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The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals

Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity)

The Gray’s sea fan, Paramuricea grayi (Johnson, 1861), typically inhabits deep littoral and circalittoral habitats of the eastern temperate and tropical Atlantic Ocean. Along the Iberian Peninsula, where P. grayi is a dominant constituent of circalittoral coral gardens, two segregating lineages (yellow and purple morphotypes) were recently identified using single-copy nuclear orthologues. The mitochondrial genomes of 9 P. grayi individuals covering both color morphotypes were assembled from RNA-seq data, using samples collected at three sites in southern (Sagres and Tavira) and western (Cape Espichel) Portugal. The complete circular mitogenome is 18,668 bp in length, has an A + T-rich base composition (62.5%) and contains the 17 genes typically found in Octocorallia: 14 protein-coding genes (atp6, atp8, cob, cox1-3, mt-mutS, nad1-6, and nad4L), the small and large subunit rRNAs (rns and rnl), and one transfer RNA (trnM). The mitogenomes were nearly identical for all specimens, though we identified a noteworthy polymorphism (two SNPs 9 bp apart) in the mt-mutS of one purple individual that is shared with the sister species P. clavata. The mitogenomes of the two species have a pairwise sequence identity of 99.0%, with nad6 and mt-mutS having the highest rates of non-synonymous substitutions

[Aim]: Marine forests of brown macroalgae create essential habitats for coastal species and support invaluable ecological services. Here, we provide the first global analysis of species richness and endemicity of both the kelp and fucoid biomes., [Location]: Global., [Time period]: Contemporary., [Major taxa studied]: Marine forests of brown macroalgae, formed by kelp (here de-fined as orders Laminariales, Tilopteridales and Desmarestiales) and fucoid (order Fucales), inhabiting subtidal and intertidal environments., [Methods]: We coupled a large dataset of macroalgal observations (420 species, 1.01 million records) with a high- resolution dataset of relevant environmental predictors (i.e., light, temperature, salinity, nitrate, wave energy and ice coverage) to develop stacked species distribution models (stacked SDMs) and yield estimates of global spe-cies richness and endemicity., [Results]: Temperature and light were the main predictors shaping the distribution of subtidal species, whereas wave energy, temperature and salinity were the main pre-dictors of intertidal species. The highest regional species richness for kelp was found in the north-east Pacific (maximum 32 species) and for fucoids in south-east Australia (maximum 53 species), supporting the hypothesis that these regions were the evolu-tionary sources of global colonization by brown macroalgae. Locations with low spe-cies richness coincided between kelp and fucoid, occurring mainly at higher latitudes (e.g., Siberia) and the Baltic Sea, where extensive ice coverage and low-salinity regimes prevail. Regions of high endemism for both groups were identified in the Galapagos Islands, Antarctica, South Africa and East Russia., [Main conclusions]: We estimated the main environmental drivers and limits shaping the distribution of marine forests of brown macroalgae and mapped biogeographical centres of species richness and endemicity, which largely coincided with the expecta-tion from previous evolutionary hypotheses. The mapped biodiversity patterns can serve as new baselines for planning and prioritizing locations for conservation, man-agement and climate change mitigation strategies, flagging threatened marine forest regions under different climate change scenarios.

Cystoseira sensu lato (s.l.) – encompassing the genera Cystoseira sensu stricto (s.s.), Ericaria and Gongolaria – is a diverse group of forest-forming brown macroalgae endemic to the warm-temperate North-east Atlantic. These algae have immense biogeographic and ecological significance and have been experiencing recent regional declines. Most Cystoseira s.l. display important morphological plasticity and can be confused with similar species. Therefore, species boundaries, geographic ranges and phylogenetic affinities remain imprecise for most. In the face of persistent taxonomic difficulties, several authors underlined the necessity for new molecular-based approaches, but studies so far lacked representativity, resolution and standardization. To fill in these gaps, in this study we sequenced a comprehensive collection of Cystoseira s.l. spanning its entire North-east Atlantic range for a ~1200 bp cox1 barcode, and sequenced selected individuals representing major genetic entities for a few additional plastid markers. Phylogeographic, phylogenetic and species delimitation methods revealed 27 Molecular Operational Taxonomic Units, including unaccounted cryptic diversity, and elucidated with unprecedented resolution species compositions and phylogenetic relationships within each genus. Some entities within the lineages Cystoseira compressa/humilis, Ericaria brachycarpa/crinita, E. selaginoides and tophulose Gongolaria, as well as among free-living algae, conflicted with a priori taxonomic assignments, and required the redefinition, reinstatement and recognition of new taxa. For some, diagnostic mutations and biogeography were more useful for species identifications than morphological characters or conventional barcoding gaps. A few species showed narrow geographic ranges and others were the sole representatives of their respective lineages. Several sister-species showed Atlantic vs Mediterranean complementary ranges. Phylogenetic signal of cox1 was nevertheless insuffic

The Global Harmful Algal Blooms (GlobalHAB, www.global hab.info) Program is aimed at fostering international cooperative research directed toward improving the prediction of harmful algal bloom (HAB) events in aquatic ecosystems, and providing sound knowledge for policy- and decision-making to manage and mitigate HAB impacts in a changing planet. GlobalHAB is sponsored by the Intergovernmental Oceanographic Commission (IOC) of UNESCO and the Scientific Committee on Oceanic Research (SCOR). GlobalHAB was launched in 2016 and will last for 10 years. The GlobalHAB scientific objectives are focused on the research of taxonomic, ecological and toxicology knowledge gaps, on the effects of climate change on HABs and their biogeographic distribution, the implementation of HABs observing systems, and overall, to promote aquatic food and water safety and security. The GlobalHAB program has an international nature, and collaborates with international entities and programs that share objectives on HABs research, management and mitigation, as was already done by the former program GEOHAB. In particular, scientists from Latin America were active participants in GEOHAB and today Latin America is key in the implementation of GlobalHAB. Extreme HAB events affecting aquaculture sites and natural environments, Sargassum beachings, HABs monitoring programs, ciguatera fish poisoning, toxin transfer through the food webs, are examples of topics where scientists in Latin America are very active and thus, contribute to the implementation of GlobalHAB. Scientists are invited to participate in GlobalHAB by designing and endorsing scientific activities linked to the goals of GlobalHAB, and by participating in other international activities

The spread of exotic species to new areas can be magnified when favored by future climatic conditions. Forecasting future ranges using species distribution models (SDMs) could be improved by considering physiological thresholds, because models solely based on occurrence data cannot account for plasticity due to acclimation of individuals to local conditions over their life-time or to adaptation due to selection within local populations. This is particularly relevant for the exotic seagrass Halophila stipulacea, which colonized the Mediterranean Sea a century ago and shifted its thermal niche, coping with a colder regime. Here, we used two hybrid models combining correlative SDMs with the thermal limits for growth of native and exotic H. stipulacea populations to predict the distribution of the species in its native (Indian Ocean and Red Sea) and exotic ranges (Mediterranean Sea and Caribbean Sea) under two scenarios forecasting limited (RCP 2.6) and severe (RCP 8.5) future climate changes by 2050 and 2100. Then, we assessed the differences between hybrid models based on native Red Sea thermal limits (niche conservatism: 17–36°C) and on exotic Mediterranean thermal limits (local adaptation: 14–36°C). At the Mediterranean exotic range, the local adaptation hybrid model accurately agreed with the present distribution of the species while the niche conservatism-based hybrid model failed to predict 87% of the current occurrences of the species. By contrast, both hybrid models predicted similar species distributions for the native range and exotic Caribbean range at present and projected that H. stipulacea will maintain its current worldwide under all future greenhouse gas emission scenarios. The hybrid model based on Mediterranean thermal limits projected the expansion of H. stipulacea through the western Mediterranean basin (except the gulf of Leon) under the most severe scenario (RCP 8.5) by 2100, increasing its distribution by 50% in the Mediterranean. The future expa

The widespread decline of canopy-forming macroalgal assemblages has been documented in many regions during the last decades. This pattern is often followed by the replacement of structurally complex algal canopies by more simplified habitats (e.g., turfs or sea urchin barren grounds). Against all odds, the fucoid Treptacantha elegans, a large Mediterranean brown macroalga, broadened its depth range to deeper and exposed environments and displayed an unexpected range expansion along the northern coast of Catalonia over the last two decades. Here, we reconstruct the spread of T. elegans in time and space and unravel ecological and demographic traits such as population dynamics and genetic patterns to provide a comprehensive and integrated view of the current status and geographical expansion for this species. Fast-growing dynamics, early fertile maturity, and high turnover rate are the main competitive advantages that allow the exposed populations of T. elegans to colonize available substrata and maintain dense and patchy populations. We also provided evidence that the deeper and exposed populations of T. elegans constitute a single group across the Catalan coast, with little genetic differentiation among populations. This seems to support the hypothesis of a unique source of spread in the last decades from the Medes Islands No-Take Zone towards both southern and northern waters.

Cystoseira sensu lato (Ochrophyta) forests are important habitat formers in the Mediterranean Sea, but they have mostly been studied in the western basin where many species are under decline. In the eastern basin, where fewer species occur, Cystoseira rayssiae Ramon was described in the year 2000 as an endemic species based on morphological characteristics from herbaria samples collected on the Israeli coast. No further investigations have been conducted on this peculiar species since, but recently it has been recorded in contiguous Lebanon and outside the Mediterranean. Our work was aimed at confi rming the taxonomic validity and endemic nature of this species, including its position among the recently split Cystoseira sensu stricto, Carpodesmia Greville and Treptacantha Kützing genera, by sequencing the mitochondrial COI gene and by examining morphological characteristics in samples from three diff erent sites in northern Israel. Notwithstanding considerable morphological plasticity, molecular analyses revealed a single unique COI sequence. Phylogenetic analyses show that Cystoseira rayssiae belongs to the resurrected genus Treptacantha and hence, the new combination Treptacantha rayssiae (Ramon) M.Mulas, J.Neiva & Á.Israel, comb. nov., is proposed. Unique sequences and a restricted range support its Levantine-endemic status. Intriguing extra-Mediterranean reports from the Red Sea and the Persian Gulf are probably misidentifi cations rather than refl ecting a disjunct distribution or recent invasion.

Pinna nobilis is an endemic bivalve of the Mediterranean Sea, and a vulnerable species registered as endangered and protected under the European Council Directive 92/43/EEC and Barcelona Convention. In early autumn 2016, a mass mortality event impacted P. nobilis populations in the south‐western Mediterranean Sea, including the Balearic Islands. At the time of this study, P. nobilis still maintained high population densities along the Balearic coasts (Western Mediterranean). This study evaluated the connectivity of P. nobilis post‐larvae and adults in seagrass habitats around the Balearic Islands and identified its source and sink populations. These objectives were reached through a multidisciplinary approach including population genetics (10 microsatellites) and hydrodynamic modelling. High genetic diversity was found and significant genetic differentiation (inferred by fixation index FST) was detected between post‐larvae samples, but not between adult populations. Significant genic and genotypic differentiation was recorded for adults and post‐larvae. This pattern was confirmed by correspondence analysis using allele frequencies. The genetic connectivity pattern was consistent with marine currents and dispersal models. This work not only improves knowledge of the P. nobilis gene pool in south‐west Mediterranean populations and their connectivity patterns, but is also crucial to help evaluate the possibility of recovery from source populations and the possibility of restocking programmes, as well as provide a solid base to establish effective marine reserve networks.

Intraspecific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial–interglacial cycles. We use ecological niche modelling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid‐Holocene (6,000 YBP), and the present. Changes in the genetic diversity within ancient refugia were projected for the future (year 2100) under two contrasting climate change scenarios (RCP2.6 and RCP8.5). Models predicted distributions that matched empirical distributions in cross‐validation, and identified distinct refugia at the low latitude ranges, which largely coincide among species with similar ecological niches. Transferred models into the future projected polewards expansions and substantial range losses in lower latitudes, where richer gene pools are expected (in Nova Scotia and Iberia for cold affinity species and Gibraltar, Alboran, and Morocco for warm‐temperate species). These effects were projected for both scenarios but were intensified under the extreme RCP8.5 scenario, with the complete borealization (circum‐Arctic colonization) of kelp forests, the redistribution of the biogeographical transitional zones of the North Atlantic, and the erosion of global gene pools across all species. As the geographic distribution of genetic variability is unknown for most marine species, our results represent a baseline for identification of locations potentially rich in unique phylogeographic lineages that are also climatic relics in threat of disappearing.

The temperate coralligenous bioconcretions are mainly built by the accumulation of encrusting coralline algae growing at low irradiance levels. They harbour approximately 10% of marine Mediterranean species (about 1600 species), including long-lived algae and invertebrates. Enhanced by climate change, several pressures affect coralligenous assemblages, leading to increased frequency of mass mortalities and dramatic loss of habitat complexity and biodiversity. The EU-funded project MERCES is developing innovative methodologies to restore macroinvertebrate habitat-forming species from three key taxonomic groups: Cnidaria/Anthozoa, Porifera/Demospongiae and Bryozoa. Restoration protocols are based on fragments/transplants from donor organisms and recruitment-enhancing devices. Collaboration with volunteers (divers and diving operators) in several phases of field activities proved crucial both to minimize underwater working time and to increase the sense of stewardship in a major users’ segment. Additionally, the MERCES project explores how to enhance restoration success by identifying the mechanisms conferring resistance to thermal stress in gorgonians. This is pursued by coupling thermotolerance experiments with next generation sequencing tools and facilitation processes (by comparing the outcomes of mono-specific vs. multi-specific transplanted assemblages). Results will be included in the strategic planning of restoration efforts in the Mediterranean in the context of global change

Saccharina latissima is an ecologically and economically important kelp species native to the coastal regions of the Northern Hemisphere. This species has considerable phylogeographic structure and morphological plasticity, but lack of resolution of available genetic markers prevents a finer characterization of its genetic diversity and structure. Here, we describe 12 microsatellite loci identified in silico in a genomic library, and assess their polymorphism in three distant populations. Allelic richness at the species level was relatively high (5–23 alleles per locus), as was gene diversity within populations (0.42 < H < 0.62). In addition, individuals readily form distinct genotypic clusters matching their populations of origin. The variation detected confirms the great potential of these markers to investigate the biogeography and population dynamics of S. latissima, and to better characterize its genetic resources for the establishing farming industry.

© 2015 International Society for Microbial Ecology All rights reserved. Functional genomics of diatom-dominated communities fromthe Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3 - uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments.

© 2015, Springer-Verlag Berlin Heidelberg. Knowledge of spatial patterns of genetic differentiation between populations is key to understanding processes in evolutionary history of biological species. Caulerpa is a genus of marine green algae, which has attracted much public attention, mainly because of the impacts of invasive species in the Mediterranean. However, very little is known about the ecological and evolutionary history of the Mediterranean native Caulerpa prolifera, a species which is currently found at sites distributed worldwide. C. prolifera provides a good model to explore the patterns of genetic diversity at different scales across the Mediterranean and Atlantic area. This study aims to investigate the biogeographical patterns of diversity and differentiation of C. prolifera in the Mediterranean, with special focus on the Mediterranean/Atlantic transition zone. We used two nuclear (ITS rDNA and the hypervariable microsatellite locus CaPr_J2) and one chloroplast (tufA) DNA markers on samples of C. prolifera from its entire range. Analyses of 51 sequences of the cpDNA tufA of C. prolifera, 87 ITS2 sequences and genotypes of 788 ramets of C. prolifera for the locus CaPr_J2 revealed three different biogeographical areas: West Atlantic, East Atlantic and a larger area representing the Mediterranean, the Mediterranean/Atlantic transition zone and a Pacific site (Bali). It was found out that the Mediterranean/Atlantic transition zone is a biogeographical boundary for C. prolifera. A lack of connectivity was revealed between Atlantic and Mediterranean types, and identical sequences found in the Mediterranean and Indo-Pacific suggest either recent gene flow along the Red Sea connection or a possible ancient Indo-Pacific origin.

Pinna nobilis is an endemic bivalve of the Mediterranean Sea whose populations have decreased in the last decades due to human pressure; as a consequence, it was declared a protected species in 1992. Despite its conservation status, few genetic studies using mitochondrial markers have been published. We report on the isolation and development of 10 microsatellite loci for the fan mussel, Pinna nobilis. All loci (2 di-nucleotide, 5 tri-nucleotide, 2 tetra-nucleotide and 1 penta-nucleotide) are characterized by high levels of polymorphism in 76 individuals tested from two populations in the Balearic Islands (Spain, Western Mediterranean Sea). The number of alleles ranged from 4 to 24 and expected heterozygosity ranged from 0.4269 to 0.9400. These microsatellites could be very useful for the assessment of the genetic diversity and connectivity patterns of P. nobilis and the establishment of new conservation strategies.

The recurrent lack of isolation by distance reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large-scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test this hypothesis by using the Genetic Diversity Spectrum (GDS) on databases containing, respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges reveals a coherent pattern of isolation by distance in contrast to the chaotic pattern previously described using allele frequencies, in particular, for the long-lived P. oceanica. These results suggest that the lack of isolation by distance, rather than the resulting from rare events of large-scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may, therefore, result predominantly from ancient events of step-by-step (re)colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS appears useful to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales by accounting for phylogenetic information borne by microsatellites, under an appropriate mutation model. This finding adds nuance to the generalization of the influence of large-scale dispersal on the dynamics of seagrasses. © 2014 The American Genetic Association. 2014. All rights reserved.

© 2014, Springer Science+Business Media Dordrecht. The Marine Park Prof. Luiz Saldanha, in the coast of Arrábida, is the first marine park in continental Portugal. This area is a Nature 2000 site and is considered to be a hotspot for European marine biodiversity. In 2005, the management plan of the park was implemented, ending several habitat menaces, thereby allowing an application to the LIFE—NATURE Programme. The LIFE-BIOMARES project aimed at the restoration and management of the biodiversity of the marine park through several actions. The restoration of the seagrass prairies that were completely destroyed by fishing activities and recreational boating, was one of the most challenging. It included the transplanting of seagrasses from donor populations and the germination of seagrass seeds for posterior plantation to maintain genetic diversity in the transplanted area. One of the most popular actions was the implementation of environmental friendly moorings to integrate recreational use of the area with environmental protection. Several dissemination and environmental education actions concerning the marine park and the project took place and contributed to the public increase of the park acceptance. The seabed habitats were mapped along the park and a surrounding area to 100 m depth in order to create a habitat cartography of the park and to help locate alternative fishing zones. Biodiversity assessments for macrofauna revealed seasonal variations and an effect of the protection status. Preliminary results are presented and show that the marine park regulations are having a positive effect on biodiversity conservation and sustainable fisheries, thereby showing that these kind of conservation projects are important to disseminate coastal conservation best practices. The Biomares project is a model project that can be followed in the implementation of marine reserves and the establishment of the Natura 2000 marine network.

Biological invasions rank amongst the most deleterious components of global change inducing alterations from genes to ecosystems. The genetic characteristics of introduced pools of individuals greatly influence the capacity of introduced species to establish and expand. The recently demonstrated heritability of microbial communities associated to individual genotypes of primary producers makes them a potentially essential element of the evolution and adaptability of their hosts. Here, we characterized the bacterial communities associated to native and non-native populations of the marine green macroalga Caulerpa racemosa through pyrosequencing, and explored their potential role on the strikingly invasive trajectory of their host in the Mediterranean. The similarity of endophytic bacterial communities from the native Australian range and several Mediterranean locations confirmed the origin of invasion and revealed distinct communities associated to a second Mediterranean variety of C. racemosa long reported in the Mediterranean. Comparative analysis of these two groups demonstrated the stability of the composition of bacterial communities through the successive steps of introduction and invasion and suggested the vertical transmission of some major bacterial OTUs. Indirect inferences on the taxonomic identity and associated metabolism of bacterial lineages showed a striking consistency with sediment upheaval conditions associated to the expansion of their invasive host and to the decline of native species. These results demonstrate that bacterial communities can be an effective tracer of the origin of invasion and support their potential role in their eukaryotic host's adaptation to new environments. They put forward the critical need to consider the 'meta-organism' encompassing both the host and associated micro-organisms, to unravel the origins, causes and mechanisms underlying biological invasions. © 2013 Aires et al.

Background The relationship between species diversity and components of ecosystem stability has been extensively studied, whilst the influence of the genetic component of biodiversity remains poorly understood. Here we manipulated both genotypic and allelic richness of the seagrass Zostera noltii, in order to explore their respective influences on the resistance of the experimental population to stress. Thus far intra-specific diversity was seldom taken into account in management plans, and restoration actions showed very low success. Information is therefore needed to understand the factors affecting resistance and resilience of populations. Results Our results show a positive influence of both allelic and genotypic richness on the resistance of meadows to environmental perturbations. They also show that at the low genotypic (i.e. clonal) richness levels used in prior experimental approaches, the effects of genotypic and allelic richness could not be disentangled and allelic richness was a likely hidden treatment explaining at least part of the effects hitherto attributed to genotypic richness. Conclusions Altogether, these results emphasize the need to acknowledge and take into account the interdependency of both genotypic and allelic richness in experimental designs attempting to estimate their importance alone or in combination. A positive influence of allelic richness on resistance to perturbations, and of allelic richness combined with genotypic richness on the recovery (resilience) of the experimental populations is supported by differential mortality. These results, on the key species structuring of one of the most threatened coastal ecosystem worldwide, seagrass meadows, support the need to better take into account the distinct compartments of clonal and genetic diversity in management strategies, and in possible restoration plans in the future.

We analyse a large data set of genetic markers obtained from populations of Cymodocea nodosa, a marine plant occurring from the East Mediterranean to the Iberian-African coasts in the Atlantic Ocean. We fully develop and test a recently introduced methodology to infer the directionality of gene flow based on the concept of geographical segregation. Using the Jensen-Shannon divergence, we are able to extract a directed network of gene flow describing the evolutionary patterns of Cymodocea nodosa. In particular we recover the genetic segregation that the marine plant underwent during its evolution. The results are confirmed by natural evidence and are consistent with an independent cross analysis.

Molecular analyses of bacteria associated with photosynthetic organisms are often confounded by coamplification of the chloroplastidial 16S rDNA with the targeted bacterial 16S rDNA. This major problem has hampered progress in the characterization of bacterial communities associated to photosynthetic organisms and has limited the full realization of the potential offered by the last generation of metagenomics approaches. A simple and inexpensive method is presented, based on ethanol and bleach treatments prior to extraction, to efficiently discard a great part of chloroplastidial DNA without affecting the characterization of bacterial communities through pyrosequencing. Its effectiveness for the description of bacterial lineages associated to the green alga Caulerpa taxifolia (M. Vahl) C. Agardh was much higher than that of the preexisting enrichment protocols proposed for plants. Furthermore, this new technique requires a very small amount of biological material compared to the other current protocols, making it more realistic for systematic use in ecological and phylogenetic studies and opening promising prospects for metagenomics of green algae, as shown by our data. © 2012 Phycological Society of America.

The maximum size and age that clonal organisms can reach remains poorly known, although we do know that the largest natural clones can extend over hundreds or thousands of metres and potentially live for centuries. We made a review of findings to date, which reveal that the maximum clone age and size estimates reported in the literature are typically limited by the scale of sampling, and may grossly underestimate the maximum age and size of clonal organisms. A case study presented here shows the occurrence of clones of slow-growing marine angiosperm Posidonia oceanica at spatial scales ranging from metres to hundreds of kilometres, using microsatellites on 1544 sampling units from a total of 40 locations across the Mediterranean Sea. This analysis revealed the presence, with a prevalence of 3.5 to 8.9%, of very large clones spreading over one to several (up to 15) kilometres at the different locations. Using estimates from field studies and models of the clonal growth of P. oceanica, we estimated these large clones to be hundreds to thousands of years old, suggesting the evolution of general purpose genotypes with large phenotypic plasticity in this species. These results, obtained combining genetics, demography and model-based calculations, question present knowledge and understanding of the spreading capacity and life span of plant clones. These findings call for further research on these life history traits associated with clonality, considering their possible ecological and evolutionary implications.

Halophila stipulacea (Forsskål) Ascherson, a tropical seagrass, is thought to be a Lessepsian immigrant that entered the Mediterranean Sea from the Red Sea after the opening of the Suez Canal (1869). Up to date, no genetic studies of H. stipulacea from Turkey are available. In order to verify the molecular identity of Turkish isolates of H, stipulacea, a part of the rDNAITS region was sequenced. Comparisons of the genetic polymorphism of this region between isolates from the Turkish coasts of the Aegean Sea and individuals from putative native (Red Sea) and introduced (Mediterranean) populations deposited previously in GenBank were performed. No intra-individual variability was found in the region considered among the isolates from Turkey.

Caulerpa spp. are clonal green marine algae which often act as invasive species when growing outside their native biogeographical borders. Over the two past decades, Caulerpa taxifolia has spread along the Mediterranean coast, presently occurring at 70 sites and covering nearly 3,000 ha of subtidal area. New genetic markers (microsatellites) have been developed to assess clonal structure and genetic diversity of recently established populations of the invasive species C. taxifolia and Caulerpa racemosa in comparison with populations of the native Caulerpa prolifera in the Mediterranean. Our results show that nine polymorphic markers have been developed for C. prolifera, seven for C. taxifolia, and three for C. racemosa. Genetic diversity in Caulerpa was assessed in two geographical scales: one at a population scale where 40 thalli units were collected from C. prolifera in Cala d'Or, Mallorca, Spain, and another at a species scale, where 30 sample units were analyzed for C. prolifera, 24 for C. taxifolia, and 24 for C. racemosa from different sites in the Mediterranean, Atlantic, and Pacific Ocean. Number of alleles, expected heterozygosity, and marker amplification success are provided in each case. © 2010 Springer Science+Business Media B.V.

Seagrasses are the structural species of one of the most important coastal ecosystems worldwide and support high levels of biodiversity and biomass production. Posidonia is one of the most ancient seagrass genera and displays a contrasting disjunct biogeographic pattern. It contains one single species in the Northern Hemisphere, P. oceanica, which is endemic to the Mediterranean Sea, and has up to 8 recognized taxa in the Southern Hemisphere, which in Australia are divided into 2 complexes, P. ostenfeldii and P. australis. A phylogeny based on a nuclear marker (rRNA-ITS) revealed an ancient split between the northern (i.e. Mediterranean) and southern (i.e. Australian) taxa, followed by a separation of the 2 recognized Australian complexes. However, the species belonging to the P. ostenfeldii complex were indistinguishable, suggesting an ecotypic origin or a recent speciation. Therefore, among the 7 morphologically described Australian species only 4 species lineages can be discriminated. The organelle markers nad7 intron, trnL-F and matK/trnK intron were not informative for reconstructing the phylogeny of this genus, and the mitochondrial markers exhibited a strikingly slow evolutionary rate relative to other genome regions.

The diversity–stability relationship is the subject of a long-standing debate in ecology, but the genetic component of diversity has seldom been explored. In this study, we analyzed the interplay between genetic diversity and demographic responses to environmental pressures. This analysis included 30 meadows formed by the Mediterranean endemic seagrass, Posidonia oceanica, showing a wide range of population dynamics ranging from a near equilibrium state to steep decline due to strong environmental pressures close to aquaculture installations. Our results show that sedimentation rates are much better predictors of mortality than clonal or genetic components. An unexpected positive trend was observed between genotypic diversity and mortality, along with a negative relationship between allelic richness and net population growth. Yet such trends disappeared when excluding the most extreme cases of disturbance and mortality, suggesting the occurrence of a threshold below which no relationship exists. These results contrast with the positive relationship between genotypic diversity and resistance or resilience observed in previous manipulative experiments on seagrass. We discuss the reasons for this discrepancy, including the difficulties in designing experiments reflecting the complexity of natural meadows.

The widespread use of Agent Orange (a mixture of phenoxyl herbicides) over Southern Vietnam by United States Forces, led to the decimation of mangrove forests in the Mekong Delta. Mangrove trees of Avicennia alba were sampled across the Mekong delta, their age was assessed using models based on internode growth and samples were genotyped for six microsatellite loci. The evolution of genetic diversity with time elapsed since local extinction was reconstructed, and compared with the genetic diversity of an unaffected population from Thailand. The results show that genetic diversity of A. alba population is still increasing in the Mekong Delta three decades following the end of the war, but is reaching an asymptotic level that is comparable to the adjacent non affected population of Thailand. This might be a sign of genetic recovery, but may also reveal a limitation, either of genetic enrichment due to current predominance of auto-recruitment, or of demographic increase due to intra-specific competition in this pioneer species. In any case these results, although encouraging, demonstrate that genetic recovery after complete or almost complete population depletion continues over a longer time-scale than apparent demographic recovery.

Aim: A central question in evolutionary ecology is the nature of environmental barriers that can limit gene flow and induce population genetic divergence, a first step towards speciation. Here we study the geographical barrier constituted by the transition zone between the Atlantic Ocean and the Mediterranean Sea, using as our model Cymodocea nodosa, a seagrass distributed throughout the Mediterranean and in the Atlantic, from central Portugal to Mauritania. We also test predictions about the genetic footprints of Pleistocene glaciations. Location: The Atlantic-Mediterranean transition region and adjacent areas in the Atlantic (Mauritania to south-west Portugal) and the Mediterranean. Methods: We used eight microsatellite markers to compare 20 seagrass meadows in the Atlantic and 27 meadows in the Mediterranean, focusing on the transition between these basins. Results: Populations from these two regions form coherent groups containing several unique, high-frequency alleles for the Atlantic and for the Mediterranean, with some admixture west of the Almeria-Oran Front (Portugal, south-west Spain and Morocco). These are populations where only one or a few genotypes were found, for all but Cadiz, but remarkably still show the footprint of a contact zone. This extremely low genotypic richness at the Atlantic northern edge contrasts with the high values (low clonality) at the Atlantic southern edge and in most of the Mediterranean. The most divergent populations are those at the higher temperature range limits: the southernmost Atlantic populations and the easternmost Mediterranean, both potential footprints of vicariance. Main conclusions: A biogeographical transition region occurs close to the Almeria-Oran front. A secondary contact zone in Atlantic Iberia and Morocco results from two distinct dispersal sources: the Mediterranean and southernmost Atlantic populations, possibly during warmer interglacial or post-glacial periods. The presence of high-frequency diagnostic

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can be represented as a network. In this paper we briefly show some properties of these complex networks of evolutionary and ecological relationships. First, we characterize large scale evolutionary relationships in the Tree of Life by a degree distribution. Second, we represent genetic relationships between individuals of a Mediterranean marine plant, Posidonia oceanica in terms of a Minimum Spanning Tree. Finally, relationships among plant shoots inside populations are represented as networks of genetic similarity.

Although clonal species are dominant in many habitats, from unicellular organisms to plants and animals, ecological and particularly evolutionary studies on clonal species have been strongly limited by the difficulty in assessing the number, size and longevity of genetic individuals within a population. The development of molecular markers has allowed progress in this area, and although allozymes remain of limited use due to their typically low level of polymorphism, more polymorphic markers have been discovered during the last decades, supplying powerful tools to overcome the problem of clonality assessment. However, population genetics studies on clonal organisms lack a standardized framework to assess clonality, and to adapt conventional data analyses to account for the potential bias due to the possible replication of the same individuals in the sampling. Moreover, existing studies used a variety of indices to describe clonal diversity and structure such that comparison among studies is difficult at best. We emphasize the need for standardizing studies on clonal organisms, and particularly on clonal plants, in order to clarify the way clonality is taken into account in sampling designs and data analysis, and to allow further comparison of results reported in distinct studies. In order to provide a first step towards a standardized framework to address clonality in population studies, we review, on the basis of a thorough revision of the literature on population structure of clonal plants and of a complementary revision on other clonal organisms, the indices and statistics used so far to estimate genotypic or clonal diversity and to describe clonal structure in plants. We examine their advantages and weaknesses as well as various conceptual issues associated with statistical analyses of population genetics data on clonal organisms. We do so by testing them on results from simulations, as well as on two empirical data sets of microsatellites of the seagrasses Posi

We explored the relationships between perturbation-driven population decline and genetic/genotypic structure in the clonal seagrass Posidonia oceanica, subject to intensive meadow regression around four Mediterranean fish-farms, using seven specific microsatellites. Two meadows were randomly sampled (40 shoots) within 1,600 m2 at each site: the >impacted> station, 5-200 m from fish cages, and the >control> station, around 1,000 m downstream further away (considered a proxy of the pre-impact genetic structure at the site). Clonal richness (R), Simpson genotypic diversity (D*) and clonal sub-range (CR) were highly variable among sites. Nevertheless, the maximum distance at which clonal dispersal was detected, indicated by CR, was higher at impacted stations than at the respective control station (paired t-test: P < 0.05, N = 4). The mean number of alleles (Â) and the presence of rare alleles ( r) decreased at impacted stations (paired t-test: P < 0.05, and P < 0.02, respectively, N = 4). At a given perturbation level (quantified by the organic and nutrient loads), shoot mortality at the impacted stations significantly decreased with CR at control stations (R2=0.86, P < 0.05). Seagrass mortality also increased with  (R 2=0.81, P < 0.10), R (R 2=0.96, P < 0.05) and D*(R 2=0.99, P < 0.01) at the control stations, probably because of the negative correlation between those parameters and CR. Therefore, the effects of clonal size structure on meadow resistance could play an important role on meadow survival. Large genotypes of P. oceanica meadows thus seem to resist better to fish farm-derived impacts than little ones. Clonal integration, foraging advantage or other size-related fitness traits could account for this effect. © 2007 Springer Science+Business Media, Inc.

Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes, such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations was examined using a combination of new tools to analyze microsatellite data in the marine angiosperm Posidonia oceanica. These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a "small-world" topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in sub-families of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.

Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species' distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes. © 2006 The Authors.

The seagrass Cymodocea nodosa forms a unique community in the Canary Islands, where it is classified as an endangered species. Biogeographic theory predicts that clonal species on islands near their distributional limits might show lower proportions of sexual (versus clonal) reproduction, lower genetic diversity, and higher differentiation. We addressed these hypotheses by comparing the genetic structure of C. nodosa from 10 meadows in the 4 main Canary Islands with 2 Iberian sites (Atlantic and Mediterranean) using microsatellites. A resampling method was proposed to standardize, among samples, genetic variability statistics estimating genotypic richness (R) and allelic richness (Â). A high degree of genotypic richness at the Canary Islands (R = 0.30 - 0.94, mean = 0.67) relative to Iberian sites revealed that C. nodosa performs effective sexual reproduction here. In contrast, lower  suggested a founder effect during the colonization of the archipelago, and similar allelic composition across all islands indicated colonization from a single source. A hotspot of genetic diversity was observed in El Medano (Tenerife), probably associated with lower drift in this meadow, the largest of the archipelago. Predominant north-south surface currents and a greater distance to the mainland could explain lower allelic richness of 2 northwestern sites on different islands and greater similarity between them. All meadows were differentiated from each other and there was no correlation between genetic and geographic distances. This non-equilibrium migration-mutation system was therefore mostly influenced by diversity resulting from genetic drift, and less by the homogenizing effects of gene flow. © Inter-Research 2006.

The extent of clonality within populations strongly influences their spatial genetic structure (SGS), yet this is hardly ever thoroughly analysed. We employed spatial autocorrelation analysis to study effects of sexual and clonal reproduction on dispersal of the dioecious seagrass Cymodocea nodosa. Analyses were performed both at genet level (i.e. excluding clonal repeats) and at ramet level. Clonal structure was characterized by the clonal subrange, a spatial measure of the linear limits where clonality still affects SGS. We show that the clonal subrange is equivalent to the distance where the probability of clonal identity approaches zero. This combined approach was applied to two meadows with different levels of disturbance, Cadiz (stable) and Alfacs (disturbed). Genotypic richness, the proportion of the sample representing distinct genotypes, was moderate (0.38 Cadiz, 0.46 Alfacs) mostly due to dominance of a few clones. Expected heterozygosities were comparable to those found in other clonal plants. SGS analyses at the genet level revealed extremely restricted gene dispersal in Cadiz (Sp = 0.052, a statistic reflecting the decrease of pairwise kinship with distance), the strongest SGS found for seagrass species, comparable only to values for selfing herbaceous land plants. At Cadiz the clonal subrange extended across shorter distances (20-25 m) than in Alfacs (30-35 m). Comparisons of sexual and vegetative components of gene dispersal suggest that, as a dispersal vector within meadows, clonal spread is at least as important as sexual reproduction. The restricted dispersal and SGS pattern in both meadows indicates that the species follows a repeated seedling recruitment strategy. © 2005 Blackwell Publishing Ltd.

The increasing use of molecular tools to study populations of clonal organisms leads us to question whether the low polymorphism found in many studies reflects limited genetic diversity in populations or the limitations of the markers used. Here we used microsatellite datasets for two sea grass species to provide a combinatory statistic, combined with a likelihood approach to estimate the probability of identical multilocus genotypes (MLGs) to be shared by distinct individuals, in order to ascertain the efficiency of the markers used and to optimize cost-efficiently the choice of markers to use for deriving unbiased estimates of genetic diversity. These results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers. © The American Genetic Association. 2005. All rights reserved.

Like most species of mangrove trees of the genus Avicennia, A. alba is widely distributed among tropical and subtropical coasts around the world. Mangroves play an essential role in ecosystem dynamics but are reported to be regressing as human pressure increases on coastal zones. Hypervariable genetic markers are useful for population genetics studies, to estimate the level of impact and the populations potential for recovery. Microsatellite markers for A. alba were obtained by screening a partial genomic library enriched for microsatellite dinucleotide repeats. Among 20 primer pairs defined, six amplified polymorphic microsatellites with a satisfying level of variability.

The seagrass Posidonia oceanica is endemic to the Mediterranean Sea, where it plays an important role in coastal ecosystem dynamics. Because of this important role and concerns about the observed regression of some meadows, population genetic studies of this species have been promoted. However, the markers used until now were not polymorphic enough to efficiently assess the level and spatial pattern of genetic variability. Hypervariable molecular markers were obtained by screening a genomic library enriched for microsatellite dinucleotide repeats. Among 25 primer pairs defined, eight amplified polymorphic micro-satellites with an encouraging level of variability at the two geographical scales sampled.