Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia.

Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.

Larval development and allometric growth of the black-faced blenny Tripterygion delaisi.

Larval development and allometric growth patterns of the black-faced blenny Tripterygion delaisi are described from a larval series (body length, LB = 3·30-12·10 mm) caught by light traps at the Arrábida Marine Park, Portugal. Larvae of T. delaisi possess distinctive morphometric and meristic characteristics which can be used to identify this species from related taxa. Pigmentation is sparse but characteristic, consisting of pigmented eyes, gas bladder pigmentation in the dorsal region, anal pigmentation and a row of regularly spaced postanal ventral melanophores. This pattern is present from as early as the yolk-sac stage and persists throughout all stages with just the addition of head and caudal pigmentation during the flexion and postflexion stages, respectively. The majority of fin development (with the exception of the caudal fin), occurs in the later stages of development. Myomere counts range between 37 and 45 for all stages. Growth is allometric during larval development. When inflexion points of growth were detected, growth was found to be biphasic with the inflexion points occurring within a very narrow range of LB (8·70-8·90 mm) close to the mean ± s.d. (9·44 ± 1·48 mm LB ) of postflexion larvae. Considering allometric growth patterns and ontogenetic descriptions together, the first developmental phase includes the preflexion and flexion stage larvae, while the second phase characterises the postflexion larvae prior to the transition from larvae to juvenile.

Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs.

Climate-driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga.

The climate-driven dynamics of species ranges is a critical research question in evolutionary ecology. We ask whether present intraspecific diversity is determined by the imprint of past climate. This is an ongoing debate requiring interdisciplinary examination of population genetic pools and persistence patterns across global ranges. Previously, contrasting inferences and predictions have resulted from distinct genomic coverage and/or geographical information. We aim to describe and explain the causes of geographical contrasts in genetic diversity and their consequences for the future baseline of the global genetic pool, by comparing present geographical distribution of genetic diversity and differentiation with predictive species distribution modelling (SDM) during past extremes, present time and future climate scenarios for a brown alga, Fucus vesiculosus. SDM showed that both atmospheric and oceanic variables shape the global distribution of intertidal species, revealing regions of persistence, extinction and expansion during glacial and postglacial periods. These explained the distribution and structure of present genetic diversity, consisting of differentiated genetic pools with maximal diversity in areas of long-term persistence. Most of the present species range comprises postglacial expansion zones and, in contrast to highly dispersive marine organisms, expansions involved only local fronts, leaving distinct genetic pools at rear edges. Besides unravelling a complex phylogeographical history and showing congruence between genetic diversity and persistent distribution zones, supporting the hypothesis of niche conservatism, range shifts and loss of unique genetic diversity at the rear edge were predicted for future climate scenarios, impoverishing the global gene pool.

New highly polymorphic microsatellite markers for the aquatic angiosperm Ruppia cirrhosa reveal population diversity and differentiation.

Ruppia cirrhosa is a clonal monoecious plant phylogenetically associated to seagrass families such as Posidoniaceae and Cymodoceaceae. It inhabits shallow waters that are important for productivity and as a biodiversity reservoir. In this study, we developed 10 polymorphic microsatellite loci for R. cirrhosa. Additionally, we obtained cross-amplification for two microsatellites previously described for Ruppia maritima. These 12 markers were tested in four R. cirrhosa populations from the southwest of Europe. The number of alleles per locus was high for most of the markers, ranging from 4 to 13. Two populations (Sicily and Cádiz) showed heterozygote deficit (p < 0.001). The four populations (Sicily, Murcia, Cádiz, and Tavira) were significantly differentiated (F(ST) ≠ 0; p < 0.001), corroborating the usefulness of these microsatellites on R. cirrhosa population genetics.

Loss of a globally unique kelp forest from Oman.

Kelp forests are declining in many regions globally with climatic perturbations causing shifts to alternate communities and significant ecological and economic loss. Range edge populations are often at most risk and are often only sustained through localised areas of upwelling or on deeper reefs. Here we document the loss of kelp forests (Ecklonia radiata) from the Sultanate of Oman, the only confirmed northern hemisphere population of this species. Contemporary surveys failed to find any kelp in its only known historical northern hemisphere location, Sadah on the Dhofar coast. Genetic analyses of historical herbarium specimens from Oman confirmed the species to be E. radiata and revealed the lost population contained a common CO1 haplotype found across South Africa, Australia and New Zealand suggesting it once established through rapid colonisation throughout its range. However, the Omani population also contained a haplotype that is found nowhere else in the extant southern hemisphere distribution of E. radiata. The loss of the Oman population could be due to significant increases in the Arabian Sea temperature over the past 40 years punctuated by suppression of coastal upwelling. Climate-mediated warming is threatening the persistence of temperate species and precipitating loss of unique genetic diversity at lower latitudes.

Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales.

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).

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic.

We examined 733 individuals of Fucusspiralis from 21 locations and 1093 Fucusvesiculosus individuals from 37 locations throughout their northern hemisphere ranges using nuclear and mitochondrial markers. Three genetic entities of F. spiralis were recovered. In northern and sympatric populations, the presence of "F. spiralis Low" in the mid-intertidal and "F. spiralis High" in the high-intertidal was confirmed and both co-occurred with the sister species F. vesiculosus. The third and newly-discovered entity, "F. spiralis South", was present mainly in the southern range, where it did not co-occur with F. vesiculosus. The South entity diverged early in allopatry, then hybridized with F. vesiculosus in sympatry to produce F. spiralis Low. Ongoing parallel evolution of F. spiralis Low and F. spiralis High is most likely due to habitat preference/local selection and maintained by preferentially selfing reproductive strategies. Contemporary populations of F. spiralis throughout the North Atlantic stem from a glacial refugium around Brittany involving F. spiralis High; F. spiralis South was probably unaffected by glacial episodes. Exponential population expansion for F. vesiculosus began during the Cromer and/Holstein interglacial period (300,000-200,000 yrs BP). Following the last glacial maximum (30,000-22,000 yrs BP), a single mtDNA haplotype from a glacial refugium in SW Ireland colonized Scandinavia, the Central Atlantic islands, and the W Atlantic.

Weak biodiversity connectivity in the European network of no-take marine protected areas.

The need for international cooperation in marine resource management and conservation has been reflected in the increasing number of agreements aiming for effective and well-connected networks of Marine Protected Areas (MPAs). However, the extent to which individual MPAs are connected remains mostly unknown. Here, we use a biophysical model tuned with empirical data on species dispersal ecology to predict connectivity of a vast spectrum of biodiversity in the European network of marine reserves (i.e., no-take MPAs). Our results highlight the correlation between empirical propagule duration data and connectivity potential and show weak network connectivity and strong isolation for major ecological groups, resulting from the lack of direct connectivity corridors between reserves over vast regions. The particularly high isolation predicted for ecosystem structuring species (e.g., corals, sponges, macroalgae and seagrass) might potentially undermine biodiversity conservation efforts if local retention is insufficient and unmanaged populations are at risk. Isolation might also be problematic for populations' persistence in the light of climate change and expected species range shifts. Our findings provide novel insights for management directives, highlighting the location of regions requiring additional marine reserves to function as stepping-stone connectivity corridors.

Global warming assessment suggests the endemic Brazilian kelp beds to be an endangered ecosystem.

Kelps are canopy-forming brown seaweed sustaining critical ecosystem services in coastal habitats, including shelter, nursery grounds, and providing food resources to a myriad of associated species. This study modeled the fundamental niche of Laminaria abyssalis along the Brazilian continental margin, an endemic species of the South Atlantic, to anticipate potential distributional range shifts under two contrasting scenarios of future environmental changes (RCP2.6 and RCP8.5). The model for fundamental niche predictions considering the "present scenario" has shown a wider potential area than the realized niche (i.e., the area where the species actually occurs) along the Brazilian coast. In both future scenarios, the models have shown niche erosion on the northern portion of the Brazilian coast and niche gains towards the south. In both scenarios, L. abyssalis populations tend to shift to deeper regions of the reef. The restricted range of occurrence (33,000 km2), intense anthropic activities along these beds (e.g., trawling fisheries, oil/gas mining, or removal for agricultural purposes) acting synergically with global warming, may drive this ecosystem to collapse faster than kelp species' ability to adapt. We propose to classify L. abyssalis as Endangered - (EN) under IUCN criteria, and highlight that long-term monitoring of kelp beds is an urgent need to develop effective conservation initiatives to protect such rare and invaluable ecosystem.

Genetic structure in the Mediterranean seagrass Posidonia oceanica: disentangling past vicariance events from contemporary patterns of gene flow.

The Mediterranean Sea is a two-basin system, with the boundary zone restricted to the Strait of Sicily and the narrow Strait of Messina. Two main population groups are recognized in the Mediterranean endemic seagrass Posidonia oceanica, corresponding to the Western and the Eastern basins. To address the nature of the East-West cleavage in P. oceanica, the main aims of this study were: (i) to define the genetic structure within the potential contact zone (i.e. the Strait of Sicily) and clarify the extent of gene flow between the two population groups, and (ii) to investigate the role of present water circulation patterns vs. past evolutionary events on the observed genetic pattern. To achieve these goals, we utilized SSR markers and we simulated, with respect to current regime, the possible present-day dispersal pattern of Posidonia floating fruits using 28-day numerical Lagrangian trajectories. The results obtained confirm the presence of the two main population groups, without any indices of reproductive isolation, with the break zone located at the level of the Southern tip of Calabria. The populations in the Strait of Sicily showed higher affinity with Western than with Eastern populations. This pattern of genetic structure probably reflects historical avenues of recolonization from relict glacial areas and past vicariance events, but seems to persist as a result of the low connectivity among populations via marine currents, as suggested by our dispersal simulation analysis.

Major shifts at the range edge of marine forests: the combined effects of climate changes and limited dispersal.

Global climate change is likely to constrain low latitude range edges across many taxa and habitats. Such is the case for NE Atlantic marine macroalgal forests, important ecosystems whose main structuring species is the annual kelp Saccorhiza polyschides. We coupled ecological niche modelling with simulations of potential dispersal and delayed development stages to infer the major forces shaping range edges and to predict their dynamics. Models indicated that the southern limit is set by high winter temperatures above the physiological tolerance of overwintering microscopic stages and reduced upwelling during recruitment. The best range predictions were achieved assuming low spatial dispersal (5 km) and delayed stages up to two years (temporal dispersal). Reconstructing distributions through time indicated losses of ~30% from 1986 to 2014, restricting S. polyschides to upwelling regions at the southern edge. Future predictions further restrict populations to a unique refugium in northwestern Iberia. Losses were dependent on the emissions scenario, with the most drastic one shifting ~38% of the current distribution by 2100. Such distributional changes might not be rescued by dispersal in space or time (as shown for the recent past) and are expected to drive major biodiversity loss and changes in ecosystem functioning.

Limited differences in fish and benthic communities and possible cascading effects inside and outside a protected marine area in Sagres (SW Portugal).

Marine protected areas (MPAs) are a relatively recent fisheries management and conservation tool for conservation of marine ecosystems and serve as experimental grounds to assess trophic cascade effects in areas were fishing is restricted to some extent. A series of descriptive field studies were performed to assess fish and benthic communities between two areas within a newly established MPA in SW Portugal. We characterized benthic macroalgal composition and determined the size, density and biomass of the main benthic predatory and herbivorous fish species as well as the main benthic herbivorous invertebrates to assess indications of top-down control on the phytobenthic assemblages. Fish species were identical inside and outside the MPA, in both cases Sarpa salpa was the most abundant fish herbivore and Diplodus spp. accounted for the great majority of the benthic predators. However, size and biomass of D. spp. were higher inside than outside the MPA. The main herbivorous invertebrate was the sea urchin Paracentrotus lividus, which was smaller and predominantly showing a crevice-dwelling behaviour in the MPA. In addition, P. lividus size frequency distribution showed a unimodal pattern outside and a bimodal pattern inside the MPA. We found significant differences in the algal assemblages between inside and outside the MPA, with higher abundance of turf and foliose algae inside, and articulated calcareous and corticated macrophytes outside the MPA, but no differences in the invasive Asparagopsis spp. The obtained results show differences in predatory fish and benthic community structure, but not in species richness, inside and outside the MPA. We hypothesize these differences lead to variation in species interactions: directly through predation and indirectly via affecting sea urchins behavioural patterns, predators might drive changes in macroalgal assemblages via trophic cascade in the study area. However due to non-biological differences between the two areas it is difficult to suggest that the MPA causes increased biological parameters of targeted species and to assess predatory control and trophic cascade effects in areas where fishing pressure is reduced. It is therefor advisable to design MPAs so that their impacts can be scientifically evaluated in a proper fashion.

A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures.

The copepod Calanus glacialis plays a key role in the Arctic pelagic ecosystem. Despite its ecological importance and ongoing climate changes, limited knowledge at the genomic level has hindered the understanding of the molecular processes underlying environmental stress responses and ecological adaptation. Transcriptome data was generated from an experiment with C. glacialis copepodite (CV) subjected to five different temperatures. We obtained a total of 512,352 high-quality 454 pyrosequencing reads, which were assembled into 55,562 contigs distributed in 128 KEGG pathways. Functional analysis revealed numerous genes related to diverse biological functions and processes, including members of all major conserved signaling pathways. Comparative analysis of acclimated individuals to experimental temperatures has provided information about gene variations observed in several pathways (e.g. genes involved in energy, lipid and amino acid metabolism were shown to be down-regulated with increasing temperatures). These mRNA sequence resources will facilitate further studies on genomics and physiology-driven molecular processes in C. glacialis and related species.

Standardizing methods to address clonality in population studies.

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 Posidonia oceanica and Cymodocea nodosa. Finally, we also propose a selection of new indices and methods to estimate clonal diversity and describe clonal structure in a way that should facilitate comparison between future studies on clonal plants, most of which may be of interest for clonal organisms in general.

Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations.

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.

Genetic entities and mating system in hermaphroditic Fucus spiralis and its close dioecious relative F. vesiculosus (Fucaceae, Phaeophyceae).

To date, molecular markers have not settled the question of the specific status of the closely related, but phylogenetically unresolved, brown seaweeds, hermaphroditic Fucus spiralis and dioecious Fucus vesiculosus, nor their propensity for natural hybridization. To test the degree of species integrity and to assess effect of the mating system on the population genetic structure, 288 individuals coming from parapatric (discontinuous) and sympatric (contiguous) spatial configurations at two sites were genotyped with five microsatellite loci. Using a Bayesian admixture analysis, our results show that F. spiralis and F. vesiculosus comprise clearly distinct genetic entities (clusters) generally characterized by cosexual and unisexual individuals, respectively. Genetic diversity within each entity suggests that F. spiralis reproduces primarily through selfing while F. vesiculosus is characterized by an endogamous breeding regime. Nevertheless, aberrant sexual phenotypes were observed in each cluster, no diagnostic alleles were revealed and 10% of study individuals were intermediate between the two genetic entities. This pattern can be explained by recent divergence of two taxa with retention of ancestral polymorphism or asymmetrical, introgressive hybridization. However, given (i) coincident monomorphism at three loci in spiralis clusters and (ii) that significantly more intermediates were observed in sympatric stations than in parapatric stations, we argue that interspecific gene flow has occurred after divergence of the two taxa. Finally, we show that whether recently separated or recently introgressive, the divergent breeding systems probably contribute to species integrity in these two taxa.

Assessing genetic diversity in clonal organisms: low diversity or low resolution? Combining power and cost efficiency in selecting markers.

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.

Intriguing asexual life in marginal populations of the brown seaweed Fucus vesiculosus.

Reproduction of attached large brown algae is known to occur only by sexual zygotes. Using microsatellites we show evolution of asexual reproduction in the bladder wrack promoting population persistence in the brackish water Baltic Sea (< 6 psu). Here a dwarf morph of Fucus vesiculosus is dominated by a single clone but clonal reproduction is also present in the common form of the species. We describe a possible mechanism for vegetative reproduction of attached algae, and conclude that clonality plays an important role in persistence and dispersal of these marginal populations, in which sexual reproduction is impaired by low salinity.

Successful external fertilization in turbulent environments.

Mathematical and experimental simulations predict that external fertilization is unsuccessful in habitats characterized by high water motion. A key assumption of such predictions is that gametes are released in hydrodynamic regimes that quickly dilute gametes. We used fucoid seaweeds to examine whether marine organisms in intertidal and subtidal habitats might achieve high levels of fertilization by restricting their release of gametes to calm intervals. Fucus vesiculosus L. (Baltic Sea) released high numbers of gametes only when maximal water velocities were below ca. 0.2 m/s immediately prior to natural periods of release, which occur in early evening in association with lunar cues. Natural fertilization success measured at two sites was always close to 100%. Laboratory experiments confirmed that (i) high water motion inhibits gamete release by F. vesiculosus and by the intertidal fucoids Fucus distichus L. (Maine) and Pelvetia fastigiata (J. Ag.) DeToni (California), and (ii) showed that photosynthesis is required for high gamete release. These data suggest that chemical changes in the boundary layer surrounding adults during photosynthesis and/or mechanosensitive channels may modulate gamete release in response to changing hydrodynamic conditions. Therefore, sensitivity to environmental factors can lead to successful external fertilization, even for species living in turbulent habitats.