Fourth International Marine Connectivity (Imarco) Conference in Heraklion, Crete, Greece

Fourth International Marine Connectivity (iMarCo) Conference in Heraklion, Crete, Greece -

8 to 9th October 2018

The challenge of asexuality in population genetics: how wrong can we be?

Sophie Arnaud-Haond

Ifremer, UMR MARBEC (Marine Biodiversity, Exploitation and Conservation), France

In the marine realm, species structuring habitat (corals, seagrasses...) and many invertebrates often exhibit a dual reproductive system, partial asexuality. The theoretical framework in population genetics is however developed only for pure asexuals or pure sexual species and interpreting genetic data on partial asexuals is a challenge. Through mathematical development and simulations, we provide new expectations as to the genotypic and genetic composition of natural populations under an increasing range of clonality. These result call for a serious revision of the interpretation of molecular data in the literature on population genetics of partial asexual in general, and seagrasses in particular.

Does genomics of parasitic sea lamprey populations provide insights to the connectivity of marine hosts?

Miguel Baltazar-Soares

Bournemouth University

The sea lamprey (Petromyzon marinus) is an ancient anadromous species and is among the last living representatives of jawless vertebrates. The life cycle is complex and includes development stages tightly linked to specific habitat needs. While adults are obligatory parasites that feed on the blood and flesh of marine or other anadromous fish species, the larvae (ammocoetes) live as free organisms in the silt-depositing zone of river banks. The migration to tidal/saltwater areas occurs progressively - from sediment bank to sediment bank - along a 7-8-year period. Full development into sexually mature parasitic individuals occurs relatively rapid, upon which attachment to potential hosts is an essential need. The intrinsic relationship between obligatory parasitism and marine-dwelling hosts allow us to test for a relationship between structure among sea-lamprey locations and a) marine fish’s biodiversity or b) population structure of predominant possible hosts as alternative hypotheses to that of complete panmixia. Here I will present first insights of a double digest RAD-seq study that screened 8 freshwater streams across the species distribution range in Europe. Approximately 200 000 loci were obtained and used to estimate genome-wide differentiation as well as preliminary correlations with biological diversity of potential hosts.

The hybrid zone theory, a universal framework for marine population genomics

Nicolas Bierne

Université de Montpellier - CNRS

Most species are subdivided by hybrid zones. Overwhelming evidences support this simple claim and the analysis of genome sequences mainly strengthened and broadens it as being a universal result of population genetics. Surprisingly, however, the consequences for the interpretation of population genetics data remains mainly ignored. In this paper I intend to highlight the importance and generality of the hybrid zone framework for population genomics. First, I will argue that hybrid zones of the pre-genomic era, studied with a few markers, represented only one small fraction at the extreme of the gradient of genomic differentiation between interacting genetic backgrounds. Genome analysis has mainly identified new cryptic hybrid zones between more loosely differentiated lineages (younger) or more loosely isolated genetic backgrounds (maintained by less efficient genetic barriers). Refraining to call them hybrid zones might unfortunately distracts us from interpreting them with the help of the hybrid zone theory. Second, I will recall two important predictions of the hybrid zone framework that well explains how genetic diversity is structured in space and within genomes. (i) Hybrid zones are expected to be trapped by barriers to dispersal or by ecotones. This explains genetic-environment associations, even when past vicariance and/or partial reproductive isolation best explain the genetic differentiation. (ii) Hybrid zones are expected to act as semi-permeable barrier to gene flow. This explains the usually much higher observed variance of differentiation than the neutral expectation, and the correlation with recombination rates. Finally, I will argue that introgression tails emanating from hybrid zones should be accounted for to interpret population genomic data within apparently well- mixed biogeographic regions. There are good reasons why introgression gradients should better correlate with ecological variables or with least cost path connectivity maps than with geographic distance. My hope is that the universality of the hybrid zone framework will be recognized and better considered when interpreting genome scans and landscape genomics analyses.

Genomic approaches and targeted genetic markers can identify fine-scale structuring in marine fish populations.

Alessia Cariani and Fausto Tinti

GenoDREAM Lab, University of Bologna, Italy

The eco-compatible management of marine bio-resources requires multidisciplinary and integrated scientific data, to which the genetic contribute is essential. The development of advanced tools (genomics and bioinformatic) for the analysis of complex data targets the identification and description of the evolutionary and environmental drivers of biodiversity in marine taxa and their application to the sustainable management of fishery resources. Weak signals of population structure are generally reported for most marine fish using neutral genetic markers as a consequence of high dispersal, connectivity and large population size. Recently, genome-wide studies and analysis of markers linked to functional gene regions have suggested that divergence might occur even when neutral markers provide genetic homogeneity, revealing patterns of fine-scale populations structuring in marine species. Significant correlation of allele frequencies at specific loci with environmental variables supports the hypothesis of local adaptation, often found to be in a delicate balance with gene flow. Seascape statistical analyses are useful tools to uncover the genetic basis of fine-scale genetic structuring across marine populations. Such findings highlight the importance of integrating information from multiple and independent disciplines, in order to develop explicit spatial models for defining management units and stock boundaries.

Abundance and distribution of the deep-sea blue and red Aristeus antennatus larvae in the North-western Mediterranean

Marta Carretón, Guiomar Rotllant, Joan B. Company

Institute of Marine Sciences (ICM-CSIC, Barcelona)

The deep-sea blue and red shrimp Aristeus antennatus (Risso, 1816) is one of the most valuable fishing resources in the Northwestern Mediterranean, currently under a local co- management plan in the port of Palamós (Spain). Gathering information about its larval distribution is a key step for the progress of its fishing stock assessment and the establishment of well-dimensioned management measures. We here present the spatial distribution of A. antennatus larvae at the peak of the species’ spawning period (July-August) along the Spanish Mediterranean coast. Zooplankton sampling was carried out in surface waters (0.5 to 1 m depth) in the summer 2016 with a 1 m-mouth neustonic sledge (mesh size: 300 µm) over bottoms of 82 to 1840 m. Samples were rinsed in distilled water, preserved in 96% ethanol and sorted in the laboratory under a stereomicroscope. Identification of the larvae was done according to the available descriptions. Over 1000 A. antennatus larvae of all known stages were found in our samples, the first protozoea representing almost 90% of the total. Results show aggregations of larvae in the Ibiza Channel and in the northern submarine canyons, concurrent with hydrographic conditions. No larvae were found below the Ibiza Channel. These data will be useful to assess the species’ larval dispersal and validate a biohydrodynamic model of the study area.

Keywords: Aristeus antennatus, larvae, ecology, fisheries

New insight on the population structure of Calanus finmarchicus in the North Atlantic using next-generation sequencing technologies

Marvin Choquet, Irina Smolina, Galice Hoarau

Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway

Calanus finmarchicus is a key species for the North Atlantic Ocean food web. Dramatic demographic reduction in Calanus has been reported in Northern Oceans, as well as large- scale northward shifts, and this might likely be associated to global warming inducing perturbations in sea temperatures and in global currents functioning. Such changes among planktonic communities are expected to have a strong impact on the higher levels of the food web. Despite a well-documented life cycle, very little is known about the population genetics of this crustacean. Such knowledge is critical to understand the dynamics of C. finmarchicus populations and their ability to cope with environmental changes. In order to better understand C. finmarchicus population connectivity, we used recently developed molecular tools to investigate genome wide genetic variation for individuals from 9 locations spanning the entire range of the species. Based on a transcriptome reference available for C. finmarchicus, we selected a set of ca. 2,000 genes for which we designed short adapter sequences. Used as baits and fixed on magnetic beads, these probes were used to sequence these particular genes in a large number of individuals. Preliminary results suggest limited genetic structure of C. finmarchicus populations in the North Atlantic.

Larval dispersion of deep-sea shrimp Aristeus antennatus in the submarine canyon of Palamós (NW Mediterranean)

M. Clavel-Henry1, J. Solé1; M.-A. Ahumada2, T. Kristiansen3, N. Bahamon1, F. Briton, G. Rotllant1, J.B. Company1

1 ICM-CSIC (Barcelona, Spain), [email protected] 2 UMAR (Puerto Escondido, Mexico), [email protected]

Individual-based model can explore the connectivity of subpopulation of the deep-sea red shrimp Aristeus antennatus in the Northwestern Mediterranean Sea through larval drifts. The species is under a unique local management plan which limits the trawling activities of fishermen. We used a Lagrangian framework with a three-dimensional hydrodynamic model to evaluate the retention capacity of the shrimp stock under fishing restriction, and therefore, the effectiveness of the local plan to expand the stock abundance. Modelled as passive particles, the larvae were retained for 44 % of them in the fishery area under restriction. This zone also received 27 % and 99 % larvae from another submarine canyon and the inter-canyons area from higher latitude, respectively. When particles had the properties to ascend to the surface, through egg buoyancy, the larvae connected with a submarine canyon at lower latitude with 39.4 % of particles; and the Balearic Islands grounds with 40 %. The two drift paths were characterized by a drift in the superficial layer (0-5 m) and a drift in the subepilagic layer (5-200 m), respectively. Connectivity intensity with Balearic Islands has slightly increased when spawning occurred at the end of summer. The retention or dispersion of larvae from the restrictive area of fishery depended mostly of the larval ecology. Above all, the vertical behavior of the species larvae could influence the recruitment and determine the effectiveness of the management plan.

Keywords: Larvae, Lagrangian, A. antennatus, Management

Sailing on the beach: genetic characterization of Velella velella and its predator Janthina pallida

Federica Costantini 1,2,3, Morello Bruno1, Bo Marzia3-4, Federico Betti4, Giorgio Bavestrello3- 4, Abbiati Marco2,3,5,6

1Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA), University of Bologna, Via Sant’Alberto 163, 48123, Ravenna, Italy 2Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), University of Bologna, Ravenna, Italy 3Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy 4 Dipartimento di Scienze della Terra dell'Ambiente e della Vita, University of Genova, Genova, Italy 5Dipartimento di Beni Culturali (DBC), University of Bologna, Ravenna, Italy 6Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine, ISMAR, Bologna, Italy

Gelatinous macrozooplankton is an ecologically and socio-economically important component of marine ecosystems. Due to their life history, they may form dense aggregations (blooms) that may be boosted by anthropic and climatic alterations of the ecosystems. In the Mediterranean Sea, the by-he-wind sailor Velella velella, a free-floating hydrozoan colony, is a well-known component of the gelatinous pleuston, forming offshore spring aggregations that may occasionally strand on the coasts under rough meteorological conditions. This phenomenon is particularly frequent in the Ligurian Sea where it is monitored since 2015. In spring 2017 blooms of V. velella were accompanied by exceptional demographic explosions, and subsequent strandings, of its purple snail predator,Janthina pallida. This poorly known holoplanktonic gastropod spends its later development stages attached to V. velella colonies and feeds on them until reproduction, when it becomes independent thanks to its floating raft. No specific study has been dedicated so far to investigate the co-evolutionary patterns of these two species. To monitor these phenomena through time and space, it is essential to implement studies to understand their origin, their evolutionary history and the genetic patterns of connectivity among populations. Samples of V. velella and J. pallida have been collected at 5 locations along the Ligurian Sea. Mitochondrial markers were used 1) to evaluate the spatial and temporal genetic variability and structure of the two species, and 2) to assess if the two species share common genetic connectivity patterns. These results will give new insight into the biological and ecological features of these species, on their interactions, dynamics and ecological role.

Combining multiple tools to investigate connectivity between marine and brackish coastal habitats during early life and its biological consequences for the seabream Sparus aurata in the NW Mediterranean.

Audrey M. Darnaude1, Maylis Labonne1, Christophe Lett2, Pierre Alexandre Gagnaire3

1 MARBEC (CNRS, Univ. Montpellier, Ifremer, IRD), Montpellier, France 2Sorbonne Universités, UPMC Université Paris 06, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes (UMMISCO), F-93143 Bondy, France 3 CNRS, Institut des Sciences de l’Evolution (UMR5554,) Montpellier, France

In coastal fishes with complex life histories, who typically inhabit different habitats during their lifespan and experience multiple environments at certain life stages (e.g. juvenile), understanding the link between genotypic diversity, environmental history and individual fitness is essential. Here, we combined three complementary techniques commonly applied to study connectivity in coastal species (population genomics, otolithometry and particle drift modelling) to explore the relative importance of genetic and environmental controls on the size-at-age and physiological condition of juvenile S. aurata in the Gulf of Lions (NW Mediterranean). In this area, the species uses both marine and brackish lagoon nursery habitats during its first year of life. Phenotypic differences among juveniles foraging in these different habitats rapidly appear a few months after recruitment, but the extent to which differential survival among genotypes (in link with the characteristics of the environment encountered) shapes these phenotypic differences remains unclear. To explore this, 50 post- larvae and 200 juveniles (100 from each lagoon type) were collected in 2013, respectively in the spring and in the autumn, i.e. at the periods when the seabreams enter and leave their lagoon nursery habitats each year. Genome-wide polymorphism was investigated in all these individuals, together with past larval and juvenile growth rates and the concomitant chemistry of the water masses inhabited (from otolith analyses). These results were complemented by Lagrangian model simulations of the possible trajectories for larval drift at sea, from different spawning locations using fish actual birth dates. Crossing all this information with the final body size, weight and condition of the fish allowed exploring the consequences of juvenile life in varied types of nurseries (marine or brackish) on the fitness of the individuals of this valuable species.

Larval dispersal and connectivity of reef-forming Sabellaria alveolata along the French Atlantic coast

Carmen David, Martin P. Marzloff, Philippe Cugier, Stanislas Dubois

The gregarious polychaete Sabellaria alveolata forms reef-like structures on tidal flats, which provide coastal protection and habitat for a wide range of species. Consistent larval settlement is locally critical to maintain good ecological status of the reefs, in particular to reinforce habitat resilience and recovery following perturbations. Thus understanding larval dispersal and connectivity between reefs represents a major challenge for long-term conservation of these biogenic constructions. The European distribution of this species expands from Morocco to Scotland, with the most widespread reefs on the French Atlantic coast. We use here the hydrodynamic model MARS3D to simulate larval dispersal under realistic hydro-climatic conditions and to generate connectivity matrices (larval exchange rates) between main reef areas. We quantify the sensitivity of connectivity patterns to inter-annual changes in environmental conditions (e.g. river outflow, wind regime) and to key features in larval ecology (e.g. spawning period, planktonic larval duration). To assess the realism of simulations, we confront estimated connectivity patterns against present and past occurrences of the species on the Atlantic French coast, based on available information (published or expert knowledge). Ultimately this study aims at targeting important geographic areas that are crucial for the seeding of larvae of this foundation species over its latitudinal distribution.

Restoring European flat oyster Ostrea edulis beds in Belgian wayers: a feasibility study

Ilse De Mesel*, Léo Barbut, Danae Kapasakali, Francis Kerckhof, Geneviève Lacroix, Laurence Vigin and Steven Degraer

Marine Ecology and Management, Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences 3de en 23ste Linieregimentsplein, 8400 Oostende, Belgium

European flat oyster Ostrea edulis beds used to be highly abundant in the Southern North Sea, ranging from Norway to Germany, France and the UK, including Belgian waters. Due to overexploitation, most oyster beds were destroyed and O. edulis populations were brought to near extinction, by the end of the 19th century. Nowadays, only a small number of relict populations are known in France, the Netherlands and the UK. Because of the major autogenic and allogenic bioengineering capacities and hence the important ecological value of oyster beds, interest in their restoration is ever growing. This project aimed at investigating the feasibility of oyster bed restoration in the Belgian part of the North Sea and developing possible restoration scenarios. After collating a wide knowledge base on oyster ecology and restoration we analysed the environmental constraints for O. edulis as to be able to identify areas suitable for oyster bed restoration in Belgian waters. We also assessed the connectivity between relict and restored beds to evaluate the long-term viability of possible restoration measures. All information was integrated to develop restoration scenarios that were scored for feasibility and sustainability. Full-coverage data on the distribution of substrate, currents and suspended particulate matter allowed delineating areas suitable for oyster settlement and growth. Connectivity modelling identified areas that possibly still receive substantial larval influxes from the oyster relict populations in the English Channel. Two dimensions were identified along which restoration scenarios could be adjusted, introduction of oysters and modulating habitat condition. We deducted 20 scenarios, which were eventually weighted based on five criteria: time to successful restoration, respecting existing biodiversity, active promotion of biodiversity, restoration cost and maintenance cost. We conclude that oyster bed restoration is still feasible in Belgian waters. We identified the gravels in the Belgian fisheries management zones (inside a Special Area of Conservation) and in the planned offshore wind farm zones to offer opportunities for oyster bed restoration.

Unraveling connectivity patterns in a highly migratory species: trans-Atlantic gene-flow and population structure of Atlantic Bluefin tuna.

Natalia Díaz-Arce, Pierre-Alexandre Gagnaire, David E. Richardson, Sophie Arnaud-Haond, Jean-Marc Fromentin, Haritz Arrizabalaga, Naiara Rodriguez-Ezpeleta

Atlantic bluefin tuna (Thunnus thynnus) is currently managed as two stocks separated by the 45oW meridian, based on the assumption of two demographically independent populations spawning respectively in the Mediterranean Sea and the Gulf of Mexico. However, evidence of regular and frequent trans-Atlantic migrations, and of a new spawning ground in the Slope Sea call for a reappraisal of the population dynamics of this species. In this study, we use thousands of single nucleotide polymorphisms (SNPs) discovered through Restriction site Associated DNA sequencing (RAD-seq) data from 527 larvae, young of the year and spawning adult samples covering the three recorded spawning grounds of Atlantic Bluefin tuna to determine its population structure and genetic connectivity. Our analyses support genetic differentiation between Mediterranean Sea and Gulf of Mexico populations, and identify Slope Sea as a genetically intermediate population. This, together with the observation of Mediterranean-like genotypes in some Gulf of Mexico spawning adults supports potential ongoing trans-Atlantic gene-flow, as well as pronounced admixture in the Slope Sea. Our findings represent a significant advance in the understanding of Atlantic Bluefin tuna genetic connectivity patterns and have important implications for the definition of more efficient management approaches of its fishery.

First approach to the age and growth of Cynoglossus senegalensis (Kaup, 1858) from the Senegalese coasts (West Africa) using otolith and perspectives to study connectivity between populations in the region.

Khady DIOUF1, Yacine NDIOUR2

1,2 IFAN Ch. A. Diop, Laboratoire de biologie marine, Université Cheikh Anta Diop de Dakar, B.P. 206, Dakar, Senegal

Senegalese tonguesole, Cynoglossus senegalensis (Kaup, 1858) is a coastal demersal species in the marine and brackish waters of the eastern Atlantic. It is encountered from Mauritania to Angola in the bathymetric fringes 10 to 110 meters, in the tropics 22° N - 18° S, 18° W - 14° E. It is a littoral species, particularly abundant on sandy and sandy-sandy bottoms, between 5 and 10 meters. It is found in estuaries and has been captured in the freshwater lagoons of western West Africa. In Senegal, this species is exploited by artisanal and industrial fisheries. Stocks of the Senegalese tongue sole are in a critical phase because heavily exploited. This situation is largely highlighted by national statistics data. However, there have not been studies of Senegalese tongue sole’s corporal growth in the area. Consequently, the objective of this work was to determine its age and growth, as determined by using sagittal otoliths, and calculate the Von Bertalanffy growth function. From January to December 2015, about 1080 Senegalese tongue sole (272 mm to 562 mm TL) were collected from three stations along the Senegalese coast and whole sagittal otoliths were removed and prepared for reading. Preliminary data would be presented in this work, which represents a baseline for future studies on Senegalese tongue sole’s population dynamics to understand the invasive process in the region.

Studying the temporal dynamics of selection acting on introgressed alleles through experimental crossing.

Maud Duranton, François Bonhomme and Pierre-Alexandre Gagnaire.

Many marine species are subdivided into genetically differentiated lineages connected through gene flow. However, gene exchange between divergent taxa can have both positive or negative effects. Foreign alleles can generate heterosis by masking recessive deleterious mutations but, they can also be maladaptive or break gene coadaptation resulting in hybrid depression. Furthermore, the intensity of these effects may depend on the time elapsed since foreign alleles introgressed the new genetic background. Identifying the impact of gene flow over short and long-time scale is therefore essential to understand populations genetic connectivity and to design appropriate conservation actions. Here, we focus on the European sea bass (Dicentrarchus labrax), which is subdivided into two lineages represented by the Atlantic and Mediterranean populations that naturally hybridize. We used experimental crossing to evaluate the short-term effect of the introgression of Atlantic alleles in the Mediterranean genetic background. We compared the relative performance in terms of survival and condition between Mediterranean and first generation Mediterranean backcrosses, which represent the principal bridge for interlineage gene flow in nature. Despite evidence that selection tends to remove Atlantic alleles after several tens of generations, first-generation Mediterranean backcrosses did not appear less fit than Mediterranean ones. Our results nevertheless indicate that residual heterosis may hide the effect of hybrid depression during the first hybrid generations. This suggests that the temporal dynamics of selection acting on introgressed alleles may be more complex than previously thought.

How strong is fisheries-induced selection? A general framework for estimating fisheries- induced selection pressures.

Bruno Ernande1,2, Asbjørn Christensen3, Ulf Dieckmann2, Mikko Heino4,2, Anne Timenes Laugen5, Suichi Matsumura6, Raul Primicerio7, Adriaan Rijnsdorp8,9, Aslak Smalås7 and the WGEVO group.

1 IFREMER, Unité Halieutique Manche Mer du Nord, Boulogne-sur-Mer, France 2 IIASA, Evolution and Ecology Program, Laxenburg, Austria 3 Technical University of Denmark, National Institute of Aquatic Resources, Kgs. Lyngby, Denmark 4 University of Bergen, Department of Biological Sciences, Bergen, Norway 5 Swedish University of Agricultural Sciences, Department of Ecology, Uppsala, Sweden 6 Gifu University, Faculty of Applied Biological Science, Gifu, Japan 7 UiT The Arctic University of Norway, Faculty of Biosciences, Fisheries and Economics, Tromsø, Norway 8 Wageningen IMARES, B IJmuiden, The Netherlands 9 Wageningen University and Research Centre, Department of Animal Sciences, , Aquaculture and Fisheries Group, Wageningen, The Netherlands

Fishing-induced evolution (FIE) changes individual traits, thus stock properties and their utility to human society. Estimating FIE prevalence and predicting its consequences are therefore necessary for complying with the ecosystem approach to ﬁsheries. While FIE has been reported for a large number of stocks, several challenges persist. One such challenge is to develop assessment tools easily deployed and allowing comparison across stocks to be included in the traditional fisheries advisory workflow. The Working Group on Fisheries-Induced Evolution (WGEVO) of the International Council for the Exploration of the Sea has developed a standardized selection-gradient approach to assess the strength of fishing-induced selection from stock-assessment output. In a quantitative genetics framework, evolutionary changes in traits are expected to be proportional to selection pressure with a proportionality constant given by traits’ heritabilities. Standardized selection gradients measure the maximum possible relative change that fishing could cause in the means of a stock’s traits if they were fully heritable. Using a general age-structured life-history model with annual transitions, the WGEVO estimated fisheries-induced selection pressures (FISP) on growth, maturation, and reproductive investment for 59 fish stocks, mostly in the North Atlantic. The main findings of this large scale analysis are that: (i) Typically, fishing induces selection pressures towards earlier maturation at smaller size, reduced growth, and increased reproductive effort. (ii) Across stocks, FSIP align along two nearly independent axes: a growth axis describing negatively covarying pressures on somatic and gonadic growth, and a maturation axis describing pressures on maturation. (iii) FISP rise with fishing intensities for the main traits, i.e., maturation propensity, growth and reproductive investment. (iv) FISP show high sensitivity to a fishery’s size selectivity. They tend to be highest when the length at which fish become exposed to significant fishing is 1-2 times larger than their maturation length. Conversely, FISP tend to be more benign in fisheries with a peaked or dome- shaped size-selectivity pattern rather than a sigmoidal one. (v) Slow growing, long-lived species maturating late and large and having costly reproduction are more prone to fisheries-induced selection. 16

Comparative patterns of connectivity among the different lineages of the giant clam Tridacna maxima found over the Indo-Pacific

Cécile FAUVELOT (1,2), HORAUD Mathilde (1), GRULOIS Daphné (1), MAGALON Hélène (1), ANDREFOUET Serge (1), WABNITZ Colette (3,4), BORSA Philippe (1).

1 UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, Noumea, New Caledonia 2 UMR LOV (Sorbonne Universités, CNRS), Institut de la Mer de Villefranche, France 3 Secretariat of the Pacific Community, Noumea, New Caledonia 4 Changing Ocean Research Unit, Institute for the Oceans and Fisheries, University of British Columbia, Aquatic Ecosystems Research Laboratory, Vancouver, Canada

Like most marine benthic organisms, the giant clam Tridacna maxima has a bipartite life cycle which includes a pelagic larval phase lasting approximately 10 days. This species is widely distributed on coral reefs, from the East African coast to French Polynesia. Using the mtDNA COI gene, the phylogeographic analysis of T. maxima across its entire distribution range revealed the presence of seven divergent lineages restricted to six biogeographic regions (two were found co-occurring in the southwestern Indian Ocean). Using 13 microsatellite loci, we further analysed the genetic variability of 1442 individuals sampled over 48 sites distributed in the Red Sea, the southwestern Indian Ocean, and the western and central Pacific Ocean. Within each province, spatial scales of larval dispersal were investigated and compared.

How do behaviour traits impact deep-sea larval dispersal and connectivity?

Alan Fox*1, Stefan Gary2, Murray Roberts1, Lea-Anne Henry1, Arne Biastoch3, C. Gabriela Mayorga Adame4, Jeff Polton4

1 School of GeoSciences, University of Edinburgh, Edinburgh, UK. 2 SAMS, Scottish Marine Institute, Oban, UK. 3 GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany. 4 National Oceanography Centre, Liverpool, UK

Many ocean bottom dwelling species release their larvae into the water column so that the larvae can both add to the local population and spread far to find other places to colonize. A better understanding of larval pathways and downstream colonization is an important factor determining population connectivity, informing studies of natural and man-made networks (results from the INSITE programme in the North Sea are used as an example), feeding into the design of Marine Protected Area networks and ultimately impacting how the marine environment is used. During their transit, larvae exhibit a range of different behaviors for maximizing their immediate survival (finding food and avoiding predation) and their long- term survival (finding a suitable spot to settle). Key strategies are pelagic duration and control of the vertical position in the water column. For deep sea species, observational evidence of the characteristics of the larval behaviour strategies are severely lacking. In these circumstances, particle tracking modelling can perhaps be most useful for predicting the larval behaviour traits which have the strongest influence on larval dispersal, and thereby helping to guide future observational work. As part of the ATLAS project, working in the North Atlantic, we try to answer two questions to help identify whether larval behaviors are impacting their long-term spreading: Is there any evidence that any of these behaviors, either alone or combined, cause greater spreading? And, do any of these behaviors cause larvae to follow particular pathways so they settle in specific locations? To answer these questions we use particle tracking with ARIANE within the VIKING20 model of the North Atlantic.

From genetic connectivity to species delimitation: the case of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites

P. Gélina, B. Postairea, L. Bigot, Ca. Fauvelotb*, H. Magalona aUMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d’excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France bUMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Nouméa cedex, New Caledonia *Present address: Université Côte d’Azur, CNRS, FRE 3729 ECOMERS, Parc Valrose, Nice, France

Studying genetic connectivity implies to know on which species we work on. Focusing on the coral genus Pocillopora, we first used species delimitation methods to explore the species diversity of this widely distributed scleractinian in the tropical belt of the Indo-Pacific. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) using two mitochondrial markers and one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). We defined at least 18 SSHs among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. Focusing on PSH09 (Pocillopora eydouxi), we assessed the genetic structure from a large sampling (2507 colonies) using 13 microsatellites loci and assignment tests (Structure and DAPC). We confirmed the three SSHs previously identified (SSH09a, SSH09b and SSH09c). SSH09a is restricted to the Western Indian Ocean, and SSH09b and SSH09c are almost exclusively in the Tropical Southwestern Pacific, suggesting that gene flow is extremely rare between the Pacific and the Western Indian Ocean. Moreover, genetic structuring analysis revealed a fractal partitioning for each SSH separately, with high gene flow between islands in the distribution range of each sub-SSH. Focusing on PSH05 (Pocillopora damicornis type β) genetic structure, we found a high clonal propagation in almost all populations and some restricted gene flow leading to diverging lineages. Thus the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning.

Marinas — not farms — drive regional connectivity and establishment in natural rocky reefs of the introduced and cultivated Pacific kelp Undaria pinnatifida

Jaromir Gunzinski, Marion Ballenghien, Claire Daguin-Thiébaut, Laurent Lévêque & Frédérique Viard

Ports and farms are introduction hotspots for marine non-indigenous species (NIS). The extent to which these anthropogenic habitats are sustainable sources of propagules in natural habitats was examined in the edible seaweed Undaria pinnatifida, a worldwide invader, native to Asia. Following its introduction 40 years ago along the French coast of the English Channel, this kelp is now found in three contrasting habitats: farms, marinas, and natural rocky reefs. We developed, for the first time in a kelp, a ddRAD-sequencing technique to genotype 738 individuals sampled in 11 rocky reefs, 12 marinas, and 2 farms located along ca. 1000 km of coastline. Habitat-specific properties of the study populations were revealed, with farms displaying very low genetic diversity and no inbreeding, conversely to populations in marinas and rocky reefs. There was however no evidence for local adaptation to any of the three habitats. A strong, but chaotic regional genetic structure, was also revealed, consistent with human-mediated dispersal (e.g., leisure boating), at a regional scale. In addition, a tight relationship between populations in rocky reefs and those in nearby marinas, but not with nearby farms, was also observed, suggesting spill-over from marinas into the wild and the need for management policies that target these marinas. Altogether, this study showed that population genomics studies can shed light on the eco- evolutionary processes sustaining successful introduction and guide policies directed towards prevention of NIS expansion.

New insights on genetic structure of great scallops (Pecten maximus) populations within the English Channel.

The great scallop (Pecten maximus) is a commercially important bivalve in Europe and particularly in the English Channel (EC), whose fisheries are managed at global, regional and local scales through regulation of fishing effort. On the long term, knowledge about larval dispersal and connectivity between populations are essential to ensure a proper stock management. Most studies have reported very low genetic differentiation of populations within the EC. In this context, we sampled scallops in the main fishing grounds along the French and English coasts of the EC (20 spatio-temporal samples, n = 1060) and conducted a population genetics study based on 13 microsatellites loci, taking into account previously published bio-physical larval dispersal modelling studies to compare empirical and simulated genetic structures. Our results revealed a lack of clear stable spatial population genetic structure but subtle genetic differentiation between SWE populations and the rest of the EC was noticed. However, discrepancies between empirical and simulated genetic structures were observed, likely resulting from uncertainties in biological parameters implemented in bio-physical and genetic models. Consequently, the role of larval dispersal in shaping the observed genetic structure cannot be clearly demonstrated. Our study provides a step forward in the understanding of great scallop population biology in the EC, underlying the fact that even in a context of potentially high gene flow and recent divergence time at regional scale, low but significant spatial genetic structure can be identified.

Keywords: gene flow, low genetic structure, microsatellites, great scallop, English Channel, genetic modelling

Defining global essential Loggerhead turtle habitat

Cheryl S Harrison1,2, Nathan F Putman3, Qingfeng Li4, Jessica Yuchao Luo5 and Matthew C Long5

(1) University of Texas, Rio Grande Valley, TX, United States, (2) National Center for Atmospheric Research, Boulder, CO, United States, (3) LGL Ecological Research Associates, Inc., Bryan, TX, United States, (4) Laramie High, Laramie, WY, United States, (5) National Center for Atmospheric Research, Climate and Global Dynamics, Boulder, CO, United States

Loggerhead turtles are an actively managed, threatened species that have a juvenile phase of basin-scale dispersal from beach nesting sites. Survivability in the first year is low, and depends on avoiding predation, cold shock, and finding adequate forage. Here we use a state-of-the-art global high-resolution ocean simulation with biogeochemistry to simulate the dispersal, feeding success, and cold shock susceptibility of Loggerhead hatchlings. The CESM-BEC Earth system model, run at 0.1º, resolves mesoscale ocean circulation consisting of jets and eddies, as well as primary and secondary production, which we use as a proxy for turtle forage. Turtles are simulated using an off-line particle transport code, modified to track turtle feeding and approximate turtle swimming behavior. We find that the majority of successful global loggerhead turtle nesting sites (8/10) are associated with boundary currents such as Western Boundary Currents and the Leeuwin Current. These currents offer rapid transport for hatchlings away from the coasts to productive subpolar-subtropical boundaries, regions where temperatures are at the cold end of Loggerheads’ thermal tolerance. The remaining two sites (Oman and Canary Islands) are in especially productive equatorial locations where temperatures and food availability are consistently high. The biogeography of best-fed turtles (top 15%) shows that juveniles in boundary currents experience significant spatial bottlenecks, information which can be used to inform sampling and management.

Differing patterns of population connectivity in two critically endangered elasmobranchs

Catherine Jones1, Michelle Frost1, Francis Neat2 & Leslie Noble3

1 University of Aberdeen, Aberdeen, UK 2 Marine Scotland Science, Aberdeen, UK 3 Nord University, Bodo, Norway

The common skate comprises two cryptic species, the flapper skate D. intermedius and the blue skate D. batis. Both species have declined drastically due to fishing pressure in the last century and are now critically endangered priority species on the UK Biodiversity Action Plan (BAP) and OSPAR List. An area from Loch Sunart to Sound of Jura is a Marine Protected Area (MPA) for common skate on the west coast of Scotland. This area has a higher than normal density of mature flapper skates and mark-recapture studies suggest it to be a mix of site attached (resident) and transient individuals. However, species abundance and population connectivity are poorly understood. Yet appropriate management measures will differ depending on whether each species exists as a single highly connected genetically uniform stock, or a collection of isolated genetically unique populations. Marker choice is crucial in studies of large marine species, whose characteristically small but significant levels of population differentiation can be masked by use of inappropriate molecular tools. Prior to this study just a handful of non-species specific microsatellite markers were available but these are not appropriate for providing accurate estimates of population metrics. Using our newly developed species-specific microsatellites for each species the first accurate estimates of genetic diversity have been obtained and clear differences in the population structure and estimates of contemporary effective population sizes in both species are revealed. These findings have implications for current conservation management.

Squaring data and models in larval connectivity studies: Conceptual differences, uncertainties and future challenges

David Kaplan (Plenary Talk)

IRD-Marbec, France

Low and asymmetrical gene flow levels in the cordonnier: geographic barrier or reproductive isolation?

Ilkser E. Kiper 1, Thierry B. Hoareau 1, Philippe Borsa 2

1 University of Pretoria, Pretoria, South Africa 2 Institut de recherche pour le développement (IRD), Montpellier, France

The cordonnier Siganus sutor is a marine fish that inhabits the estuaries, rock reefs, and the inner, pavement areas of coral-reef flats of the Western Indian Ocean (WIO). We investigated the genetic structure of the cordonnier using nuclear (11 microsatellite) and mitochondrial markers from seven localities in the WIO. Based on their geographic distribution, we identified two genetically distinct ensembles, one in the Mozambique Channel (MZC) and one in the Mascarene Islands (MAS). The reconstructed gene flow between MZC and MAS was bidirectional for nuclear markers but unidirectional for the mitochondrial marker. Although weak, the gene flow occurred predominantly from MZC to MAS, which was opposite to the main westward oceanographic circulation. Bayesian structure assignment showed little admixture, leading us to suspect that the cordonnier may alternatively consist of two species. Under the latter hypothesis, the weak gene flow would correspond to occasional hybridization, also offering an alternative explanation for asymmetrical gene flow at the mitochondrial locus.

Keywords: Geographic barrier; Reproductive barrier; Asymmetrical gene flow; Cryptic species; Siganus sutor

Diel vertical migratory behaviour impact on the retention patterns of the early life stages of S. aurita in the northern Gulf of Guinea. A modelling study.

Vamara Koné1, Christophe Lett2, Sandrine Djakouré3

1 Centre de Recherches Océanologiques (CRO), 29 Rue des Pêcheurs, BPV 18, Abidjan, Côte d’Ivoire 2 Sorbonne Université, IRD, Unité de Modélisation Mathématiques et Informatique des Systèmes Complexes, UMMISCO, F-93143, Bondy, France 3 Laboratoire de Physique de l’Atmosphère et Mécanique des fluides (LAPA-MF), Université Félix Houphouet Boigny, Cote d’Ivoire

The small pelagic fishes, S. aurita particularly have adapted their reproductive strategies to the environmental conditions in the northern Gulf of Guinea. In order to characterize the main processes controlling the retention dynamics of S. aurita early life stages in the northern Gulf of Guinea, we developed a biophysical model of S. aurita early life history by coupling offline an individual-based model (Ichthyop) with the regional Oceanic Modelling System (ROMS). We used this model to investigate the role of Diel Vertical Migration (DVM) on S. aurita spatio-temporal retention patterns by performed different simulations. The first simulation called “Reference Simulation” (RSIM) represents a case where the vertical migratory behavior is not included. Three others simulations were performed using three different DVM depth (25, 50 and 75 m) thresholds, called DVM 25, DVM 50 and DVM 75, respectively. The results show that DVM does not change the most favorable spawning areas patterns, regardless the depth threshold used. However, DVM reinforce the seasonal patterns since the retention of individuals occurring only during both the minor and the major upwelling seasons. In addition, DVM affects the spawning depth effect on the larval retention, since the layer of 25-50 m becomes the optimum depth for larval retention in all DVM 25, DVM 50 and DVM 75 simulations contrary to RSIM where larval retention increases with depth.

Keywords: Biophysical model, S. aurita early life stages, Diel vertical migration, retention, upwelling, Gulf of Guinea.

Connectivity patterns of free-living marine nematodes

Nikolaos Lampadariou

Hellenic Centre for Marine Research, PO Box 2214, 71003 Heraklion, Crete, Greece

Patterns of population structure and connectivity are increasingly considered for the management of marine ecosystems in both shallow and deep water. For most benthic marine populations, connectivity is achieved primarily through the exchange of individuals during the pelagic larval stage, although there are many exceptions. Here, we review the case of free-living marine nematodes, one of the most abundant and diverse groups of metazoans on the planet, which are characterised by a direct benthic development, i.e. they do not have a planktonic or a pelagic larvae phase. They are also considered as exceedingly poor swimmers, and their body size is so small that active dispersal over large distances is likely to be very limited. Yet, many nematodes genera and even species are considered cosmopolitan, inhabiting a large variety of habitats and oceans. Nevertheless, the eurytopic, cosmopolitan character of most taxa is mainly based on their simple anatomy, thus making the inter-specific differences often difficult to detect by light microscopy. More recently, the application of complementary molecular techniques to improve identification accuracy of marine nematodes, has uncovered an overwhelming amount of unrecognized cryptic diversity. These studies showed that while dispersal capabilities in marine nematodes seems to be quite substantial at small geographic scales, gene flow declines with geographic distance, resulting in an increase in genetic dissimilarity between populations that are more distant from each other. Analyses of life history and habitat preference of specific nematode species have shown that other environmental factors may be more important drivers for their dispersal. The patterns of population genetic structure, gene flow and connectivity of marine nematodes at a range of spatial scales indicate that flexible spatial management approaches are required for the conservation of marine habitats.

Flatfish comparative genomic in a transition zone: example of the Baltic Sea

Alan Le Moan1, Dorte Bekkevold1 & Jakob Hemmer-Hansen1

1 Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, Silkeborg, DK-8600, Denmark

The connection between the Baltic Sea and the Atlantic was only recently established (app. 20kyo), and today represents an important ecological gradient. Numerous species display a high genetic structure within this area. Here, we used comparative population genomics with ddRAD sequencing to study the colonization of the Baltic Sea by marine organisms. We sampled populations along the environmental gradient for 4 different flatfish species: the European flounder (Platichthys flesus), the European plaice (Pleuronectes platessa), the turbot (Scophthalmus maximus) and the common dab (Limanda limanda). Importantly, these closely related species show contrasting distribution patterns in the Baltic Sea with half of them that have colonized the entire gradient whereas the other half are only found in the south-western part of the Baltic Sea. We obtained one dataset per species containing between 7521 and 19521 independent SNPs. For each species, the genetic differentiation between the populations from the North Sea and populations from the Baltic Sea is highly heterogeneous. Fst varied between 0 and 0.45-0.82 across the SNPs despite a relatively low average Fst (around 0.02 for all species). The majority of the allelic clines between the divergent lineages are located along the eastern Danish coast. Interestingly, in the case of the European flounder, three divergent lineages occurred in the area and another hybrid zone seems to be located between the northern and southern population of the Baltic Sea. In order to understand the evolutionary processes involved during the colonization and population diversification of the Baltic Sea populations, we will also discuss the extent of bottleneck effects and positive selection in different colonization scenarios of the novel marginal habitat in the Baltic Sea.

Integrating Lagrangian modelling with otolith analyses to investigate larval dispersal and fish natal origins: a case-study for Diplodus sargus and Diplodus vulgaris in the Adriatic Sea

Térence Legrand1, Antonio Di Franco2, Enrico Ser-Giacomi3, Vincent Rossi1

1: Mediterranean Institute of Oceanography (MIO, UMR 7294, UM110), CNRS, Aix Marseille Univ., Toulon Univ., IRD, 13288 Marseille, France. 2: Nice Sophia Antipolis Univ., CNRS, FRE 3729 ECOMERS, 28, Avenue Valrose, 06108 Nice, France. 3: LOCEAN (UMR 7159); CNRS / IRD / UPMC / MNHN; 4, place Jussieu 75252 PARIS Cedex, France.

In the marine realm, larval dispersal induced by ocean currents results in complex patterns of connectivity among fish subpopulations; it thus has implications for population dynamics as well as conservation and management. Our target species, the white seabream (Diplodus sargus) and the two-banded seabream (Diplodus vulgaris), play a crucial ecological role in Mediterranean ecosystems and have important socio-economic values as they are exploited by professional and recreational fisheries. Otolith geochemical analyses of both species, sampled along the Apulian coast in the Adriatic Sea, allowed determining their early-life traits (spawning date and pelagic larval duration, PLD), and estimating the relative proportion of a few distinct natal origins but without providing any spatial information. Using Lagrangian modelling and Network Theory tools, we characterize the localisations and extensions of these natal origins by examining connectivity matrices through four levels of analysis which impose successively both physical and biological constraints inferred from the otolith analyses and from their biological traits (e.g. preferential habitat). We found that the backward dispersal plume of D. vulgaris is four times bigger than D.sargus, inducing coast- to-coast connectivity and suggesting that the scale of dispersion is not linearly related to the PLD. The most relevant putative larval sources are situated along the Italian shores, from 43°N to the Apulian coast. These connectivity patterns are well explained by hydrodynamical factors such as the average and seasonal surface circulation as well as the flow turbulence. Connectivity information is then exploited for conservation purposes by investigating the effectiveness of the network of marine protected areas in the Adriatic Sea. By clustering the putative larval sources and comparing the natal origin attributions inferred from both approaches, we discussed the consistency and limitations of our results, which could be partly addressed by improving the partitioning algorithm and by performing more extensive sampling.

Keywords: Larval dispersal; connectivity; otolith; Lagrangian modelling; Adriatic Sea; coastal fishes.

Marine connectivity in Africa

Christophe Lett

Sorbonne Université, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, F-93143, Bondy, France. [email protected]

In a recent literature review of marine population connectivity research, it was recommended that researchers refocus their efforts towards under-studied regions, including Africa (Bryan-Brown et al. 2017). To participate to this need, the IRD (French National Research Institute for Sustainable Development, http://en.ird.fr/) decided to support financially the involvement of African researchers and students in our iMarCo group. The expected benefits for them and their institutions include the promotion of their work more internationally and the establishment of new collaborations enabling to mobilize the group's forces towards their own needs. The expected benefits for the group include their active participation in the structuring of an international multidisciplinary scientific community around the theme of marine connectivity. Here I will briefly review marine connectivity studies conducted in Africa and open the floor to the presentations of our African colleagues.

Connectivity in coastal bottlenose dolphins, Tursiops truncatus, in the British Isles and implications for conservation

Marie Louis*, Milaja Nykänen*, Eileen Dillane, Simon Berrow, Rod Deaville, François Gally, Simon N. Ingram, Vincent Janik, Joanne O’Brien, Rod Penrose, Emer Rogan, Oscar E. Gaggiotti * these authors contributed equally

Protecting species often requires the designation of protected areas, wherein suitable management strategies are applied either at the taxon or ecosystem level. Specials Areas of Conservation (SACs) have been created in European waters under the Habitats Directive (92/43/EEC) to protect two cetacean species including the bottlenose dolphin, Tursiops truncatus, which forms two ecotypes, pelagic and coastal. SACs have been designated in coastal waters based on photo-identification studies indicating that the species had relatively high site fidelity and formed localized coastal communities. However, some communities can carry out relatively long-distance movements, which suggest potential demographic connectivity between the designated SACs. Previous studies used different sets of genetic markers and therefore fine-scale population structure and demographic connectivity could not be investigated at a large scale. Here, we provide the first comprehensive analyses of the genetic structure of the species in coastal waters of the UK, Ireland and northern France. We applied ddRAD sequencing on 96 samples collected from free-ranging (N=86) and stranded bottlenose dolphins (N=10) from the six main coastal communities in the studied area and identified 56,377 SNPs. Genetic structure was defined at an unprecedented fine-scale. Identified populations corresponded to the different local communities that are the Shannon estuary, the West Ireland, the English Channel, the East Scotland, the Wales and the West Scotland populations. Each local community should therefore be managed and monitored separately. These results support the need to protect bottlenose dolphins’ habitat through a network of protected areas such as the SACs. However, given that the range of some populations spans several hundreds of kilometers, habitat modelling and photo-identification studies are needed to define borders for the protected areas that are the most suitable for this species.

Shrimp larval dispersal on the Sofala Bank, Mozambique

Bernardino S. Malauenea,b,*, Coleen L. Moloneyb, Michael .J. Robertsc,d, Fransic Marsace,f, Christophe Lettg aInstituto Nacional de Investigação Pesqueira, Av. Mao Tse Tung 309, Maputo, Mozambique bDepartment of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa cOcean Science and Marine Food Security, Nelson Mandela University, Port Elizabeth, South Africa dNational Oceanography Centre, European Way, Southampton, UK eICEMASA, Department of Oceanography, University of Cape Town, South Africa and fIRD, UMR 248 Marbec, Avenue Jean Monnet, 34203 Sete Cedex, France gSorbonne Universités, UPMC Université Paris 06, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes (UMMISCO), F-93143, Bondy, France

The Sofala Bank, located between 16 and 21oS off the Mozambican coast, is a key tropical habitat for six native species and recently two invasive species of penaeid shrimps in the Western Indian Ocean. These shrimps, particularly the co-occurring Penaeus indicus and Metapenaeus monoceros, support important fisheries. Shrimp larvae dispersal and settlement on the Sofala Bank was investigated by coupling a high-resolution hydrodynamic ROMS model to the biophysical Ichthyop model. Simulations consisted in tracking larvae trajectories during their pelagic life and provided information about their state: position, age and status (alive and dead). Simulated larvae could either be retained over the banks settlement zones (considered as success) or be transported outside (considered as lost). Most larvae were retained on the bank, but some were occasionally advected out by the energetic offshore mesoscale eddy activity. Most lost larvae were transported to the South, exhibiting unidirectional connectivity, in the same direction as the dominant propagating eddies. However, some larvae were occasionally transported offshore, suggesting a possible connectivity between Mozambique and Madagascar.

Assessing sardines and anchovies population structure with ddRAD Sequencing

Tereza Manousaki, Costas S. Tsigenopoulos, Panagiotis Kasapidis, Alessia Cariani, Rita Cannas, Marta Coll and the SPELMED consortium

Adequate fisheries stock assessment is of high priority for sustainable management. Sardines and anchovies represent the main targets of the Mediterranean small pelagic fisheries industry, and when scrutinized in view of the climate change, these species are facing serious threats that may lead to population reduction and loss of genetic diversity. Modern genomic tools provide the means to assess the population structure of species in high resolution and get a detailed view of populations’ status. Here, we sampled 12 populations from each of the two focal species, summing up to 800 samples, from a wide geographic range covering the species distributions in the W. Mediterranean. Sampled populations were used for building ddRAD libraries and Illumina sequencing, which yielded many thousands of SNPs per species. This will allow the assessment of the two species population structure and connectivity providing an overall view of their genetic diversity. Our analysis is expected to unveil the genome-wide genetic profile of sardine and anchovies populations and may serve as a guide for proper management of the studied populations.

Assessing resilience of beaked whale populations to human impacts: population structure and genetic diversity in impacted and semi-pristine areas.

Aubrie Onoufriou, Natacha Aguilar de Soto, Morten Olsen, Oscar Gaggiotti, Emma Carroll

Beaked whales (family Ziphiidae) are one of the most speciose and least-studied cetacean families. Of the 21 recognized species by the IUCN, 19 are classified as data-deficient. Globally distributed, these animals have come into the public eye due to their exceptional diving behaviour and dramatic behavioural responses linking certain anthropogenic sounds to mass stranding events. Little has been published about beaked whale populations on local or global scales and the few that are studied are small and isolated, thus susceptible to genetic erosion. The recognized susceptibility to noise pollution and substantial knowledge gap regarding abundance and population structure, strongly highlight that more information is required for effective management and conservation of these species. This project investigates global population structure and genetic diversity of two sympatric beaked whale species commonly found in mass stranding events, Blainville’s (Mesoplodon densirostris) and Cuvier’s (Ziphius cavirostris). High-resolution genomic profiles generated for each individual consist of single nucleotide polymorphisms (SNPs) discovered using double-digest restriction associated digest (ddRAD) tag sequencing, genetically identified sex and mitochondrial control region haplotypes. Incorporating mitochondrial DNA with nuclear SNPs has generate the most comprehensive dataset for understanding of the global population structure and genetic diversity of Cuvier’s and Blainville’s beaked whales. Future genomic analyses with these data will provide a context for fine-scale population studies that are critical to identifying population-level effects of mass stranding events.

Passive larval transport explains recent gene flow in a Mediterranean gorgonian

Mariana Padrón1, Federica Costantini2,3, Sandra Baksay4, Lorenzo Bramanti1, Katell Guizien1

1 Sorbonne Université, CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques, LECOB, 66650 Banyuls-sur-Mer, France. 2 Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA) & Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Università di Bologna, Via S. Alberto 163, 48123 Ravenna, Italy. 3 CoNISMa, Piazzale Flaminio, 9, 00196 Rome, Italy. 4 Laboratoire Evolution et Diversité Biologique EDB, CNRS, Université Toulouse III Paul Sabatier, 31062 Toulouse, France

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.

Population connectivity of key-species in the Marine Protected Area (MPA) of Karpathos (Greece)

Pavloudi C1, Sarafidou G2, Apostolaki ET3, Chatzigeorgiou G1, Chatzinikolaou E1, Keklikoglou K1, Arvanitidis C1*

1 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece, [email protected] 2 Biology Department, University of Crete, Greece 3 Institute of Oceanography, Hellenic Centre for Marine Research, Greece

The project “Regional cooperation for the transnational ecosystem sustainable development” (RECONNECT) aims to develop strategies for sustainable management of Marine Protected Areas (MPAs) and Natura 2000 sites. The creation of a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, under a common approach, is the overall goal of this project. The main outputs of RECONNECT will provide information concerning habitat attributes, as well as the essential biodiversity (using ecological and genetic methodologies), socio- economic and cultural variables, which will be freely available as tools through a web-based platform. The aim of RECONNECT is the protection and conservation of areas with high ecological and economical value under a harmonized socio-economic and legal framework. Regarding the estimation of biodiversity using genetic tools, 5 sampling stations were chosen in the regional marine park of northern Karpathos, Saria and Astakidonision (Greece). Key- species, i.e. Pinna nobilis, Posidonia oceanica and Cymodocea nodosa, were collected by non-destructive sampling. DNA was extracted, following PCR amplification and sequencing of selected barcoding genes. The results of the project will shed light on the distribution of the populations of the selected key-species and on the degree of connectivity between the different sampling stations. In addition, the results will unravel possible relationships of the populations to environmental variables, which could be used as a proxy for monitoring the population distribution and ecosystem resilience.

Keywords: Marine Protected Areas (MPAs); Natura 2000; biodiversity; conservation; Pinna nobilis; Posidonia oceanica; Cymodocea nodosa

Acknowledgements: RECONNECT (MIS code: 5017160) is funded by the Transnational Cooperation Programme Interreg "Balkan-Mediterranean 2014-2020" (Subcidy Contract Number: BMP1/2.1/2581/2017). More details can be found in the project's website (http://reconnect.hcmr.gr/).

Temperature anomalies influence larval cohesion in a southern African temperate sparid, the hottentot seabream

Kerry Reid 1, Paulette Bloomer1, Estelle Crochelet2, Thierry B Hoareau1

1 Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa. 2 Institut de Recherche pour le Développement (IRD), UMR 228 ESPACE-DEV, Sainte Clotilde, Réunion, France.

Endemic marine species with relatively sedentary adults and vagile pelagic larvae provide models to assess the effects of local oceanographic features and climatic fluctuations on regional connectivity. Here, we studied the population genetic variation of an endemic sparid, the hottentot seabream Pachymetopon blochii, to evaluate the role of environmental factors on pelagic larval dispersal along the west coast of South Africa. We analysed thirteen microsatellites of 480 samples from various locations collected in 2001 and 2009. A single population was identified, with evidence of weak genetic structuring among locations. Overall, age-class cohorts showed higher genetic relatedness values than within locations which suggests an effect of the large variance in individual reproductive success. Moreover, the genetic relatedness of age-class cohorts increase with the sea surface temperature (SST) anomalies suggesting the influence of oceanographic conditions on the larval cohesion of P. blochii. Specifically, we suggest that the variation in SST and related wind-stressed currents along the west coast of southern Africa affect the dispersal and mixing of larval pools originating from different locations.

Keywords: chaotic genetic patchiness, gene flow, larval cohesion, microsatellites, Pachymetopon blochii, SST

Modelling early-life stages connectivity to better understand marine population structure and inform fisheries management

Vincent Rossi1,4, Ehsan Sadighrad2, Manuel Hidalgo3, Enrico Ser-Giacomi4,5, Bettina Fach2 and Emilio Hernandez-Garcia4

1: Mediterranean Institute of Oceanography (MIO, UMR 7294, UM110), CNRS, Aix Marseille Univ., Toulon Univ., IRD, 13288 Marseille, France. 2: Institute of Marine Sciences, Middle East Technical University, Erdemli, 33731 Mersin, Turkey. 3: Instituto Español de Oceanografía, Centre Oceanogràfic de les Balears, Moll de Ponent s/n, 07015 Palma de mallorca, Spain. 4: Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain. 5: LOCEAN (UMR 7159) ; CNRS / IRD / UPMC / MNHN; 4, place Jussieu 75252 PARIS Cedex, France.

There is growing evidence that the spatial structures of marine populations are often more complex than currently accounted for in management frameworks. Large fish stocks are usually assessed independently within each sub-area while overlooking demographical dynamics within and across transnational boundaries and neighboring stocks. Due to the highly dispersive abilities of the early-life stages (ELS) for many marine organisms, a good description of ELS large-scale connectivity is of paramount importance to better understand the dynamics and structural complexity of marine populations. We present a novel modelling approach to assess ELS connectivity and infer large-scale biogeographical patterns. Our target-species, the European hake, is one of the most commercially and ecologically important demersal species in the Mediterranean Sea. By combining estimated spawning areas, ensemble of realistic connectivity matrices (current-driven larval dispersal) and predicted settlement grounds of juveniles, it provides insights into the basin-scale structure of hake population. A clustering algorithm provides a scientifically-based separation of the seascape that do not necessarily match the established fisheries assessment units nor the most accepted eco-regions. Identified communities illustrate how connectivity and habitats shape hake’s subpopulations in the entire Mediterranean basin and reveal spatial mismatches between hake´s population structure and the current delimitation of fisheries assessment units. Merging concepts and tools from fishery sciences, oceanography, population dynamics and network-theory, our modeling framework allows comparing putative large-scale population structure and management areas, thus providing pertinent information for a better effectiveness of area-based management of marine species.

Keywords: Early-life stages; Connectivity; Larval dispersal; Population Structure; Spatial Management.

Assessing the sensitivity of coral connectivity modelling to mesh resolution in the Great Barrier Reef (or "How fine is fine enough?")

Antoine Saint-Amand1, Jonathan Lambrechts2, Christopher Thomas2, Emmanuel Hanert1

1Earth & Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium 2Institute of Mechanics, Materials and Civil Engineering, Université Catholique de Louvain, Louvain-la-Neuve, Belgium

Over the past decade, constant efforts have been put in modelling the connectivity between the 3000+ individual reefs composing the Great Barrier Reef (GBR). However, the computing cost of such models compared to the vastness of the GBR often leads to use coarse resolution models. In this study, we use the 2D unstructured-mesh coastal ocean SLIM model to assess the impact of mesh resolution on model results. SLIM uses unstructured meshes that offer the flexibility to vary the spatial resolution so that computational resources can be allocated where they are most useful: the level of detail is set at a high precision near reefs, islands and along the coast, but is coarser in open seas. More particularly, this work is an attempt to assess the effect of the highest level of detail of the mesh on the resulting connectivity estimates. For this purpose, we built five different meshes for which the highest resolution ranges from 250m to 4km. For each setup, we model the ocean currents to simulate larval dispersal. We then compare the effect of mesh resolution on different connectivity indicators (number of reefs resolved, average connectivity length, community structure, …). Our results suggest that a 500m resolution is at least required to have solid estimates of coral connectivity.

Influence of the Siculo-Tunisian Strait (Central Mediterranean Sea) and early-life-history traits on genetic patterns of two Labridae species

Shili A. and L. Bahri-Sfar

Université de Tunis El Manar, Faculté des Sciences de Tunis, UR 11ES08 Biologie Intégrative et Ecologie évolutive et Fonctionnelle des Milieux aquatiques, 2092, Tunis, Tunisie

In marine fishes, several factors like historical events (glaciations), ecological and biological traits (population size, larval dispersion) or even geophysical ones like ocean currents shape the spatial structure of genetic variation. In the Mediterranean Sea, the Siculo-Tunisian Strait (STS) constitute a zone of transition between western and eastern basins that can affect gene flow and influence the connectivity among populations. Therefore, we aimed in this study to shed light on how biological traits in such particular area can influence the spatial patterns of the genetic diversity of two Labridea species: Symphodus tinca (Linnaeus, 1758) and Coris julis (Linnaeus, 1758). Indeed, the Labridae family presents the most morphologically and ecologically diversified fishes in size, shape and life history traits. Symphodus tinca is characterized by a shorter larval dispersal phase (9-13 days) than Coris julis (45 days). For this, we sampled several localities from either side of the STS for both of the two species and used two type of molecular markers: mitochondrial DNA and Inter Simple Sequence Repeats markers, ISSR (only for Symphodus tinca) to study their genetic diversity. The preliminary phylogeographic analyses have shown different genetic patterns between the targeted species and a more heterogeneous pattern was highlighted for Symphodus tinca than for Coris julis which emphasizes a likely influence of larval dispersal duration.

Population genomics of repeated invasions of genetically admixed mussels in ports

Alexis Simon1,*, Khalid Belkhir1, John Welch2, Frédérique Viard3, Nicolas Bierne1

1. Institut des Sciences de l’Évolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE- UM, France. 2. Department of Genetics, University of Cambridge, Downing St. Cambridge, CB23EH, UK. 3. UPMC Université Paris 6, CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, équipe DIVCO, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France.

Colonization of new regions by alien species, intentional or not, is a bypass of natural connectivity. When the alien species can hybridize with a native relative, gene flow of alien genes can further impact the genetic connectivity of local populations. This gene flow can often go unnoticed due to cryptic divergence. Ports are highly modified environments presenting anthropogenic disturbances and increased propagule pressures, favorable for alien species establishment. In addition, ports can act as connectivity hubs creating secondary invasion events. We studied the genomics of introduced Mediterranean mussel populations, Mytilus galloprovincialis, in five French ports. M. galloprovincialis is listed in the 100 world's worst invasive alien species and is part of a complex of hybridizing species, together with M. edulis and M. trossulus. M. galloprovincialis found in the sampled ports show an unforeseen rate of introgression with native mussels (~30%). Colonized ports present different characteristics in terms of layout (impacting in/out connectivity) and of local Mytilus genetic backgrounds. We performed low-coverage whole genome sequencing of 144 mussels including reference samples, introgressed port mussels and other comparable naturally introgressed populations. First, the assembly of mitogenomes will allow us to study the diversity and the origin of port populations. This step will help us answer questions related to routes of propagation, bottlenecks and shared history of invasion events. Then, the architecture of admixed genomes and introgression will be studied to uncover common or different patterns between introduction events. The objectives will be to (i) uncover the origin of the introgression, either local or historic, (ii) investigate the relative role of contingency and parallel processes of introgression by comparing repeated instances of established port mussels in contact with different local genetic backgrounds.

Defining connectivity of exploited octopus and shrimp populations across the Mediterranean

Anamaria Štambuk1, Iva Sabolić1, Miguel Baltazar-Soares2, Óscar Mira1, Robert Bakarić1, Sasa Raicevich3, Marta Albo4, Pietro Battaglia3, Jakša Božanić5 , Joan B. Company4, Rute Cegonho6, Maria Rosario Partidario6, Guiomar Rotllant4, Margarida Barros6, Matea Špika5, Sandra Hudina1

1Department of Biology, Faculty of Science, University of Zagreb, Roosveltov trg 6, 10000 Zagreb; Croatia 2Faculty of Science and Technology, Bournemouth University, Christchurch House, Talbot Campus, Poole, Dorset BH12 5BB 3Institute for Environmental Protection and Research, Loc. Brondolo, 30015 Chioggi, Italy 4Institute of Marine Sciences, Spanish National Research Council, Calle República Árabe Saharawi, 4, 11519 Puerto Real, Cádiz, Spain 5Association for Nature, Environment and Sustainable Development Sunce, Obala Hrvatskog narodnog preporoda 7, 21000 Split, Croatia 6Centre for Management Studies, Instituto Superior Técnico Lisboa, Av. Rovisco Pais, 1049- 001 Lisboa, Portugal

In this era of fast global change, defining connectivity and adaptive potential of exploited marine stocks is a key requirement towards sustainability of fisheries. However, management of exploited marine species is often limited to the geopolitical boundaries, and stocks are perceived as static, non-evolving units. Though the use of genetics tools is not very pervasive in fisheries management, evolutionary concepts that derive from its use provide the much needed information regarding stock structure and its adaptation capacity. In our study, we examine the integration of evolutionary-based knowledge in fisheries conservation of two target species: common octopus, Octopus vulgaris and red shrimp Aristeus antennatus. To that end, we sampled 19 octopus and 12 red shrimp populations across the Mediterranean and collected data on their distribution, status and fisheries. Populations were genotyped using genotying-by-sequencing approach and a number of polymorphic genetic markers (SNPs) was validated for each species and population. In order to assess the stock structure, genetic differentiation among populations was estimated with F-statistics and patterns of genomic variation across spatial scales were obtained, providing evidence of connectivity. To investigate occurrences of local adaptation, the data set was tested for evolution under selection. Here we provide perspective on stock structure, connectivity and local adaptation of octopus and red shrimp in the Mediterranean and indicate fishery areas that are critical to preserve, contributing directly to the sustainable management of Mediterranean fishery populations.

Next-generation marine biodiversity research using environmental DNA

Philip Thomsen (Plenary Talk)

Department of Bioscience, Aarhus University, Denmark

Determining effective connectivity: developing models that go beyond structural and functional estimates

Justin Travis (Plenary Talk)

The Institute of Biological and Environmental Sciences, University of Aberdeen, UK

Close-kin methods to estimate census size and effective population size

Robin S. Waples (Plenary Talk)

University of Washington, USA

Close-kin mark-recapture (CKMR) uses genetic methods to identify close relatives, which are then analyzed in the standard capture-mark-recapture (CMR) statistical framework to estimate adult census size (N). Unlike traditional CMR, it is not necessary to capture the same individuals more than once to apply CKMR; instead, the method relies on the fact that genes are shared naturally among close relatives through Mendelian inheritance. In the CKMR framework, pairs of close relatives (parent-offspring (POPs) or half-siblings (HSPs)) are considered “recoveries.” In the first large-scale application of CKMR, Bravington et al. (2016 Nature Communications 7:13162) produced an estimate of N ≈ 2x106 for southern bluefin tuna (SBT; Thunnus maccoyii) that was both larger than expected and much more precise (CV = 17%) than had been possible with traditional methods. This result, which was obtained using POPs identified by 26 microsatellite loci, has attracted a great deal of interest globally. Furthermore, the ready availability of many thousands of SNP loci, even for non- model species, opens up the possibility of also using siblings to increase precision. However, extension of CKMR to incorporate siblings introduces a number of complexities, not the least of which is that there is already a widely-used method based on siblings to estimate effective population size (Ne) or the effective number of breeders per year (Nb). I review the CKMR methodology for POPs and siblings and discuss factors that can affect bias and precision of the estimates, including changes in survival and fecundity with age; selectivity in sampling; overdispersed variance in reproductive success; skewed sex ratio; skip breeding; persistent individual differences; and population subdivision. I show that HSPs from different cohorts can be used to estimate N, whereas siblings from the same cohort estimate Nb. Because precision depends on the number of close-kin pairs identified, robust estimates for large populations will require extensive sampling efforts.