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Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar- Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation. Stylophora sequence files for DryadAligned sequence files used for phylogeny analysis. ReadMe files also included.

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)

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

Aim The introduction of aquatic non-indigenous species (ANS) has become a major driver for global changes in species biogeography. We examined spatial patterns and temporal trends of ANS detections since 1965 to inform conservation policy and management. Location Global Methods We assembled an extensive dataset of first records of detection of ANS (1965-2015) across 49 aquatic ecosystems, including the i) year of first collection, ii) population status and iii) potential pathway(s) of introduction. Data were analysed at global and regional levels to assess patterns of detection rate, richness, and transport pathways. Results An annual mean of 43 (± 16 S.D.) primary detections of ANS occurred – one new detection every 8.4 days for 50 years. The global rate of detections was relatively stable during 1965-1995, but increased rapidly after this time, peaking at roughly 66 primary detections per year during 2005-2010, then declining marginally. Detection rates were variable within and across regions through time. Arthropods, molluscs and fishes were the most frequently reported ANS. Most ANS were likely introduced as stowaways in ships’ ballast water or biofouling, although direct evidence is typically absent. Main conclusions This synthesis highlights the magnitude of recent ANS detections, yet almost certainly represents an underestimate as many ANS go unreported due to limited search effort and diminishing taxonomic expertise. Temporal rates of detection are also confounded by reporting lags, likely contributing to the lower detection rate observed in recent years. There is a critical need to implement standardized, repeated methods across regions and taxa to improve the quality of global-scale comparisons and sustain core measures over longer timescales. It will be fundamental to fill in knowledge gaps given that invasion data representing broad regions of the world's oceans are not yet readily available and to maintain knowledge pipelines for adaptive management. At least one co-author with extensive regional knowledge of ANS carefully reviewed and edited each regional dataset for accuracy, checking scientific peer-reviewed publications, reports, books and personal collections to confirm: i) year of first collection; ii) current population status and; iii) potential pathway(s) of introduction (as known up to July 15, 2020). Level of Certainty was not critically reviewed.Records were compiled only for ANS collected from the natural environment while those reported exclusively on or within pathways were excluded (e.g., taxa sampled during surveys of ships’ ballast water and biofouling, tsunami debris and other marine litter). Only species considered fully aquatic were included including marine stenohaline, marine euryhaline, diadromous and freshwater-euryhaline species, but excluding, for example, shoreline plants and aquatic birds. Freshwater stenohaline species were included for the Laurentian Great Lakes and Baltic Sea but excluded from all other estuarine and marine ecosystems as being ‘inland’ introductions. We also excluded records for cryptogenic species (whose status as indigenous or non-indigenous is unresolved) and taxa poorly studied or otherwise presenting challenges for taxonomic identification and assessment of historical biogeographic origin (e.g., fungi, protists, parasitic and free-living flatworms, viruses and microbes). Note that Level of Certainty was not assigned in a uniform manner and may be unreliable, except for the 'Direct Evidence' category. We assembled an extensive dataset of primary detection events of ANS (i.e. the first recorded collection of each species in each region) across global (primarily coastal marine, but also estuarine and freshwater) aquatic ecosystems for the period 1965-2015 using online ANS databases as primary data sources, including AquaNIS (http://www.corpi.ku.lt/databases/index.php/aquanis/), GLANSIS (https://www.glerl.noaa.gov/glansis/), Marine Biosecurity Porthole (https://www.marinebiosecurity.org.nz/) and NEMESIS (http://invasions.si.edu/nemesis/). In addition, we conducted a literature search using the Web of Science to locate published datasets not available online, using the search terms “nonindigenous” or “non-indigenous” or “nonnative” or “non-native” or “alien” AND “aquatic” or “marine” AND “database” or “dataset” or “list” or “inventory”. Datasets were included only if dedicated, expert research on ANS had been conducted such that an up-to-date comprehensive and reliable inventory exists; datasets comprised of only a single taxonomic group, or not listing dates of first collection, or covering a shorter time period than this analysis were not included. 

This is the source code of the chemistry-transport model TM5-MP model used for the simulations presented in the revised manuscript entitled: "Description and evaluation of a detailed gas-phase chemistry scheme in the TM5-MP global chemistry transport model" authored by S. Myriokefalitakis et al.

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.