ABSTRACT. Aim Understanding relationships at the root of the animal tree is key to clarify animal evolution and the origin of modern marine ecosystems. Traditionally the sponges were seen as the sister group to all the other animals and the last common ancestor of all animals was assumed to be a sponge-like organism. However, standard analyses of amino acid data failed to provide a consistent support for this hypothesis, frequently finding support for Ctenophora (comb jellies), as the sister group of all the other animals instead (the Ctenophora-sister hypothesis). I will summarise current evidence and recent advances bearing on the topic and discuss how they impact our understanding of early animal evolution.

Methods A diversity of published amino acid data sets were analysed using a multiple models and data transformations, in a Bayesian context, to evaluate changes in support, fit and adequacy. Morphological datasets including both fossils and extant taxa were analysed using Bayesian and other methods and presence/absence of individual orthogroups and protein families were analysed using Bayesian methods.

Results A clear pattern of consilience exists and different data types (Genome content, Morphology and Amino Acid data analysed using well-fitting models) can be shown to discriminate against the Ctenophora-sister hypothesis. Amino acid data analyses are more variable and strongly model-dependent; implying that model selection and model adequacy should be the guiding principle when amino acid data are used.

Main Conclusion While there is still significant uncertainty on the relationships at the root of the animal tree, the Porifera-sister hypothesis is supported by multiple lines of evidence. While several amino acid models support Ctenophora-sister, support for this hypothesis is invariably maximised under the worst fitting models.

ABSTRACT. Sea turtles comprise seven extant species, and six are classified as endangered. These species have diverged for at least 20 million years, and despite their long divergence time, four species are known to hybridize on the Brazilian coast. In the largest nesting population in Brazil, 30-40% of nesting females morphologically identified as hawksbills (Eretmochelys imbricata) are genetically identified F1 hybrids between loggerheads (Caretta caretta) and hawksbills. First generation hybrids between loggerheads and olive ridleys (Lepidochelys olivacea) are also found, although not as frequently. Hybridization is possibly driven by the population decline that reduces the chance to find a mate of the right species. Hybrids can backcross with both parental species and produce viable offspring. Previous research has shown that loggerhead x hawksbill hybrids and pure species have similar reproductive output, hybrids are noticeably bigger than pure species, and the hybrid offspring have the same fitness as pure offspring from both species. To study and understand species hybridization under the extreme conditions of a secondary contact between highly divergent genomes, we are using whole genome sequences from five sea turtle species including population data for loggerheads, hawksbills, and their F1 hybrids. We will present preliminary results on population dynamics reconstructed from genomic data, which can be useful to understand the impact of population size changes on the hybridization process. Phylogenies from five species show that chromosomes have unique evolutionary rates and different putative signs of hybridization. We will also present a general description of the genetic diversity of all species and putative genomic regions associated with ancient hybridization events. Our goal is to understand the consequences of hybridization for the conservation of the Brazilian sea turtle population.

ABSTRACT. Aim As a consequence of the 2007 European Union Maritime Policy, the European Marine Observation and Data Network (EMODnet) was established to improve access to high quality marine data. From 2009 to 2012, a set of preparatory actions led to the development of an online portal which allowed for the access and download of these data European marine biological data. Methods EMODnet Biology is currently a partnership between 22 organisations, but it has connections with other international initiatives such as OBIS and GBIF, ensuring that the data is not duplicated but can be widely accessed. We will show how the partnership is organised and the various ways data providers can submit their data and the different procedures we undertake to make data FAIR. EMODnet Biology data includes and encourages the use of the World Register of Marine Species (WoRMS) for species scientific names, British Oceanographic Data Centre NVS2 for measurements or facts that accompany the data and Marine Regions for the sample locations, thus improving standardisation and interoperability with other data. Results Over the last 20 years, the European marine biological landscape has changed significantly. MarBEF included 94 marine institutes in its network and gave rise to EurOBIS and ERMS (which became WoRMS). With the setup of EMODnet Biology (meta)data interoperability and standardisation has been the main aim alongside the free and open access to the data. EMODnet Biology currently provides access to almost 25 million records from over 1000 datasets of various taxonomic groups. It also provides access to an ever-growing portfolio of data products and various tools. Main conclusion EMODnet Biology data have been used in several assessments (UN World Ocean Assessments and IPBES regional and global assessments, both via OBIS) and have also contributed to an OSPAR assessment on the introduction of non-indigenous species.

ABSTRACT. Aim DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The COI is a standard universal barcode marker for animals, however a comprehensive, updated and accurate reference dataset of animal COI sequences has not been available so far. Here, we are presenting preliminary work on constructing such a reference. So far we have constructed a reference dataset of all Metazoa excluding Hexapoda.

Methods We retrieved 1 004 333 sequences from NCBI, and extracted the COI sequence. We have quality checked the sequences by excluding those shorter than 300 bp, those with ambiguous nucleotides, human, bacterial and non-metazoan contaminations, and those sequences identified only above genus level. We clustered the remaining sequences at a 100% similarity and manually checked and resolved taxonomic discrepancies appearing above the family level, while we used the taxonomy of the last common ancestor for the discrepancies bellow this level.

Results At the moment our reference dataset includes 445 731 COI sequences clustered at 100% similarity belonging to 114 614 taxa. Of these, 348 914 are singleton clusters, while 83 403, 11 740 and 1258 clusters share a species, genus or family taxonomy, respectively. We have tested the curated database on already published DNA metabarcoding projects targeting marine, freshwater and terrestrial ecosystems.

Main conclusion A curated and updated reference database is a first step for the standardization of animal DNA metabarcoding studies enabling comparison of different DNA metabarcoding projects. In the future, we plan to expand the curated reference dataset to include Hexapoda sequences. Furthermore, we will cluster all the sequences in the dataset at 99% similarity to reduce redundancy and computational effort.

ABSTRACT. Aim The Northern-Central Adriatic Sea is one of the most productive areas of the Mediterranean Sea including a broad diversity of habitats. Within this basin, the Pomo Pit is one of the most important areas of aggregation and is an important spawning/nursery area in the Northern and Central Adriatic for the stock of European hake (Merluccius merluccius), a species of relevant commercial value heavily exploited by fishing activities. In this study we applied a metabarcoding approach to study the feeding habits of European hakes sampled within the Pomo Pit and to compare this feeding behaviour to the diet of hakes caught outside the Pomo area. Methods European hake specimens were collected in 2016, between 46 to 260 m depth along the coast of the Adriatic Sea from the Gulf of Trieste to Pomo/Jabuka pit. Ten individuals each of the five size classes in the two different habitat (shallow water outside the Pomo Pit and deep water within the Pomo Pit) for a total of 100 individuals were selected for the metabarcoding analyses. Results Our metabarcoding analyses proved the presence of specific niche partitioning and food preferences between hakes living inside and outside the Pomo Pit confirming the ontogenetic shift from a diet based mainly on crustaceans for juveniles to a more piscivorous feeding behaviour for adult fish. These results for the first time highlighted the crucial role played by the Pomo Pit in Merluccius merluccius feeding behaviour and ontogenetic development strengthening the hypothesis of the presence of an Essential Fish Habitat and promoting a careful management of this ecosystem through focused conservation measures. Main conclusions These outcomes emphasize the need of updated scientific methods as metabarcoding or DNA-based methods to study marine food webs and integrate the current information about the feeding behaviour of marine organisms.

ABSTRACT. An integrative approach is crucial in discrimination of species, especially for taxa that are difficult to identify based on morphological characters. In this study, we combine genetics and morphology to assess the diversity of Pterasteridae, a sea star family diversified in deep-sea and polar environments. Because of their derived anatomy and the frequent loss of characters during preservation, Pterasteridae are a suitable case for an integrative study. The molecular identification of 191 specimens (mostly from the Southern Ocean) suggests 26–33 species in three genera (Diplopteraster, Hymenaster and Pteraster), which match the morphological identification in 54–62% of cases. The mismatches are either different molecular units that are morphologically indistinguishable (e.g. Pteraster stellifer units 2 and 4) or, conversely, nominal species that are genetically identical (e.g. Hymenaster coccinatus/densus/praecoquis). Several species are shared between the Northern and Southern Hemispheres (e.g. Pteraster jordani/affinis). In conclusion, the taxonomic status of some groups is confirmed, but for others we find the need to re-evaluate the taxonomy at both genus and species levels. This work significantly increases the DNA barcode library of the Southern Ocean species and merges taxonomic information into an identification key that could become a baseline for future studies (pterasteridae-so.identificationkey.org).

ABSTRACT. Zooplankton molecular analysis by DNA-barcoding allows for species identification with a proper molecular signature, and complements classic phenotypic taxonomy. This study underlines the effectiveness of DNA-barcoding to assess the biodiversity of the zooplankton community of the Gulf of Naples. We analysed more than one hundred organisms, mostly Copepods, the main components of the Mediterranean zooplankton. After taxonomy identification, carried out by morphological analysis, DNA extraction of single organisms was performed and metazoan barcode was obtained by amplification of the mitochondrial gene, cytochrome c oxidase I (COI). We obtained the first COI consensus sequences from the Gulf of Naples for eight copepod species, three euphausiids, and one chaetognath. We identified individuals at different stages of development such as eggs and larvae of E. krhonii. The COI sequences will be deposited in GenBank and be used as reference sequences for other zooplankton works through DNA barcoding.

ABSTRACT. Aim Pseudo-nitzschia is a cosmopolitan marine diatom genus. It encompasses more than 50 species, with several cases of cryptic and pseudo-cryptic species. Many of the taxa are toxic, so it is important to correctly identify them. Here we used meta-barcoding data collected at the LTER Station MareChiara in the Gulf of Naples to explore the genetic structure of the genus. Methods We used the V4-region of the 18S rDNA as reference to retrieve Pseudo-nitzschia reads from 48 environmental DNA samples collected along three years. The reference sequences were used as queries in blast analysis, phylogenetic building and SWARM clustering to assign metabarcode haplotypes to species. Haplotype frequency distributions, haplotypic and nucleotidic diversity and temporal patterns of occurrence were analysed within each species. Median-joining networks and sequence divergence were used to assess interspecific relationships within and among cryptic species complexes. Results The V4 barcode showed good resolution power in most cases. Haplotype assignment to known species was usually straightforward. Signs of incomplete lineage sorting and/or introgression between species were nevertheless observed within the “delicatissima” and the “galaxiae” species-complex. Moreover, a highly abundant, intermediate haplotype between two of the “delicatissima” species was found. The frequency spectrum of the haplotypes showed a highly abundant haplotype and many low frequency ones within single taxa. Values of mean distance between taxa were different among species complexes. Almost all taxa showed a regular seasonal pattern among years. Conclusions - Metabarcoding possesses a high resolution, allowing a deeper look on the relationships within and between species complexes. - Cryptic species occur in offset or different periods, suggesting ecophysiological differentiation, which could be used in combination with blast analysis for a correct assignment of the reads. - Signs of incomplete lineage sorting and/or introgression between species suggest lingering hybridization events. Thematic Areas Populations and species, Biodiversity

ABSTRACT. Aim Accurate delimitation of species and their relationships is a fundamental question in evolutionary biology and systematics and provides essential implications for conservation and management. Scleractinian corals are difficult to identify because of their morphological plasticity. Furthermore, little is known about their distribution and biogeography. For example, many coral species are thought to be widely distributed in the Indo-Pacific but limited genomic information are available to verify this hypothesis. Methods Here, we applied the genome-wide technique Restriction-site Associated DNA sequencing (ezRAD) to investigate phylogenetic relationships and biogeography within two common reef coral genera of the Indo-Pacific, namely Leptastrea and Cyphastrea. We collected 180 colonies from several localities across the Indo-Pacific, from the Red Sea to French Polynesia, and subjected them to genomic analyses. A combination of de novo clustering and reference mapping was used to obtain coral and holobiont SNPs and to retrieve nearly complete coral mitochondrial genomes. Results Phylogenetic analyses reveal high diversity within the two genera, with some lineages in agreement with morphology-based taxonomy and several lineages representing undescribed species. Only a minor fraction of the genomic lineages occurs across the Indo-Pacific, displaying strong clustering and isolation by distance between the Indian and Pacific populations. Most lineages are found either in the Indian or Pacific basin, with the seas around the Arabian Peninsula as a region of high endemism. Main conclusion This study suggests that an important fraction of hard coral biodiversity is yet to be discovered and that actual coral distributions are narrowed than traditionally thought.

ABSTRACT. Aim Monitoring zooplankton biodiversity is crucial when studying marine ecosystem processes as well as a support for ecosystem-based management efforts. However, as the morphological assessments of zooplankton biodiversity are labour intensive, and therefore the characterization of its spatio-temporal variability would often require an unsustainable effort, there is a rising need for fast and more cost-effective methods. After having successfully evaluated the suitability of DNA metabarcoding for zooplankton biodiversity assessments by comparing it to the morphological identification, this study aims to apply this molecular method on a monitoring project with high spatial and temporal frequency in the Venice Lagoon (Italy). Methods In 16 stations within the Venice Lagoon zooplankton samples were monthly collected with a 200 µm standard net from April 2018 to March 2019 together with environmental parameters. From the resulting 192 samples, the DNA was extracted, a fragment of the COI gene was amplified, and the sequencing was performed with the Ion Torrent PGM System. The bioinformatic pipeline included quality filtering, sequence corrections as well as different similarity thresholds to recover possibly all putative metazoan sequences. Results The analysis resulted in over ten million raw sequences and about 7 million sequences assigned more than 500 taxa belonging to 15 different phyla. The ecological analysis of the zooplankton community showed a differentiation both between different locations and months, following the seasonality of environmental changes throughout the year. Main conclusion The results highlight that DNA metabarcoding, with the advantage of increased sample processing speed and the broad taxonomic coverage, is a promising tool for surveying marine biodiversity, especially in large-scale monitoring programs and biodiversity assessments of ecosystems with high spatial and temporal variability.

ABSTRACT. Aim The pressure of anthropogenic activities on marine ecosystem has increased in recent decades. Biodiversity assessment is often restricted to groups studied in greater detail, usually popular and charismatic species. The majority of biodiversity consists, on the other hand, in little known and inconspicuous species. The Hydrozoa taxon includes organisms that are particularly sensitive to climate change. The aim of this work is to review the knowledge about the diversity of the Mediterranean non-Siphonophora Hydrozoan (NSH) fauna and examine whether species might have become extinct.

Methods The list of NSH species of the Mediterranean Sea is based on taxonomic revisions and recent papers. To determinate historical series and distribution, 785 faunistic studies published between 1850 and 2020 have been consulted and a database with 8,385 records was organized so as to provide the information.

Results The list of NSH species of the Mediterranean Sea has about 400 species, including 69 non-indigenous species. Global warming is favoring the tropical contingent, while the boreal one is in a stressful condition. The change in biodiversity is often decoupled from the richness of species: the rate of introduction of alien species often exceeds that of the extinction of native species in the same habitat, leading to erroneous interpretations of local biodiversity. In fact, while some populations of hydroids are in decline or disappear (more than 10% of the Mediterranean NSH have not been reported in the last 40 years), other ones invade new areas and habitats.

Main conclusion The species lists are dynamic and require continuous updating that considers both the subtraction of the species with non-contemporary reports and addition of the introduced species. In conclusion, the role of the naturalist in today's society should be re-evaluated by recovering traditional scientific methods such as long-term observations that provide valuable information on changes in ecosystems.

ABSTRACT. Aim The opening of the Suez Canal, in 1869, connected the Red Sea and the Mediterranean, involuntarily creating a grand experiment in biological invasion science. At first, few species migrated from the Red Sea into the Mediterranean (termed Lessepsian bioinvaders), yet the rate of invasion kept increasing with time. While the expectation of few individual invaders should result in signatures of genetic bottlenecks, this is seldom observed. The goal of our studies is to identify the genetic patterns of Lessepsian bioinvaders, and determine the role of natural selection in the invasion success.

Methods A combination of classical Sanger sequencing and genomic RAD sequencing was used on a panel of fish species. Samples were obtained for both early invaders and more recent ones, as well as from sites that are very close to the Suez Canal as well as far from it.

Results For the most part, we have found that successful invaders do not show a signature of bottlenecks, instead, their genetic diversity is similar to what is seen in natural Red Sea populations. Blue spotted cornetfish, in contrast, shows reduced genetic diversity and evidence for genes under selection, in particular for genes that are related to osmoregulation, a key factor in being able to breach the barrier of the Canal.

Main Conclusion While most Lessepsian migrants do not show evidence of bottlenecks and founder effects, a combination of population size and local adaptation seem to play essential roles in successful invasions.

ABSTRACT. Antarctic notothenioid fishes, the predominant fish group of the sub-zero degree Southern Ocean, represent a dramatic example of vertebrate adaptive radiation with >100 species diversifying in the last 15MY. We have generated 24 new whole genome assemblies representing five notothenioid families to help understand the radiation and genome evolution in extreme cold. For the basal non-Antarctic notothenioid Cottoperca gobio (Bovichtidae) (fCotGob3, size 609Mb, scaffoldN50 14.74Mb), and the highly derived Antarctic icefish Pseudochanichthys georgianus (Channichthyidae) (fPseGeo1, size 1.03G, scaffoldN50 43Mb) we have completed reference assemblies assigned to chromosomes. Gene completeness for these and three other long-read assemblies (Trematomus bernacchii, Harpagifer antarcticus, Gymnodraco acuticeps) averages 95%, and gene annotation identified 21,662 (fCotGob3) - 23,222 (fPseGeo1) coding genes. Comparative analysis demonstrated a 65% expansion in genome size from the basal to derived species, with size ranging from 609Mb – 1.02Gb. The majority of this size expansion can be attributed to transposable element (TE) insertions (repeat content 28-46%), with multiple TE classes contributing to the expansion (DNA elements: CACTA, PiggyBac, hAT; retrotransposons: Copia, Gypsy, I, Pao). With these highly contiguous assemblies we have reconstructed the history of the expansion of the antifreeze gene family among notothenioids and the degeneration of globin genes in the white-blooded icefishes. This work provides a deep genomic characterisation of this iconic group and a platform to investigate the mechanisms of fish cold adaptation and genome evolution.

ABSTRACT. Among the four classes of Porifera, three of them construct siliceous skeletons but through divergent enzymatic pathways. In demosponges, the silicification occurs by polycondensation of silica using silicases around an axial filament formed by a protein called silicatein. Most demosponges can produce more than one spicule type, in some occasions with convoluted ornamentations. Some demosponges have more than one silicatein gene (with highly divergent evolutionary pathways). In calcareous sponges, the many alpha-carbonic anhydrases present in the group are linked to the production of several spicule types. Whether the diversity of siliceous spicules is linked to larger molecular complexity in demosponges, is completely unknown. Here we used complete transcriptomes of 72 sponges (19 newly assembled) to create a sound phylogenomic framework to explore the evolution of biosilicification within demosponges. The enzymes required to produce siliceous spicules including silicases, silicateins, and silicon transporters, were screened within our transcriptomic and other datasets available and their expression quantified using bowtie2/RSEM. Character reconstructions were performed in our datasets to understand the evolution of the molecular machinery. Finally, we used BAMM tools to detect and quantify heterogeneity in evolutionary rates across sponges with diverging silicification levels, in terms of number of spicule types and spicule total content.

ABSTRACT. Aim Anguilliform fishes are an ecologically diverse clade distributed in all marine habitats, from deep sea trenches to oceanic pelagic ecosystems, from tropical coral reefs to coastal sandy bottoms. Recent molecular phylogenies have dramatically changed our understanding of the relationships among major eel lineages, and provided us with a better understanding of the timeline of eel evolution. Little is known, however, about how the repeated habitat shifts that have occurred within this group may have influenced evolutionary rates and contributed to the present diversity of eels.

Methods I generated a new relaxed clock timetree for enguilliforms using a new molecular dataset (7 loci for 272 species), and used several phylogenetic comparative methods in combination with ecological and morphological data (habitat type, depth, body size) to test whether habitat shifts affected rates of diversification within anguilliforms.

Results The new time-calibrated phylogeny suggests that eels likely originated in marine coastal habitats during the late Cretaceous, with several lineages independently invading deep sea environments during the Eocene or Oligocene. While multiple invasions of coral reef habitats did not produce significant shifts in the rate of lineage or body size diversification, habitat shifts towards the deep-sea led to dramatic increases in rates of lineage diversification compared to their shallow water relatives. The highest rates of both lineage and body size diversification, however, occur within the true eels (Anguillidae), the only group to have successfully colonized freshwater habitats.

Main conclusion Habitat shifts towards deep-sea or freshwater environments appear to significantly increase the rate of lineage diversification in eels, while invasion of tropical coral reefs does not. True eels are a very young and diverse group that is likely experiencing an adaptive radiation

ABSTRACT. Abstract Photoreceptors are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in their complexity and diversification are a matter of great interest in the field. By using transgenic and reverse genetics approaches on the Ciona robusta model system, we aimed to identity the Oc downstream-acting factors that mediate specific tasks in the differentiation of photoreceptor cells. In this study, we contribute in understanding the cascade of events that direct the formation of the increasingly complex eye structures of chordates. Methods We used transgenic perturbation of the Ciona Oc protein to show its requirement for ciliary photoreceptor cell differentiation. Then, we performed a RNAseq analysis between the trans-activation and trans-repression Oc phenotypes and an in silico comparison of the C. robusta and mouse mutant RNA-Seq datasets. Results The Oc transcription factor emerges as a key element for Ciona photoreceptors differentiation Transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis and neurotransmission. In particular, its downstream genetic pathway evidenced core components of the molecular machinery for neurotransmission of retinal cell types in chordates. Finally, comparison of RNA-Seq datasets in C. robusta and mouse identified a set of Oc downstream genes conserved between tunicates and vertebrates. Main conclusions -The transcription factor Oc is necessary for ciliary photoreceptor cells differentiation in ascidians. -Comparative transcriptomics of Oc perturbation in ascidian and mouse highlights the existence of effector genes involved in neurotransmission of retinal cell types. -Full comprehension of Oc role in photoreceptor differentiation could represent an important turning point to understand the process that contributed to cone and rod diversification in vertebrates.

ABSTRACT. Abstract Aim The availability of high-quality reference genomes has led to great advancements in comparative and functional genomics and has uncovered several aspects of the evolution of physiological adaptations. Despite many reference genomes are available both for vertebrate and invertebrate species, some taxa remain deeply underrepresented. Among these taxa there is the decapod infra-order Brachyura, including all the extant true crabs, for which only two genomes have been assembled so far. The deficiency of genomic data on Brachyura can certainly not be attributed to a lack of interest in this taxa, since its ecological and economic value is unquestionable. On the contrary, this depends on some critical technical difficulties in the assembly production due to crustacean genome organization. Here we present the preliminary steps we performed to assemble the genome of the tropical crab Chiromantes haematocheir. This species has a terrestrial life style, and it was specifically chosen to investigate the biological and physiological processes involved in the sea-land transition of brachyuran crabs.

Methods Fundamental prerequisite to perform a correct assembly of sequencing data is to get information on the genome size and chromosome organization of the target species. For this, we measured the genome size of C. haematocheir using flow cytometry, and performed cytogenetic analyses to determine its chromosome number. Then we performed initial sequencing of C. haematocheir genome using PacBio facilities.

Results and Conclusions Despite some technical difficulties, we managed to obtain a draft genome for C. haematocheir. Our research goal is to use the genome assembly to investigate the evolutionary processes involved in the sea-land transition of this species. Thus we will investigate possible genes, or groups of genes, selected under the environmental pressures due to terrestrialization, shedding light on the genomic adaptation that led marine crabs to adapt to a terrestrial ecosystem.

Thematic Areas Macroevolution, Adaptation

ABSTRACT. Aim Concerted evolution describes the mode of evolution of certain repetitive sequences that evolve in concert within a genome. Classically, concerted evolution has been inferred indirectly from phylogenetic studies as “noise” in electropherograms and analysed through cloning and sequencing of limited subsamples of PCR-amplified products. We designed an experiment to reveal the occurrence of concerted evolution by means of metabarcoding data and discuss its potential impact on ecological and evolutionary studies.

Methods We performed high-throughput sequencing (HTS) of the V4-18S rDNA region of monoclonal strains of six Chaetoceros species (marine planktonic diatoms) and analysed them together with a time-series environmental metabarcode dataset and Chaetoceros Sanger reference barcodes previously generated. Data were analysed by means of abundance plots, analysis of similarity and phylogenetic haplotype networks.

Results The 18S rDNA region was under concerted evolution in the Chaetoceros species here analysed and that homogenisation was highly efficient at maintaining nearly identical 18S rDNA copies. Some intragenomic variation represented by the minor haplotypes was observed at the threshold of similarity of 99% with respect to a dominant haplotype. Minor haplotypes were not just technical artefacts because they were found in multiple independent environmental samples as well as in single strains obtained from the same locality. The distribution of haplotypes in both time-series and single strain data fitted Zipf’s law.

Main conclusion Concerted evolution occurs in Chaetoceros. The dominant haplotype perfectly matches the Sanger reference sequence, validating the use of the metabarcoding technique for ecological studies. We highlight that the high number of sequences occurring at low abundances (minor haplotypes) could inflate diversity assessments, but they are intragenomic variation.

ABSTRACT. Aims Most organisms reproduce sexually and individuals maintain a fixed sex throughout their life (gonochorism). In some species, however, individuals can produce male and female gametes at the same time (simultaneous hermaphroditism) or reproduce initially as one sex and later in life switch to the other (sequential hermaphroditism, with female being the first sex in protogyny and male the first sex in protandry). Theoretical models, initially developed for plants, suggest that gonochorism and simultaneous hermaphroditism are evolutionary stable conditions, but if this is the case in animals is unclear, especially in sexually plastic taxa such as teleosts. Methods and results Using Bayesian phylogenetic comparative methods and 4740 teleost species, we show that gonochorism is likely to be the ancestral condition from which protogyny, protandry and simultaneous hermaphroditism evolve at a moderate evolutionary rate. While all forms of hermaphroditism revert as quickly or faster to gonochorism, protogyny and simultaneous hermaphroditism are evolutionarily more stable than protandry, as the latter is quickly lost to other sexual systems. Moreover, we report for the first time a direct pathway from gonochorism to simultaneous hermaphroditism, without the need of intermediary evolutionary transitions (e.g., androdioecy or sequential hermaphroditism). Finally, we expanded the theoretical framework of the evolution of hermaphroditism investigating how life history traits change among sexual systems: as predicted, protogynous fish live longer, allowing individuals to take advantage of the reproductive value of dominant males, while protandrous species are bigger, maximizing the fecundity of females. Conclusions While including life history traits is important, it is not sufficient to explain the distribution of hermaphroditism among teleosts (Williams’ paradox). We propose the use of a comprehensive framework, which includes mating systems, sex determining mechanisms and developmental gonadal plasticity, to gather a better understanding of the unique evolution and distribution of hermaphroditism in the largest radiation of vertebrates.

ABSTRACT. In the ocean, microbes influence biogeochemistry, climate and overall planet functioning. They outnumber any other living organism by far, with recent estimates of microbial biomass on Earth between 9 and 31×10^29 cells, and control all major biogeochemical cycling of elements. Over time, they have influenced the overall redox state of the surface of our planet and permanently bioengineered the environment. Besides controlling biogeochemical cycles, microbes also affect human and animal health. Microorganisms that comprise both beneficial strains and potential pathogens colonize the exposed areas of our bodies and our gastrointestinal tract. Understanding how microbes have adapted to colonize every available environmental niche, including the outside and inside of other organisms, may hold the clue to a more efficient fight against microbial diseases. The reconstruction of the evolutionary history of key biochemical functions is critical to understand this process. Given that animals and mammals are comparatively new-comers compared to ocean ecosystems, especially geothermal influenced ones, it is plausible to hypothesize that that beneficial and pathogenic microorganisms that today colonize the inside and outside of higher organisms, including ourselves, have evolved recently. We will discuss how the comparative genomic of marine microbes can help understand the evolutionary journey of pathogens, and present a case study from the ubiquitous marine class Epsilonproteobacteria. Understanding which portion of the pathogens’ metabolic machinery has been conserved and adapted to new conditions and what portion of their genomes is an acquired trait is fundamental in delineating the evolutionary journey from environmental strains to human pathogens.