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Larval dispersal enables demographic and genetic connectivity among marine populations. For many sessile species, it is the only natural mechanism for resilience after major population disturbances, as those that have been affecting Mediterranean gorgonian species inside and outside Marine Protected Areas (MPAs). Larval dispersal simulation is a powerful tool to anticipate connectivity among populations which might be altered by modelling choices. We assessed how flow representation (resolution and vertical turbulence) and larval traits (pelagic larval duration, release timing and duration, larval vertical behaviour) influenced populations connectivity among five coastal rocky locations in the northwestern Mediterranean, four of them being designated as MPAs. We used a finer (0.3 km) and coarser (1.5 km) flow resolution in two years to assess, using a hierarchical simulation approach, the sensitivity of connectivity patterns to the above parameters. Larval traits corresponded to two gorgonian species, the neutrally buoyant Eunicella singularis and the passive sinker Paramuricea clavata. Ocean model resolution was the most influential factor on resulting connectivity patterns. When using the finer flow model resolution, connectivity patterns were equally influenced by all larval traits while vertical turbulence could be neglected. Hence, advising the design of coastal MPAs with regional connectivity estimates requires adequate flow simulation resolution. [ABSTRACT FROM AUTHOR]

Ocean circulation is the engine of dispersal and population connectivity in marine ecosystems, knowledge of which is essential for conservation planning. Understanding connectivity patterns at a large scale can help define the spatial extent of metapopulations. In this study, we built connectivity networks from Lagrangian transport simulations of neutrally buoyant particles released along the Indian coastline, a significant region in the Indian Ocean. We assessed the variation in connectivity networks across release periods for the major drivers of oceanography including the two monsoonal seasons, El Niño–Southern Oscillation (ENSO) years and for the entire range of region‐specific pelagic larval durations (PLDs) for marine invertebrates. We detected well‐connected communities, mapped frequent connectivity breaks, and assessed the functional role of coastal areas within the connectivity network using node metrics. Network characteristics did not differ based on the ENSO year, but varied with season and PLD. Connectance for the Indian coastline was relatively low, ranging from 0.5% to 3.4%, and increased significantly for PLD larger than 20 d. The number of cohesive coastal communities decreased gradually from 60 (PLD < 4 d) to 30 (PLD > 20 d) with increasing PLD. Despite variation in the location of connectivity breaks with the time of particle release within a monsoonal season, four disconnected provinces were consistently identified across the entire PLD range, which partially overlapped with observed genetic and biogeographic breaks reported along the Indian coastline. Our results support the adoption of a coordinated management framework within each of the four provinces delineated in the present study. [ABSTRACT FROM AUTHOR]

Representing data as networks cuts across all sub-disciplines in ecology and evolutionary biology. Besides providing a compact representation of the interconnections between agents, network analysis allows the identification of especially important nodes, according to various metrics that often rely on the calculation of the shortest paths connecting any two nodes. While the interpretation of a shortest paths is straightforward in binary, unweighted networks, whenever weights are reported, the calculation could yield unexpected results. We analyzed 129 studies of ecological networks published in the last decade that use shortest paths, and discovered a methodological inaccuracy related to the edge weights used to calculate shortest paths (and related centrality measures), particularly in interaction networks. Specifically, 49% of the studies do not report sufficient information on the calculation to allow their replication, and 61% of the studies on weighted networks may contain errors in how shortest paths are calculated. Using toy models and empirical ecological data, we show how to transform the data prior to calculation and illustrate the pitfalls that need to be avoided. We conclude by proposing a five-point check-list to foster best-practices in the calculation and reporting of centrality measures in ecology and evolution studies. [ABSTRACT FROM AUTHOR]

Microphytobenthos (MPB) from intertidal mudflats are key primary producers at the land–ocean interface. MPB can be more productive than phytoplankton and sustain both benthic and pelagic higher trophic levels. The objective of this study is to assess the contribution of light, mud temperature, and gastropod Peringia ulvae grazing pressure in shaping the seasonal MPB dynamics on the Brouage mudflat (NW France). We use a physical–biological coupled model applied to the sediment first centimetre for the year 2008. The simulated data compare to observations, including time-coincident remotely sensed and in situ data. The model suggests an MPB annual cycle characterised by a main spring bloom, a biomass depression in summer, and a moderate fall bloom. In early spring, simulated photosynthetic rates are high due to mud surface temperature (MST) values close to the MPB temperature optimum for photosynthesis and because increasing solar irradiance triggers the onset of the MPB spring bloom. Simulated peaks of high P. ulvae grazing (11 days during which ingestion rates exceed the primary production rate) mostly contribute to the decline of the MPB bloom along with the temperature limitation for MPB growth. In late spring–summer, the MPB biomass depression is due to the combined effect of thermo-inhibition and a moderate but sustained grazing pressure. The model ability to infer biotic and abiotic mechanisms driving the seasonal MPB dynamics could open the door to a new assessment of the export flux of biogenic matter from the coast to the open ocean and, more generally, of the contribution of productive intertidal biofilms to the coastal carbon cycle. [ABSTRACT FROM AUTHOR]

Habitat-forming species sustain biodiversity and ecosystem functioning in harsh environments through the amelioration of physical stress. Nonetheless, their role in shaping patterns of species distribution under future climate scenarios is generally overlooked. Focusing on coastal systems, we assess how habitat-forming species can influence the ability of stress-sensitive species to exhibit plastic responses, adapt to novel environmental conditions, or track suitable climates. Here, we argue that habitat-former populations could be managed as a nature-based solution against climate-driven loss of biodiversity. Drawing from different ecological and biological disciplines, we identify a series of actions to sustain the resilience of marine habitat-forming species to climate change, as well as their effectiveness and reliability in rescuing stress-sensitive species from increasingly adverse environmental conditions. [ABSTRACT FROM AUTHOR]

Abstract: Larval transport by ocean circulation and its emerging property at the population level, i.e. connectivity, has received increasing attention thanks to the Aichi target 11 of protecting 10% of ocean surfaces through well‐connected marine protected area (MPA) networks. Furthermore, it is also important to investigate retention within a site, as it determines the self‐persistence of a population in an isolated MPA. Mediterranean rocky substrates host a conspicuous and diverse biota, which explains why MPA designations have targeted rocky habitat. Retention rates in the fragmented rocky habitat of the Gulf of Lion were established at two spatial scales (10 and 1 km2) using dispersal simulations. To this end we computed three‐dimensional flow simulations with high spatial resolution nearshore (80 m), combined with a high density of release spots (every 100 m). This study shows that among the six rocky 10‐km2 patches, the four with highest average retention rates for pelagic larval duration (PLD), of up to 42 days, were designated MPAs. Furthermore, within each MPA, small zones where special protection measures are applied correspond to 1‐km2 subpatches where the highest local retention rates were found. Yet the 2% most retentive subpatches of the rocky habitat do not exhibit retention rates large enough to ensure the local persistence of most species. [ABSTRACT FROM AUTHOR]

Abstract: Climate‐induced threats are increasingly affecting marine populations worldwide. In the last few decades, several gorgonian species have been affected by mass mortality events in the north‐west Mediterranean, putatively linked to local sea temperature increases during heatwaves. For many benthic sessile species, recovery after disturbances depends upon larval supply shaping the connections among populations. In the Ligurian Sea, genetic analyses showed that some Paramuricea clavata populations recovered after mass mortality events; however, the patterns of connectivity, and the potential role of migration in supporting the recovery of the populations of P. clavata, across its distribution range within the Ligurian Sea are still unknown. In this study, the population genetic structure and migration patterns of P. clavata populations have been analysed across seven sites in the Ligurian Sea, some of which have been affected by mass mortality events. Evidence of a population bottleneck was found in most of the populations studied. Significant genetic differentiation was found among P. clavata populations, reflecting habitat fragmentation at a regional scale, except for two populations found 20 km apart. Continuing gene flow between distant populations was also revealed. Empirical data suggest that gene flow among populations may have contributed to support their recovery from mass mortality events. The study identified populations in the central part of the Ligurian Sea that can be strategic for the regional persistence of the species. These findings highlight that the preservation of key populations could maintain connectivity and gene flow in the metapopulation, and increase the resilience of the species. [ABSTRACT FROM AUTHOR]

Microphytobenthos (MPB) from intertidal mudflats are key primary producers at the land-ocean interface. MPB can be more productive than phytoplankton and sustain both benthic and pelagic higher trophic levels. The objective of this study is to assess the contribution of light, mud temperature, and gastropod Peringia ulvae grazing pressure in shaping the seasonal MPB dynamics on the Brouage mudflat (NW France). We use a physical-biological coupled model applied to the sediment first centimeter for the year 2008. The simulated data compare to observations including time-coincident remotely sensed and in situ data. The model suggests a MPB annual cycle characterized by a main spring bloom, a biomass depression in summer, and a moderate fall bloom. In early spring, high simulated photosynthetic rates due to mud surface temperature (MST) values close to the MPB temperature optimum for photosynthesis and to increasing solar irradiance trigger the onset of the MPB spring bloom. After the bloom, high MST values lead to synoptic events when MPB thermo-inhibition (39.5 % of summer) and limitation by P. ulvae grazing (8.7 % of summer) superimpose. During these synoptic events of thermo-inhibition and grazing combination, 14 % of the simulated annual MPB primary production is channeled towards the P. ulvae secondary production through ingestion. The model suggests that such a combined effect is highly linked to the MPB biomass depression in summer. The model ability to infer on biotic and abiotic mechanisms driving the seasonal MPB dynamics could open the door to a new assessment of the export flux of biogenic matter at the land-ocean interface and, more generally, of the contribution of productive intertidal biofilms to the coastal carbon cycle. [ABSTRACT FROM AUTHOR]

Understanding the patterns of connectivity is required by the Strategic Plan for Biodiversity 2011-2020 and will be used to guide the extension of marine protection measures. Despite the increasing accuracy of ocean circulation modelling, the capacity to model the population connectivity of sessile benthic species with dispersal larval stages can be limited due to the potential effect of filters acting before or after dispersal, which modulates offspring release or settlement, respectively. We applied an interdisciplinary approach that combined demographic surveys, genetic methods (assignment tests and coalescent-based analyses) and larval transport simulations to test the relative importance of demographics and ocean currents in shaping the recent patterns of gene flow among populations of a Mediterranean gorgonian (Eunicella singularis) in a fragmented rocky habitat (Gulf of Lion, NW Mediterranean Sea). We show that larval transport is a dominant driver of recent gene flow among the populations, and significant correlations were found between recent gene flow and larval transport during an average single dispersal event when the pelagic larval durations (PLDs) ranged from 7 to 14 d. Our results suggest that PLDs that efficiently connect populations distributed over a fragmented habitat are filtered by the habitat layout within the species competency period. Moreover, a PLD ranging from 7 to 14 d is sufficient to connect the fragmented rocky substrate of the Gulf of Lion. The rocky areas located in the centre of the Gulf of Lion, which are currently not protected, were identified as essential hubs for the distribution of migrants in the region. We encourage the use of a range of PLDs instead of a single value when estimating larval transport with biophysical models to identify potential connectivity patterns among a network of Marine Protected Areas or even solely a seascape. [ABSTRACT FROM AUTHOR]

Betweenness has been used in a number of marine studies to identify portions of sea that sustain the connectivity of whole marine networks. Herein we highlight the need of methodological exactness in the calculation of betweenness when graph theory is applied to marine connectivity studies based on transfer probabilities. We show the inconsistency in calculating betweeness directly from transfer probabilities and propose a new metric for the node-to-node distance that solves it. Our argumentation is illustrated by both simple theoretical examples and the analysis of a literature data set. [ABSTRACT FROM AUTHOR]

Disturbance strongly impacts patterns of community diversity, yet the shape of the diversity-disturbance relationship remains a matter of debate. The topic has been of interest in theoretical ecology for decades as it has practical implications for the understanding of ecosystem services in nature. One of these processes is the remineralization of organic matter by microorganisms in coastal marine sediments, which are periodically impacted by disturbances across the sediment-water interface. Here we set up an experiment to test the hypothesis that disturbance impacts microbial diversity and function during the anaerobic degradation of organic matter in coastal sediments. We show that during the first 3 weeks of the experiment, disturbance increased both microbial production, derived from the increase in microbial abundance, and diversity of the active fraction of the community. Both community diversity and phylogenetic diversity increased, which suggests that disturbance promoted the cohabitation of ecologically different microorganisms. Metagenome analysis also showed that disturbance increased the relative abundance of genes diagnostic of metabolism associated with the sequential anaerobic degradation of organic matter. However, community composition was not impacted in a systematic way and changed over time. In nature, we can hypothesize that moderate storm disturbances, which impact coastal sediments, promote diverse, and productive communities. These events, rather than altering the decomposition of organic matter, may increase the substrate turnover and, ultimately, remineralization rates. [ABSTRACT FROM AUTHOR]

Accounting for connectivity is essential in marine spatial planning and the proper design and management of marine protected areas, given that their effectiveness depends on the patterns of dispersal and colonization between protected and non-protected areas. The genetic structure of populations is commonly used to infer connectivity among distant populations. Here, we explore how population genetic structure is affected by pre- and settlement limitations with a spatially explicit coupled metapopulation-gene flow model that simulates the effect of demographic fluctuations on the allele frequencies of a set of populations. We show that in closed populations, regardless of population growth rate, the maintenance of genetic diversity at saturating initial population density increases with species life expectancy as a result of density-dependent recruitment control. Correlatively, at low initial population density, the time at which a population begins to lose its genetic diversity is driven larval and post-settlement mortality (comprised in the recruitment success parameter) —the larger the recruitment success, the stronger the genetic drift. Different spatial structures of connectivity established for soft bottom benthic invertebrates in the Gulf of Lions (NW Mediterranean, France) lead to very different results in the spatial patterns of genetic structuration of the metapopulation, with high genetic drift in sites where the local retention rate was larger than 2%. The effect of recruitment failure and the loss of key source populations on heterozygosity confirm that transient demographic fluctuations help maintain genetic diversity in a metapopulation. This study highlights the role of intraspecific settlement limitations due to lack of space when the effective number of breeders approaches saturating capacity, causing a strong reduction in effective reproduction. The present model allows to: (i) disentangle the relative contribution of local demography and environmental connectivity in shaping seascape genetics, and (ii) perform in silico evaluations of different scenarios for marine spatial planning. [ABSTRACT FROM AUTHOR]

In shallow environments, common unsteady flows, such as tides, waves or wind-driven currents modulate the diffusive boundary layer thickness that controls the exchange of electron acceptors for mineralization and oxidation processes in surficial sediment. This study demonstrated the ability of an oscillating grid mesocosm to (1) produce homogenous turbulence at the sediment-water interface of multiple sediment cores (between-core variability < within core variability; 16% on average); (2) simulate diffusive boundary layer thickness dynamics on different timescales by easy control of turbulence intensity and (3) study transient oxygen dynamics of organic matter mineralization under varying turbulent conditions. The relationship between turbulence intensity and oxygen diffusive boundary layer thickness, and oxygen penetration depth in the sediment was investigated with different organic matter enrichments and sediment permeability. Oxygen diffusive boundary layer thickness decreased linearly as URMS increased. Oxygen penetration depth increased with turbulence intensity, and converging to an upper limit with a larger value for low (3.28 mm ± 5.8%) than for high (1.77 mm ± 11.8%) organic matter content in muddy sediment. In sandy sediment, advective flows and resuspension led to a continuous increase of oxygen penetration depth with turbulence intensity, up to 13.2 mm ± 19% for turbulent velocities of 9.6 cm s−1. This mesocosm device will enable the experimental study of microbial dynamics under transient oxygen dynamics, to improve early diagenesis modeling under unsteady flows. [ABSTRACT FROM AUTHOR]

The average bed shear stress and bed friction factor of samples with any roughness was derived from the head loss between upstream and downstream of a test section in an erosion tunnel. The method was validated in both hydraulically smooth (plexiglass; Reynolds number less than 25,000) and rough regimes (calibrated particles with known roughness). As a first step toward using this method on natural sediment, this method was tested with experimental mesocosms assembled from field collected materials (sieved sediments; diatoms). Bed shear stress measurement precision was high enough in the experiments to detect a positive significant relationship between bed friction factor and core roughness. The observed bed friction factor increase could be related to diatom growth but not to diatoms biomass. [ABSTRACT FROM AUTHOR]

In this paper, we compare experiments on short gravity wave phase shifting by surface solitary waves to a Wentzel–Kramers–Brillouin–Jeffreys (WKBJ) refraction theory. Both weak interactions (head-on interaction) and strong interactions (overtaking interaction) are examined. We derive a dispersion relation and wave action conservation relation which are similar to the ones obtained for short waves refraction on slowly varying media. The model requires an exact solitary wave solution. To this end, a steady wave solution is numerically computed using the algorithm devised by Byatt-Smith [Proc. R. Soc. London, Ser. A 315, 405 (1970)]. However, two other solitary wave solutions are incorporated in the model, namely the classical Korteweg and De Vries (KdV) [Phil. Mag. 39, 422 (1895)] solution (weakly nonlinear/small amplitude solitary wave) and the Rayleigh [Phil. Mag. 1, 257 (1876)] solution (strongly nonlinear/large amplitude solitary wave). Measurements of the short wave phase shift show better agreement with the theoretical predictions based on the Byatt-Smith numerical solution and the Rayleigh solution rather than the Korteweg and De Vries one for large amplitude solitary waves. Theoretical phase shifts predictions based on Rayleigh and Byatt-Smith numerical solutions agree with the experiments for A/h[sub 0]≼0.5. A new heuristic formula for the phase shift allowing for large amplitude solitary waves is proposed as a limiting case when the short wave wave number increases. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The migratory shorebirds of the East Atlantic flyway land in huge numbers during a migratory stopover or wintering on the French Atlantic coast. The Brouage bare mudflat (Marennes-Oléron Bay, NE Atlantic) is one of the major stopover sites in France. The particular structure and function of a food web affects the efficiency of carbon transfer. The structure and functioning of the Brouage food web is crucial for the conservation of species landing within this area because it provides sufficient food, which allows shorebirds to reach the north of Europe where they nest. The aim of this study was to describe and understand which food web characteristics support nutritional needs of birds. Two food-web models were constructed, based on in situ measurements that were made in February 2008 (the presence of birds) and July 2008 (absence of birds). To complete the models, allometric relationships and additional data from the literature were used. The missing flow values of the food web models were estimated by Monte Carlo Markov Chain – Linear Inverse Modelling. The flow solutions obtained were used to calculate the ecological network analysis indices, which estimate the emergent properties of the functioning of a food-web. The total activities of the Brouage ecosystem in February and July are significantly different. The specialisation of the trophic links within the ecosystem does not appear to differ between the two models. In spite of a large export of carbon from the primary producer and detritus in winter, the higher recycling leads to a similar retention of carbon for the two seasons. It can be concluded that in February, the higher activity of the ecosystem coupled with a higher cycling and a mean internal organization, ensure the sufficient feeding of the migratory shorebirds. [ABSTRACT FROM AUTHOR]