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The relationships between parasites and their hosts are intimate, dynamic and complex; the evolution of one is inevitably linked to the other. Despite multiple origins of parasitism in the Cnidaria, only parasites belonging to the Myxozoa are characterized by a complex life cycle, alternating between fish and invertebrate hosts, as well as by exceptionally high species diversity. This inspired us to examine the history of reciprocal interactions and adaptive radiations in myxozoans and their hosts by determining the degree of congruence between their phylogenies and by timing the emergence of myxozoan lineages in relation to their hosts. Recent genomic analyses suggested a common origin of Polypodium hydriforme, a cnidarian parasite of acipenseriform fishes, and the Myxozoa, and proposed fish as original hosts for both sister lineages. We clearly demonstrate that the Myxozoa emerged long before fish populated Earth and that phylogenetic congruence with their invertebrate hosts is evident down to the most basal branches of the tree, indicating bryozoans and annelids as original hosts and challenging previous hypothesis. We provide evidence that, following invertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogenetic lineages. We identify the acquisition of vertebrate hosts that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. The results of this study transform our understanding of the origins and evolution of parasitism in the most basal metazoan parasites known. Trees for cophylogeny reconciliationHost and parasite trees (24) used for cophylogeny reconciliation and based on the alignments of 18S rDNA and 16S rRNA gene sequences deposited in the same dryad folder.trees for cophylogeny reconciliation.nexMolClock_alignmentAlignment of 6 concatenated protein-coding genes, i.e. aldolase (200 aa), triosephosphate isomerase (217 aa), phosphofructokinase (175 aa), methionine adenosyltransferase (348 aa), elongation factor 1 alpha (418 aa) and ATP synthase beta chain (430 aa), for molecular clock analysis of myxozoan and other metazoan taxa.18S rDNA aligment_myxozoans_in_vertebrate_hostsCut alignment of 18S rDNA sequences of 682 taxa of myxozoans from vertebrate hosts in fasta format18S_myxozoans_in_vertebrate_hosts.fasta18S rDNA_myxozoans_from_invertebrate_hostsCut alignment of 18S rDNA sequences of 124 taxa of myxozoans from invertebrate hosts in fasta format18S_myxozoans_from_invertebrates_53M.fasta18S rDNA alignment_invertebrate hostsCut alignment of 18S rDNA sequences of 25 taxa of invertebrate hosts of myxozoans in fasta format18S_invertebrate hosts.fasta16S rRNA_vertebrate_hostsCut alignment of 16S rRNA gene sequences of 246 taxa of vertebrate hosts of myxozoans in fasta format16S_vertebrate_hosts.fastafull__mitogenome_vertebrate_hostsCut alignment of full mitogenome sequences of 105 taxa of invertebrate host families of myxozoans in fasta format

All experimental trials were performed in 12-well polystyrene plates. Three food choice treatment groups were defined: (1) Artemia sp. nauplii only (n = 10 nauplii in each replicate); (2) microplastic particles only (n = 10 microplastic particles in each replicate); (3) evenly split food choice of Artemia sp. nauplii and microplastic (n = 5 each). A total of 12 replicates of each treatment group were set up, and a randomized design was created to assign treatments to wells. A total of five specimens of A. gibbosa were placed into each well. Approximately 24 hours after the initiation of the experiment, feeding activity of A. gibbosa on nauplii and microplastic was assessed visually under a Leica binocular microscope, by counting the number of remaining nauplii and feeding attempts on microplastic particles and nauplii. For the purpose of this experiment, feeding on microplastic is defined as any physical interaction with the LBFs’ pseudopodia. Two trials were conducted, with a total of 24 replicates (12 per trial) in each treatment. None of the specimens were used in both trials. To ensure counting accuracy, an additional four counting controls per treatment were established, in which no LBF were placed in the well. Increasing marine microplastic pollution has detrimentally impacted organismal physiology and ecosystem functioning. While previous studies document negative effects of microplastics on coral reef animals, the potential responses of organisms such as Large Benthic Foraminifera (LBF) are largely unknown. Here, we document the impact of microplastics on heterotrophic feeding behavior of LBF. Specimens of Amphistegina gibbosa were incubated in three experimental treatments: (1) Artemia sp. nauplii only; (2) pristine microplastic particles only; (3) choice of nauplii and pristine microplastic. Feeding rates were observed 24 h after initiation of treatments. A separate experiment was conducted to compare the effect of conditioned vs. pristine microplastic. Our results indicate that A. gibbosa is able to selectively feed on Artemia, avoiding interactions with pristine microplastic. However, the presence of conditioned microplastic causes similar feeding interaction rates as with Artemia. This suggests microplastics with longer residence times may have a larger impact on facultative detritivores. There are no missing values in the dataset. Pristine Microplastic, Exp. 1 trial refers to the time points at which the Experiment was conducted (trial 1 vs. trial 2) Food choice refers to the food source that was presented to the foraminifera (Artemia sp. Nauplii vs. Pristine Microplastic) Treatment represents the food choices that were offered to the foraminifera (single choice vs. Mixed choice) Feeding rate represents the number of particles ingested and/or pseudopodal interactions (Particles fed upon day-1) Soaked Microplastic, Exp. 2 trial refers to the time points at which the Experiment was conducted (trial 1 vs. trial 2) Food choice refers to the food source that was presented to the foraminifera (Artemia sp. Nauplii vs. soaked Microplastic) Treatment represents the food choices that were offered to the foraminifera (single choice vs. Mixed choice) Feeding rate represents the number of particles ingested and/or pseudopodal interactions (Particles fed upon day-1)

The positive effect of fully protected Marine Protected Areas (MPAs) on marine biodiversity, specifically on fishes, has been widely documented. In contrast, the potential of MPAs to mitigate the impact of adverse climatic conditions has seldom been investigated. Here, we assessed the effectiveness of MPAs, quantified as increasing fish biomass, across wide geographic and environmental gradients across the Mediterranean Sea. We performed underwater visual surveys within and outside MPAs to characterize fish assemblages in 52 rocky reef sites across an extent of over 3,300 km. We used the steep spatial temperature gradient across the Mediterranean as a ‘space-for-time’ substitution to infer climate-driven temporal changes. We found that, as expected, Mediterranean MPAs increased fish biomass. At the same time, higher seawater temperatures are associated with decreased fish biomass, changes in species composition, and shifts towards more thermophilic species. Importantly, we found that the rate of decrease in fish biomass with temperature was similar between protected and fished sites. Taken together, these results suggest that the capacity of MPAs to harbor higher fish biomass, compared to surrounding areas, is maintained across a broad temperature range. At the same time, MPAs will not be able to offset larger-scale biotic alterations associated with climate change. Policy implications: Our results suggest that sustained warming will likely reduce fish biomass in the Mediterranean Sea and shift community structure, requiring more conservative targets for fishery regulations. At the same time, protection from fishing will remain an important management tool even with future high-water temperatures, and MPAs are expected to continue to provide local-scale benefits to conservation and fisheries.

In the framework of the EU-FP7 BACCHUS (impact of Biogenic versus Anthropogenic emissions on Clouds and Climate: towards a Holistic UnderStanding) project, an intensive field campaign was performed in Cyprus (March 2015). Remotely piloted aircraft system (RPAS), ground-based instruments, and remote-sensing observations were operating in parallel to provide an integrated characterization of aerosol–cloud interactions. Remotely piloted aircraft (RPA) were equipped with a five-hole probe, pyranometers, pressure, temperature and humidity sensors, and measured vertical wind at cloud base and cloud optical properties of a stratocumulus layer. Ground-based measurements of dry aerosol size distributions and cloud condensation nuclei spectra, and RPA observations of updraft and meteorological state parameters are used here to initialize an aerosol–cloud parcel model (ACPM) and compare the in situ observations of cloud optical properties measured by the RPA to those simulated in the ACPM. Two different cases are studied with the ACPM, including an adiabatic case and an entrainment case, in which the in-cloud temperature profile from RPA is taken into account. Adiabatic ACPM simulation yields cloud droplet number concentrations at cloud base (approximately 400 cm−3) that are similar to those derived from a Hoppel minimum analysis. Cloud optical properties have been inferred using the transmitted fraction of shortwave radiation profile measured by downwelling and upwelling pyranometers mounted on a RPA, and the observed transmitted fraction of solar radiation is then compared to simulations from the ACPM. ACPM simulations and RPA observations shows better agreement when associated with entrainment compared to that of an adiabatic case. The mean difference between observed and adiabatic profiles of transmitted fraction of solar radiation is 0.12, while this difference is only 0.03 between observed and entrainment profiles. A sensitivity calculation is then conducted to quantify the relative impacts of 2-fold changes in aerosol concentration, and updraft to highlight the importance of accounting for the impact of entrainment in deriving cloud optical properties, as well as the ability of RPAs to leverage ground-based observations for studying aerosol–cloud interactions.

Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on Single Nucleotide Polymorphisms (SNPs) allele frequencies. We used Moran’s Eigenvector Maps (db-MEMs) and Asymmetric Eigenvector Maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (> 1,000km) while larval dispersal was the major predictor at smaller spatial scale (< 1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history or multi-generational stepping stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected areas network that would efficiently enhance protection and persistence capacity of marine species. SNPs dataAllele frequencies of the 47 sites at 1123 neural SNPs locifq_data_neutre_1123.txtEnvironmental dataMean, maximal and minimal salinity and temperature at the 47 sites.Data_enviro_sans47.txt

Marine organisms normally swim at elevated speeds relative to cruising speeds only during strenuous activity, such as predation or escape. We measured swimming speeds of 29 ram ventilating sharks from 10 species and of three Atlantic bluefin tunas immediately after exhaustive exercise (fighting a capture by hook-and-line), and unexpectedly found all individuals exhibited a uniform mechanical response, with swimming speed initially 2 times higher than the cruising speeds reached approximately 6 hours later. We hypothesised that elevated swimming behaviour is a means to increase energetic demand and drive the removal of lactate accumulated during capture via oxidation. To explore this hypothesis, we estimated the mechanical work that must have been spent by an animal to elevate its swim speed, and then showed that the amount of lactate that could have been oxidized to fuel it comprises a significant portion of the amount of lactate normally observed in fishes after exhaustive exercise. An estimate for the full energetic cost of the catch-and-release event ensued.

Solitary ascidians found on complex settlement plates in the Red Sea and the MediterraneanWe constructed unique settlement plates, each representing six different niches, to assess ascidian niche breadth, and deployed them in similar habitats in the Red Sea and the Mediterranean. Settlement plate design: To estimate and compare habitat niche breadth between species, we designed settlement plates each representing different niches, based on six substrate squares measures 10 x 10 cm as our basic units. The base of the plate was built from stainless steel, and the substrate squares were glued to the base. We used three substrate types within two current /light regimes to allocate six different "niches” to each settlement plate, with total measurement of 30 x 20 cm. The three substrate types were constructed from three materials: cement with sea shells, non-glazed ceramic and recycled plastic. Since substrate is a major factor for fouling species, we selected three materials that differ substantially from each other: plastic is smooth, the non-glazed ceramic is rough but homogenous, and the cement with sea shells is complex and heterogeneous. The two current and light regimes were achieved by placing the plates facing the pillars, and leaving the upper part of the plate open from three directions (from above and from either side) while the lower part remained open from the bottom only and was thus dark and with restricted water flow. We were interested in the relative patterns across species to these niche differences, and hence do not attempt to quantify the exact differences in light and flow between the upper and lower sections. Nevertheless, light measurements confirm the lower side was ~10 time darker than the upper side. We used all possible permutations (36 in total) of substrate type ordering within each current and light regime treatment in constructing the settlement plates. Study sites: The same experimental designs were used in the eastern Mediterranean Sea and northern Red Sea to facilitate direct comparisons. In the Mediterranean, the settlement plates were deployed on three pillars of the Israel Electric Company pier (32°28′ N 34°53 E), and in the Red Sea, on three pillars of the Israeli oil port (29°31′ N 34°56′ E), with minimal distance of 10 meters between pillars. At both sites, the plates were deployed at about 15 meters depth, with the seabed at 20 meters, in order to avoid any bottom effects such as sedimentation. The depth of 15 meters was chosen in order to minimize disturbance to the experiment by the strong winter storms, while still providing sufficient underwater work time when using scuba. As public entrance to both sites is prohibited, the experiment was subjected to minimal human disturbance. Pillars at both sites are located in the open sea (as opposed to closed harbors) and are >30 years old, therefore the fauna found on them represent a climax community. Study design: The experiment lasted one year, from February 2014 to February 2015. For analyses, we combined two types of plates, seasonal and full-year. We deployed 15 full-year plates at each site and these remained undisturbed for the entire year of the experiment. In addition, 10 seasonal plates were replaced every three months, totaling 40 seasonal settlement plates at each site. At the end of each experiment, the settlement plates were removed and taken to the lab for taxonomic identification (using Nikon SMZ18 stereomicroscope and dissection tools). Solitary ascidians were counted and identified to species level where possible (649 out of 658 individuals). In addition, we took monthly underwater photos of all settlement plates. Plates were photographed from the exact same distance and angle using a custom-made tripod. These photos were used in order to identify individuals that were present on the plates during the experiment but did not survive to the point of plate removal, in order to increase sample size for the niche breadth calculations. Unfortunately, only four individuals were added using these photos. We categorized the species found in the Red Sea as Lessepsian (species that are known to establish populations in the Mediterranean) or non-Lessepsian species (species that have not yet been recorded in the Mediterranean, i.e., non-invaders). In the Mediterranean we categorized the species as non-indigenous or indigenous. We included Styela plicata with the indigenous species of the Mediterranean for analysis although it possibly invaded from the Atlantic Ocean (Pineda et al., 2011; Maltagliati et al., 2015) as it is clearly not of tropical origin, unlike the rest of the non-indigenous species, and has been found in the Mediterranean for at least a century (de Barros et al., 2009). Data file structure: plate – id for each settlement plate (reminder: the six different habitats described above are within each plate). site – Mediterranean or Red Sea species type – ‘Lessepsian’ and ‘non Lessepsian’ for the species found on plates in the Red Sea site. ‘indigenous’ and ‘non-indigenous’ for species found on plates in the Mediterranean site. season – ‘spring’, ‘summer’, ‘autumn’, ‘winter’ for the seasonality plates. ‘long term’ for the long term (full year) plates. And ‘added by pictures’ for three records of P. nigra we added in order to increase its sample size for our niche breadth calculations. niche – ‘su’ for shells-up, ‘cu’ for ceramics-up, ‘pu’ for plastic-up, ‘sd’ for shells down etc… substrate – shells, ceramics or plastic light – up – upper part of the plate or down – the lower part of the plate. number of individuals – the actual data – number of individuals foundSolitaryAscdians_DryAdVersion.csv A major focus of invasion biology is understanding the traits associated with introduction success. Most studies assess these traits in the invaded region, while only few compare non-indigenous species to the pool of potential invaders in their native region. We focused on the niche-breadth hypothesis, commonly evoked but seldom tested, which states that generalist species are more likely to become introduced since they are capable of thriving under a wide set of conditions. Based on the massive introduction of tropical species into the Mediterranean via the Suez Canal (Lessepsian migration), we defined ascidians in the Red Sea as the pool of potential invaders. We constructed unique settlement plates, each representing six different niches, to assess ascidian niche breadth, and deployed them in similar habitats in the native and invaded regions. For each species found on plates, we evaluated its abundance, relative abundance across successional stages and niche breadth, and then compared (1)species in the Red Sea known to have been introduced into the Mediterranean (Lessepsian species) and those not known from the Mediterranean (non-Lessepsian); and (2)non-indigenous and indigenous species in the Mediterranean. Lessepsian ascidians identified on plates in the Red Sea demonstrated wider niche breadth than non-Lessepsian ascidians, supporting the niche-breadth hypothesis within the native region. No differences were found between Lessepsian and non-Lessepsian species in species abundance and successional stages. In the Mediterranean, non-indigenous species numerically dominated the settlement plates. This precluded robust comparisons of niche breadth between non-indigenous and indigenous species in the invaded region. In conclusion, using Red Sea ascidians as the pool of potential invaders, we found clear evidence supporting the niche-breadth hypothesis in the native region. We suggest that such patterns may often be obscured when conducting trait-based studies in the invaded regions alone. Our findings indicate that quantifying the niche breadth of species in their native regions will improve estimates of invasiveness potential.

Depth sections of two short sediment cores were analyzed in the Radioactivity measurements Laboratory at the University of Bremen by gamma spectrometry to determine the activities of natural and artificial gamma emitting radionuclides. The core chronology was based on a combination of two radiotracers, 210Pb and 137Cs, due to their suitable half-lives 22.2 and 30 years. A robust time-frame will enable to track the rapid changes in the sedimentation pattern of the Nile River along a S-N gradient observed in the cores GC and BC as a part of the project Rapid changes along the Israeli Mediterranean coast following the damming of the Nile and their influence on the Israeli inner shelf. In order to understand causes of recent sharp changes in sedimentation pattern on the inner Israeli shelf, dating of cores collected in the region is important.

Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months. Mediterranean gap analysis in environmental spaceThis .zip folder contains the data and an R script to reproduce the gap analysis documented in Mannocci et al. 2018.Data_Scientific_Reports.zip