified on these two species, though 1 to 5 loci were monomorphic., Conclusion: These new markers will not only be relevant for further analyses on the population structure of the green turtle and the two other species, but they will also be invaluable for parentage studies, for which a high number of polymorphic loci are necessary. This can provide important insight into male reproductive behavior and migration, an aspect of sea turtle biology that is of critical importance for the conservation of the species., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, Pinna nobilis , which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, Haplosporidium pinnae . In this context, we focused on a single population (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in 2011, 2015, and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities ( H o ) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011-2015 and 2015-2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9% of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that P. nobilis exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by H. pinnae , these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans., Competing Interests: The authors declare that they have no competing interests., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype., (© 2021. The Author(s).)

Although human thinking is often biased by erroneous intuitions, recent de-bias studies suggest that people's performance can be boosted by short training interventions, where the correct answers to reasoning problems are explained. However, the nature of this training effect remains unclear. Does training help participants correct erroneous intuitions through deliberation? Or does it help them develop correct intuitions? We addressed this issue in three studies, by focusing on the well-known Bat-and-Ball problem. We used a two-response paradigm in which participants first gave an initial intuitive response, under time pressure and cognitive load, and then gave a final response after deliberation. Studies 1 and 2 showed that not only did training boost performance, it did so as early as the intuitive stage. After training, most participants solved the problems correctly from the outset and no longer needed to correct an initial incorrect answer through deliberation. Study 3 indicated that this sound intuiting sustained over at least two months. The findings confirm that a short training can boost sound reasoning at an intuitive stage. We discuss key theoretical and applied implications., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The fan mussel, Pinna nobilis, endemic to the Mediterranean Sea, is a critically endangered species facing mass mortality events in almost all of its populations, following the introduction of the parasite Haplosporidium pinnae. Such a unique pandemic in a marine organism, which spreads rapidly and with mortality rates reaching up to 100%, could lead to the potential extinction of the species. Only few regions, involving lagoon habitats, remain healthy throughout the entire Mediterranean Sea. This study describes the genetic structure of P. nobilis across the Gulf of Lion, including confined locations such as lagoons and ports. A total of 960 samples were collected among 16 sites distributed at 8 localities, and then genotyped using 22 microsatellite markers. Genetic diversity was high in all sites with mean allele numbers ranging between 10 and 14.6 and with observed heterozygosities (Ho) between 0.679 and 0.704. No genetic differentiation could be identified (F ST ranging from 0.0018 to 0.0159) and the percentages of related individuals were low and similar among locations (from 1.6 to 6.5%). Consequently, all fan mussels, over the entire coastline surveyed, including those in the most geographically isolated areas, belong to a large genetically homogeneous population across the Gulf of Lion. Considering the ongoing mass mortality context, this result demonstrates that almost all of the genetic diversity of P. nobilis populations is still preserved even in isolated lagoons, which might represent a refuge habitat for the future of the species.

Recently, Pinna nobilis pen shells population in Mediterranean Sea has plummeted due to a Mass Mortality Event caused by an haplosporidian parasite. In consequence, this bivalve species has been included in the IUCN Red List as "Critically Endangered". In the current scenario, several works are in progress to protect P. nobilis from extinction, being identification of hybrids (P. nobilis x P. rudis) among survivors extremely important for the conservation of the species.Morphological characteristics and molecular analyses were used to identify putative hybrids. A total of 10 individuals of each species (P. nobilis and P. rudis) and 3 doubtful individuals were considered in this study. The putative hybrids showed shell morphology and mantle coloration intermingled exhibiting both P. nobilis and P. rudis traits. Moreover, the analyses of 1150 bp of the 28S gene showed 9 diagnostic sites between P. rudis and P. nobilis, whereas hybrids showed both parental diagnostic alleles at the diagnostic loci. Regarding the multilocus genotypes from the 8 microsatellite markers, the segregation of two Pinna species was clearly detected on the PCoA plot and the 3 hybrids showed intermediate positions.This is the first study evidencing the existence of hybrids P. nobilis x P. rudis, providing molecular methodology for a proper identification of new hybrids. Further studies testing systematically all parasite-resisting isolated P. nobilis should be undertaken to determine if the resistance is resulting from introgression of P. rudis into P. nobilis genome and identifying aspects related to resistance.

To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species' evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

Cetaceans are large mammals widely distributed on Earth. The fin whale, Balaenoptera physalus, is the second largest living animal. In the 20th century, commercial whaling reduced its global population by 70%, and in the Mediterranean Sea not only was their overall population depleted but the migration between the Mediterranean Sea and the Atlantic Ocean was reduced. Previous genetic studies identified isolation between these two regions, with a limited gene-flow between these adjacent populations based on nuclear and mitochondrial markers. However, only limited information exists for the Mediterranean population as genetic diversity and abundance trends are still unknown. In this study, 39 highly polymorphic microsatellite markers were tested, including 25 markers developed de novo together with 14 markers previously published. An average allelic diversity of 8.3 alleles per locus was reported, ranging from 3 to 15 alleles per locus, for B. physalus. Expected heterozygosity was variable among loci and ranged from 0.34 to 0.91. Only two markers in the new set were significantly deviant from the Hardy Weinberg equilibrium. Cross-species amplification was tested in four other cetacean species. A total of 27 markers were successfully amplified in the four species (Balaenoptera acutorostrata, Megaptera novaeangliae, Physeter macrocephalus and Globicephala melas). A multivariate analysis on the multilocus genotypes successfully discriminated the five species. This new set of microsatellite markers will not only provide a useful tool to identify and understand the genetic diversity and the evolution of the B. physalus population, but it will also be relevant for other cetacean species, and will allow further parentage analyses. Eventually, this new set of microsatellite markers will provide critical data that will shed light on important biological data within a conservation perspective.

Lionfish ( Pterois volitans ) have rapidly invaded the tropical Atlantic and spread across the wider Caribbean in a relatively short period of time. Because of its high invasion capacity, we used it as a model to identify the connectivity among nine marine protected areas (MPAs) situated in four countries in the Gulf of Mexico and the Caribbean Sea. This study provides evidence of local genetic differentiation of P. volitans in the Gulf of Mexico and the Caribbean Sea. A total of 475 lionfish samples were characterized with 12 microsatellites, with 6-20 alleles per locus. Departures from Hardy-Weinberg equilibrium (HWE) were found in 10 of the 12 loci, all caused by heterozygous excess. Moderate genetic differentiation was observed between Chiriviche, Venezuela and Xcalak, México localities ( F ST  = 0.012), and between the Los Roques and the Veracruz ( F ST  = 0.074) sites. STRUCTURE analysis found that four genetic entities best fit our data. A unique genetic group in the Gulf of Mexico may imply that the lionfish invasion unfolded both in a counterclockwise manner in the Gulf of Mexico. In spite of the notable dispersion of P. volitans , our results show some genetic structure, as do other noninvasive Caribbean fish species, suggesting that the connectivity in some MPAs analyzed in the Caribbean is limited and caused by only a few source individuals with subsequent genetic drift leading to local genetic differentiation. This indicates that P. volitans dispersion could be caused by mesoscale phenomena, which produce stochastic connectivity pulses. Due to the isolation of some MPAs from others, these findings may hold a promise for local short-term control of by means of intensive fishing, even in MPAs, and may have regional long-term effects., Competing Interests: The authors declare no conflict of interest., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m 2 of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance., (© 2020 John Wiley & Sons Ltd.)

The fan mussel, Pinna nobilis is a highly endangered bivalve species endemic to the Mediterranean Sea. During the last few decades, populations have been greatly reduced due to anthropic impacts and they are now under strict protection in most Mediterranean countries. Today, the species is facing a major crisis following the introduction of an haplosporidan parasite which is driving mass mortality in almost all P. nobilis populations throughout the Mediterranean Sea. Gathering additional knowledge regarding dynamics and connectivity patterns of P. nobilis populations is now more than ever critical. Here, we describe the development of 26 highly polymorphic microsatellite markers. Average allelic diversity of 10.9 alleles per locus was reported and heterozygosity ranged from 0.0294 to 0.9737. We tested cross-species amplification in four Pinna species for the new markers together with 10 already published markers, and analysed its success according to the genetic distances among species. Cross-species transferability success ranged from 3 to 38% and had a negative relationship with the genetic distance between the target species and the tested species. The establishment of this new set of high-resolution markers provides a useful tool to understand processes driving gene flow and genetic diversity in P. nobilis populations and the closest congeneric species.

Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (F ST  = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., Competing Interests: The authors have declared that no competing interests exist.

The fire coral Millepora platyphylla Hemprich Ehrenberg, 1834 (Cnidaria, Hydrozoa) has a widespread Indo-Pacific distribution observed from the surface to 40 m (Razak Hoeksema 2003). However, its extirpation from the East Pacific (Gulf of Chiriqui, Panama) was documented after the 1982-1983 bleaching event (Glynn Weerdt 1991). Here, we report the discovery of 5 colonies of M. platyphylla from the eastern Pacific, specifically at Clipperton Atoll, during the TARA Pacific expedition (www.taraexpeditions.org).

Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus Ophiocoma, as currently constituted, is paraphyletic on our trees and required revision. Four genera are recognised herein: an expanded Ophiomastix (now including Ophiocoma wendtii, O. occidentalis, O. endeani, O. macroplaca, and Ophiarthrum spp), Ophiocomella (now including the non-fissiparous Ophiocoma pumila, aethiops and valenciae) and Breviturma (now including Ophiocoma pica, O. pusilla, O. paucigranulata and O. longispina) and a restricted Ophiocoma. The resulting junior homonym Ophiomastix elegans is renamed O. brocki. The genus Ophiomastix exhibits relatively high rates of morphological disparity compared to other lineages. Ophiomastix flaccida and O. (formerly Ophiarthrum) pictum have divergent mitochondrial genomes, characterised by gene-order rearrangements, strand recoding, enriched GT base composition, and a corresponding divergence of nuclear mitochondrial protein genes. The new phylogeny indicates that larval and developmental transitions occurred rarely. Larval culture trials show that species with abbreviated lecithotrophic larval development occur only within Ophiomastix, although the possible monophyly of these species is obscured by the rapid early radiation within this genus. Asexual reproduction by fission is limited to one species-complex within Ophiocomella, also characterised by elevated levels of allelic heterozygosity, and which has achieved a relatively rapid global distribution. The crown ages of the new genera considerably predate the closure of the Tethyan seaway and all four are distributed in both the Atlantic and Indo-Pacific Oceans. Two species pairs appear to reflect the closure of the Panama Seaway, although their fossil-calibrated node ages (12-14 ± 6 my), derived from both concatenated sequence and multispecies coalescent analyses, considerably predate the terminal closure event. Ophiocoma erinaceus has crossed the East Pacific barrier and is recorded from Clipperton Island, SW of Mexico., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium , a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM&#95;VAR&#95;5.8S2/SYM&#95;VAR&#95;REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium , as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM&#95;VAR&#95;5.8S2/SYM&#95;VAR&#95;REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol's ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes., Competing Interests: Xavier Pochon is an Academic Editor for PeerJ.

Coral reef ecosystems worldwide are immediately threatened by the impacts of climate change. Here we report on the condition of coral reefs over 83 km of coastline at the island of Upolu, Samoa in the remote South West Pacific in 2016 during the Tara Pacific Expedition. Despite the distance to large urban centers, coral cover was extremely low (<1%) at approximately half of the sites and below 10% at 78% of sites. Two reef fish species, Acanthurus triostegus and Zanclus cornutus, were 10% smaller at Upolu than at neighboring islands. Importantly, coral cover was higher within marine protected areas, indicating that local management action remains a useful tool to support the resilience of local reef ecosystems to anthropogenic impacts. This study may be interpreted as cautionary sign for reef ecosystem health in remote locations on this planet, reinforcing the need to immediately reduce anthropogenic impacts on a global scale., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies., (© 2017 John Wiley & Sons Ltd.)

In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005-0.064) and mean interspecific genetic distances within genera (0.056-0.316) were concordant with previous echinoderm studies. This study revealed that brittle-star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo-West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.

Intracolonial genotypic variability is described in many colonial organisms and arises from mosaicism (somatic mutation) and/or chimerism (allogenic fusion). Both processes provide an additional source of genotypic variation in natural populations and raise questions on the biological significance of colonies having more than one genotype. Using fifteen microsatellite markers, we screened for potential genetic heterogeneity within Millepora platyphylla colonies, a hydrocoral species known for its extensive morphological plasticity among reef habitats. We aimed to determine whether mosaicism and chimerism were related to specific reef habitats and/or colony morphologies. Our results show that intracolonial genotypic variability was common (31.4%) in M. platyphylla at Moorea, French Polynesia, with important variations in its frequency among habitats (0-60%), while no effect of morphology was observed. Mosaicism seemed responsible for most of the genetic heterogeneity (87.5%), while chimerism was rarer. Some mosaics were shared among fire coral clones indicating that mutations could be spread via colony fragmentation. Further, the genotypic variability among clones suggests that colonies produced asexually through fragmentation have the potential to accumulate their own mutations over time. Such mutation dynamics might have important implications for the adaptive potential of long-lived reef-builder populations that are predominantly sustained through asexual reproduction.

Clonal populations are often characterized by reduced levels of genotypic diversity, which can translate into lower numbers of functional phenotypes, both of which impede adaptation. Study of partially clonal animals enables examination of the environmental settings under which clonal reproduction is favoured. Here, we gathered genotypic and phenotypic information from 3,651 georeferenced colonies of the fire coral Millepora platyphylla in five habitats with different hydrodynamic regimes in Moorea, French Polynesia. In the upper slope where waves break, most colonies grew as vertical sheets ("sheet tree") making them more vulnerable to fragmentation. Nearly all fire corals in the other habitats are encrusting or massive. The M. platyphylla population is highly clonal (80% of the colonies are clones), while characterized by the highest genotype diversity ever documented for terrestrial or marine populations (1,064 genotypes). The proportion of clones varies greatly among habitats (≥58%-97%) and clones (328 clonal lineages) are distributed perpendicularly from the reef crest, perfectly aligned with wave energy. There are six clonal lineages with clones dispersed in at least two adjacent habitats that strongly demonstrate phenotypic plasticity. Eighty per cent of the colonies in these lineages are "sheet tree" on the upper slope, while 80%-100% are encrusting or massive on the mid slope and back reef. This is a unique example of phenotypic plasticity among reef-building coral clones as corals typically have wave-tolerant growth forms in high-energy reef areas., (© 2017 John Wiley & Sons Ltd.)

We studied the diversity within the former genus Gymnangium in the South West Indian Ocean by using an integrative approach of both traditional (morphology-based) and modern molecular taxonomy. Nine species were recorded in the material collected. A total of 97 16S mitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differences in the studied Gymnangium species that make it necessary to split the genus. It is proposed to revalidate the genus Taxella which is currently regarded as a synonym of Gymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until now regarded as distinct species based on morphological characteristics, cluster together in one phylogenetic clade. Possible explanations are discussed. Two species from Madagascar new to science are herein described and rare species from the Indian Ocean islands are re-described.

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla , an important reef-builder of Indo-Pacific reefs . We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2-13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs., Competing Interests: The authors declare there are no competing interests.

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level., (© 2016 John Wiley & Sons Ltd.)

Despite their importance in marine biodiversity, invertebrates are far less studied than vertebrates. Given the current global biodiversity crisis and insufficient taxonomic resources, sustained efforts need to be undertaken to assess species diversity, especially in the highly threatened 'biodiversity hotspots'. Réunion is a young volcanic island lying in the Mascarene Islands (south-western Indian Ocean, SWIO), a marine biodiversity hotspot. A substantial sampling effort was conducted around Réunion Island to document shallow water reef-associated ophiuroid (brittle-stars) diversity, a class recognised as the most diverse among echinoderms. A total of 33 species were documented, increasing the known species richness of the island by 56%. Findings include 15 new records for Réunion, 11 for the Mascarene Islands and 8 for the Indian Ocean. The most diverse family was Ophiocomidae, a family of large, abundant and conspicuous tropical species. Even in this well studied family, a new species was revealed by this survey. Morphological variants together with DNA sequence variations within several species revealed cryptic species. We compared our results with the known fauna of other Mascarene Islands and discuss biogeographic implications for the region.

The order Botryosphaeriales represents several ecologically diverse fungal families that are commonly isolated as endophytes or pathogens from various woody hosts. The taxonomy of members of this order has been strongly influenced by sequence-based phylogenetics, and the abandonment of dual nomenclature. In this study, the phylogenetic relationships of the genera known from culture are evaluated based on DNA sequence data for six loci (SSU, LSU, ITS, EF1, BT, mtSSU). The results make it possible to recognise a total of six families. Other than the Botryosphaeriaceae (17 genera), Phyllostictaceae (Phyllosticta) and Planistromellaceae (Kellermania), newly introduced families include Aplosporellaceae (Aplosporella and Bagnisiella), Melanopsaceae (Melanops), and Saccharataceae (Saccharata). Furthermore, the evolution of morphological characters in the Botryosphaeriaceae were investigated via analysis of phylogeny-trait association. None of the traits presented a significant phylogenetic signal, suggesting that conidial and ascospore pigmentation, septation and appendages evolved more than once in the family. Molecular clock dating on radiations within the Botryosphaeriales based on estimated mutation rates of the rDNA SSU locus, suggests that the order originated in the Cretaceous period around 103 (45-188) mya, with most of the diversification in the Tertiary period. This coincides with important periods of radiation and spread of the main group of plants that these fungi infect, namely woody Angiosperms. The resulting host-associations and distribution could have influenced the diversification of these fungi., Taxonomic Novelties: New families - Aplosporellaceae Slippers, Boissin & Crous, Melanopsaceae Phillips, Slippers, Boissin & Crous, Saccharataceae Slippers, Boissin & Crous.

Understanding the evolutionary histories of invasive species is critical to adopt appropriate management strategies, but this process can be exceedingly complex to unravel. As illustrated in this study of the worldwide invasion of the woodwasp Sirex noctilio, population genetic analyses using coalescent-based scenario testing together with Bayesian clustering and historical records provide opportunities to address this problem. The pest spread from its native Eurasian range to the Southern Hemisphere in the 1900s and recently to Northern America, where it poses economic and potentially ecological threats to planted and native Pinus spp. To investigate the origins and pathways of invasion, samples from five continents were analysed using microsatellite and sequence data. The results of clustering analysis and scenario testing suggest that the invasion history is much more complex than previously believed, with most of the populations being admixtures resulting from independent introductions from Europe and subsequent spread among the invaded areas. Clustering analyses revealed two major source gene pools, one of which the scenario testing suggests is an as yet unsampled source. Results also shed light on the microevolutionary processes occurring during introductions, and showed that only few specimens gave rise to some of the populations. Analyses of microsatellites using clustering and scenario testing considered against historical data drastically altered our understanding of the invasion history of S. noctilio and will have important implications for the strategies employed to fight its spread. This study illustrates the value of combining clustering and ABC methods in a comprehensive framework to dissect the complex patterns of spread of global invaders., (© 2012 Blackwell Publishing Ltd.)

Compared to endemics, widespread species are of particular interest to retrace recent evolutionary history. These species have a large population size which provides a clearer genetic signature of past events. Moreover, their wide geographic range increases the potential occurrence of evolutionary events (expansion, divergence, etc.). Here, we used several coalescent-based methods to disentangle the evolutionary history of a widespread amphidromous goby (Sicyopterus lagocephalus), in the light of sea-level variations during the Pleistocene. Using 75 samples recovered from three biogeographic regions (Western Indian Ocean, Melanesia and Polynesia), we analysed a portion of the cytochromeb gene and confirmed three major haplogroups, each specific to a region. Furthermore, we found that: (1) the Melanesian haplogroup was the oldest while the two peripheral regions hosted daughter haplogroups; (2) two centrifugal colonisation events occurred from Melanesia to the periphery, each synchronised with periods of strong paleo-ENSO episodes; (3) the demographic contraction-expansion events were linked to Pleistocene sea-level changes; (4) Melanesia and Polynesia acted as efficient refuges during the Last Glacial Maximum. These results highlight the importance of studying widespread species to better understand the role of climate changes and paleo-oceanography on the evolution of biodiversity., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Over the last decade, cryptic speciation has been discovered in an increasing number of taxa. Species complexes are useful models for the understanding of speciation processes. Motivated by the discovery of brooding specimens in the common Atlanto-Mediterranean broadcast spawning brittle star, Ophioderma longicauda, a recent study revealed the occurrence of divergent mitochondrial lineages. We analysed 218 specimens from 23 locations spread over the geographic range of the species with partial Cytochrome c Oxidase subunit I (COI) sequences. A subset of this sample was also surveyed with the internal transcribed spacer of the ribosomal DNA cluster (nuclear ITS-1). Our study revealed six highly divergent mitochondrial lineages, and the ITS-1 data confirmed that they most likely represent a species complex. Geographic ranges, abundances and genetic structures are contrasted among the putative cryptic species. Lineages in which brooding specimens have been found form a monophyletic group and are restricted to the Eastern Mediterranean basin, an oligotrophic zone. A phylogeny-trait association analysis revealed a phylogenetic signal for low 'chlorophyll a' values (our proxy for oligotrophy). An ecological shift related to the hyper oligotrophy of the Eastern Mediterranean region is therefore likely to have played a role in the evolution of brooding. This study revealed that a complex mixture of vicariance, population expansion, adaptive divergence and possibly high local diversification rates resulting from brooding has shaped the evolution of this species complex. The dating analysis showed that these events probably occurred in the Pleistocene epoch., (© 2011 Blackwell Publishing Ltd.)

Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing., (© 2010 Blackwell Publishing Ltd.)

Background: Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families., Results: In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals., Conclusions: Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.