Systematics and phylogeography of the deep-sea coral Desmophyllum dianthus (Anthozoa, Hexacorallia): morphological and molecular evidences

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 28-11-2014

Editorial : The sustainability series : the plastics problem - pathways towards sustainable solutions against plastic pollution

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The origin and correlated evolution of symbiosis and coloniality in Scleractinian corals

Symbiosis and coloniality are ecologically important traits for corals of the order Scleractinia. Symbiotic (zooxanthellate) species are highly successful in shallow waters of tropical and subtropical seas and most of them are colonial. On the other hand, azooxanthellate species present wide distribution ranges and expand to the deep-sea at more than 6,000 m depth. These are mostly solitary, with only few species colonial that form extensive deep reefs. Each ecologically distinctive group encompasses half of the biodiversity of the order and they are not grouped into differentiated monophyletic clades. Paleontologists and evolutionary biologists have debated for decades whether modern scleractinian corals have evolved from symbiotic or colonial ancestors and how these traits have evolved and being involved in the diversification process in corals. Previous comparative analyses throw evidence in favor of coevolution of these characters and toward repetitive loss of symbiosis and coloniality. Nevertheless, the discovery of the origin of the group deep in the Paleozoic, with a deep divergent clade composed of only azooxanthellate corals has questioned these findings. With this work, we disentangle the patterns in the evolution of symbiosis and coloniality, testing if they are correlated and if they follow a gradual or episodic mode of evolution. To this end, we first produce the most complete time-calibrated phylogenetic tree for the order Scleractinia, including new sequences of never-before sampled species and genera. These novel sequences contribute to alleviate the current molecular under sampling of azooxanthellate species. Incorporating phylogenetic uncertainty, we obtained strong evidence in favor of a correlated and episodic model of evolution. This model led to the inference of an azooxanthellate and solitary most recent ancestor of scleractinians. Transition rates between the four different combinations of the two traits showed that while coloniality is gained and lost multiple times, symbiosis first appears around 282 Ma and is never lost. Also, coloniality seems to have appeared before symbiosis in azooxanthellate lineages. Thus, azooxanthellate corals, and especially colonial lineages, have been acting as a source of biodiversity for shallow zooxanthellate coral communities, highlighting the uniqueness of shallow and deep species and the need to preserve them

EU Marine Beach Litter Baselines

Measures against marine litter require quantitative data for the assessment of litter abundance, trends and distribution. While beach litter monitoring has been ongoing in some European areas since years, so far it was yet not possible to obtain an overview and to analyse litter abundance, litter category distribution and trends at the different spatial scales from local to EU. Therefore, the EU Marine Directors and the Marine Strategy Coordination Group mandated, in the context of the MSFD implementation, to the MSFD Technical Group on Marine Litter and the JRC, the compilation and analysis of an EU beach litter dataset. Aim was to derive EU Marine Beach Litter Baselines at different spatial levels. After collection of European beach litter data from EU Member States via the EMODNET chemistry module database, harmonisation of data formats, clean-up a 2012-2016 dataset was derived. Following the spatio-temporal aggregation of data and the identification of possible litter category analysis, different scenarios for baseline setting have been tested and evaluated. The application of agreed scenario parameters has enabled the calculation of marine beach litter baselines for the years 2015 and 2016 at spatial scales ranging from country and country –region level to sub-regional, regional and EU level. Litter categories have been aggregated and allow analysis of group categories up to EU level, whereas the analysis of single categories could not include all received data due to non-comparable litter type category descriptions. The resulting set of baselines enables the future monitoring of progress in reduction, as well as compliance checking developed using the dataset. Furthermore, it provides valuable information for future improving harmonised monitoring through updated guidance, common data treatment and agreed data reporting formats. Beach litter abundance has been found to be very high in large areas of Europe, requiring joint and strong action in Europe and with the neighbours in shared marine basins.JRC.D.2-Water and Marine Resource

Cruise Summary Report - MEDWAVES survey. MEDiterranean out flow WAter and Vulnerable EcosystemS (MEDWAVES)

The MEDWAVES (MEDiterranean out flow WAter and Vulnerable EcosystemS) cruise targeted areas under the potential influence of the MOW within the Mediterranean and Atlantic realms. These include seamounts where Cold-water corals (CWCs) have been reported but that are still poorly known, and which may act as essential “stepping stones” connecting fauna of seamounts in the Mediterranean with those of the continental shelf of Portugal, the Azores and the Mid-Atlantic Ridge. During MEDWAVES sampling has been conducted in two of the case studies of ATLAS: Case study 7 (Gulf of Cádiz-Strait of Gibraltar-Alboran Sea) and Case study 8 (Azores). The initially targeted areas in the Atlantic were: the Gazul Mud volcano, in the Gulf of Cádiz (GoC) area, included in the case study 7, and the Atlantic seamounts Ormonde (Portuguese shelf) and Formigas (by Azores), both part of the case study 8. In the Mediterranean the targeted areas were The Guadiaro submarine canyon and the Seco de los Olivos (also known as Chella Bank) seamount. Unfortunately it was not possible to sample in Guadiaro due to time constraints originated by adverse meteorological conditions which obligate us to reduce the time at sea focusing only in 4 of the 5 initially planned areas. MEDWAVES was structured in two legs; the first leg took place from the 21st September (departure from Cádiz harbour in Spain) to the 13th October 2016 (arrival in Ponta Delgada, São Miguel, Azores, Portugal took place the 8th of October due to the meteorological conditions that obligated to conclude the first leg earlier as planned). during the Leg 1 sampling was carried out in Gazul, Ormonde and Formigas. The second leg started the 14th October (departure from Ponta Delgada) and finished the 26th October (arrival in Málaga harbour, Spain). MEDWAVES had a total of 30 effective sampling days, being 6 days not operative due to the adverse meteorological conditions experienced during the first leg which forced us to stay in Ponta Delgada from the 08th to the 13th October. During MEDWAVES the daily routine followed a similar scheme, depending of course on the weather and sea conditions. The main activity during the day, starting early in the morning (around 08:00 AM, once the night activities were finished), was the ROV deployment. Generally a single ROV dive of around 8 hours was performed, however in several occasions two dives were carried out in the same day (see General station list, Appendix II). After the ROV (and sometimes between two dives) the Box Corer and/or Van Veen Grab and/or Multicore was deployed. After these activities, during the night CTD-Rosette deployments and MB was conducted. Accordingly to this schema the scientific personnel worked in the day or in the night watch. A total of 215 sampling stations have been covered in MEDWAVES, using the following sampling gears: Multibeam echosounder, CTD-Rosette, LADCP, Box Corer, Van Veen Grab, Multicorer and a Remotely Operated Vehicle (ROV). Table 1 sumamrised the number of sampling stations conducted with each gear in each sampling zone. Additionally MB surveys have been conducted during the transits between area

Toward the integrated marine debris observing system

Plastics and other artificial materials pose new risks to the health of the ocean. Anthropogenic debris travels across large distances and is ubiquitous in the water and on shorelines, yet, observations of its sources, composition, pathways, and distributions in the ocean are very sparse and inaccurate. Total amounts of plastics and other man-made debris in the ocean and on the shore, temporal trends in these amounts under exponentially increasing production, as well as degradation processes, vertical fluxes, and time scales are largely unknown. Present ocean circulation models are not able to accurately simulate drift of debris because of its complex hydrodynamics. In this paper we discuss the structure of the future integrated marine debris observing system (IMDOS) that is required to provide long-term monitoring of the state of this anthropogenic pollution and support operational activities to mitigate impacts on the ecosystem and on the safety of maritime activity. The proposed observing system integrates remote sensing and in situ observations. Also, models are used to optimize the design of the system and, in turn, they will be gradually improved using the products of the system. Remote sensing technologies will provide spatially coherent coverage and consistent surveying time series at local to global scale. Optical sensors, including high-resolution imaging, multi- and hyperspectral, fluorescence, and Raman technologies, as well as SAR will be used to measure different types of debris. They will be implemented in a variety of platforms, from hand-held tools to ship-, buoy-, aircraft-, and satellite-based sensors. A network of in situ observations, including reports from volunteers, citizen scientists and ships of opportunity, will be developed to provide data for calibration/validation of remote sensors and to monitor the spread of plastic pollution and other marine debris. IMDOS will interact with other observing systems monitoring physical, chemical, and biological processes in the ocean and on shorelines as well as the state of the ecosystem, maritime activities and safety, drift of sea ice, etc. The synthesized data will support innovative multi-disciplinary research and serve a diverse community of users

Mapping and Assessment of Ecosystems and their Services: An EU ecosystem assessment

This report presents an ecosystem assessment covering the total land area of the EU as well as the EU marine regions. The assessment is carried out by Joint Research Centre, European Environment Agency, DG Environment, and the European Topic Centres on Biological Diversity and on Urban, Land and Soil Systems. This report constitutes a knowledge base which can support the evaluation of the 2020 biodiversity targets. It also provides a data foundation for future assessments and policy developments, in particular with respect to the ecosystem restoration agenda for the next decade (2020-2030). The report presents an analysis of the pressures and condition of terrestrial, freshwater and marine ecosystems using a single, comparable methodology based on European data on trends of pressures and condition relative to the policy baseline 2010. The following main conclusions are drawn: - Pressures on ecosystems exhibit different trends. - Land take, atmospheric emissions of air pollutants and critical loads of nitrogen are decreasing but the absolute values of all these pressures remain too high. - Impacts from climate change on ecosystems are increasing. - Invasive alien species of union concern are observed in all ecosystems, but their impact is particularly high in urban ecosystems and grasslands. - Pressures from overfishing activities and marine pollution are still high. - In the long term, air and freshwater quality is improving. - In forests and agroecosystems, which represent over 80% of the EU territory, there are improvements in structural condition indicators (biomass, deadwood, area under organic farming) relative to the baseline year 2010 but some key bio-indicators such as tree-crown defoliation continue to increase. This indicates that ecosystem condition is not improving. - Species-related indicators show no progress or further declines, particularly in agroecosystems. The analysis of trends in ecosystem services concluded that the current potential of ecosystems to deliver timber, protection against floods, crop pollination, and nature-based recreation is equal to or lower than the baseline value for 2010. At the same time, the demand for these services has significantly increased. A lowered potential in combination with a higher demand risks to further decrease the condition of ecosystems and their contribution to human well-being. Despite the wide coverage of environmental legislation in the EU, there are still large gaps in the legal protection of ecosystems. On land, 76% of the area of terrestrial ecosystems, mainly forests, agroecosystems and urban ecosystems, are excluded from a legal designation under the Bird and Habitat Directives. Freshwater and marine ecosystems are subject to specific protection measures under the Water Framework and Marine Strategy Framework Directives. The condition of ecosystems that are under legal designation is unfavourable. More efforts are needed to bend the curve of biodiversity loss and ecosystem degradation and to put ecosystems on a path to recovery. The progress that is made in certain areas such as pollution reduction, increasing air and water quality, increasing share of organic farming, the expansion of forests, and the efforts to maintain marine fish stocks at sustainable levels show that a persistent implementation of policies can be effective. These successes should encourage us to act now and to put forward an ambitious plan for the restoration of Europe’s ecosystems.JRC.D.3-Land Resource

Sistemática y filogeografía del coral de profundidad Desmophyllum dianthus (Anthozoa, Hexacorallia): Indicios morfológicos y moleculares

[EN] Scientific knowledge on phylogeny, phylogeography and genetic population of Scleractinia is mainly based on shallow and tropical corals, and only few works involved deep-sea and azooxanthellate corals, whose species composed half of the total number of corals identified so far. Just recently, the scleractinian species Desmophyllum dianthus (Esper, 1794) has received some attention in biological studies, but its phylogeny and population genetics has been slightly explored. The aim of this Thesis is to analyse its phylogenetic relationship at inter and intra-family level, and its population structure, through a multidisciplinary approach. In order to achieve the phylogenetic objective and because the genus belongs to the well known polyphyletic Caryophylliidae family, distinct caryophylliids species are analysed with molecular markers commonly used in the studies of phylogenetic relationships of Scleractinia, and additionally new ones are here developed by high-throughput Illumina sequencing. At intraspecific level, since D. dianthus is one of few corals widespread distributed, several individuals from different areas of both northern and southern hemispheres are analysed, with 30 new microsatellites developed by pyrosequencing 454, giving a picture of its population genetics on a global scale. Additional analyses are performed with morphological characters of skeleton and polyps to define the high level of morphological variability that characterized D. dianthus. Furthermore, the complete mitochondrial genome of two specimens from Mediterranean Sea and southwestern Pacific are also sequenced and comparative analyses are performed in order to clarify phylogenetic relationship of closely related species. Data revealed that D. dianthus belongs phylogenetically to scleractinian “robust group” in one of the Caryophylliidae polyphyletic clades, and its extremely high morphology variability has not showed ecological or geographical pattern. Specific population structures are detected for northern and southern hemispheres, with an isolation by distance model of gene flow (IBD). Moreover, deep currents play a key role on larval dispersal, creating peculiar genetic barriers or genetic connectivity between D. dianthus populations, such as New Zealand and Chile, whose populations presented own genetic characteristics, or Australia and Argentina, whose gene flow is detected despite the large geographic distance between them. Finally, a surprising genetic similarity, throughout several nuclear and mitochondrial molecular markers characterized by different mutation rates and polymorphism level, was found between D. dianthus and the main deep-water coral reef builder Lophelia pertusa, Even though scientific community still have to face several unanswered questions over phylogeny and phylogeography of Scleractinia, and overall much more additional data and analyses are needed, the results of this study provide the first detailed insight on phylogeny and genetic population of the deep-sea coral species D. dianthus. Moreover, genetic similarity between D. dianthus and L. pertusa demonstrated the need for a complete taxonomic revision of the genera and family Caryophylliidae. In this Thesis new molecular tools are provided to tackle this goal, both at phylogeny and phylogeographic level.[ES] El conocimiento científico de la filogenia, filogeografía y genética de poblaciones de Scleractinia, se basa principalmente en estudios llevados a cabo en corales de aguas someras y tropicales, y sólo unos pocos incluyen corales azooxantelados y de aguas profundas, si bien sus especies constituyen la mitad del número total de las especies de corales identificadas hasta el momento. Sólo recientemente, la especie escleractinia Desmophyllum dianthus (Esper, 1974) ha sido objeto de cierta atención en estudios biológicos, aunque han sido marginalmente explorados aspectos sobre sus relaciones filogenéticas y la estructura genética de sus poblaciones. Por tanto, el objetivo central de esta Tesis es precisamente analizar la relación filogenética de la especie a nivel inter y intra-familiar, y la genética de sus poblaciones, todo ello a través de un enfoque multidisciplinario. Con el fin de alcanzar el objetivo filogenético, teniendo en cuenta que el género pertenece a la familia Caryophylliidae, bien conocida por su carácter polifilético, distintas especies de cariofílidos han sido analizadas con marcadores moleculares comúnmente utilizados en los estudios de relaciones filogenéticas de Scleractinia y, además, nuevos marcadores han sido aquí desarrollados gracias a la aplicación de metodologías de secuenciación masiva. A nivel intraespecífico, puesto que D. dianthus es uno de los escasos corales ampliamente distribuidos, se han podido analizar individuos de distintas áreas de ambos hemisferios, norte y sur. Para este estudio de diferenciación genética poblacional a escala global, se han empleado 30 nuevos microsatélites desarrollados a través de técnicas de pirosecuenciación. Por otra parte, y con el fin de delimitar el alto nivel de variabilidad morfológica que caracteriza a D. dianthus, se han llevado a cabo análisis de los esqueletos y de los pólipos con caracteres morfológicos. Finalmente, se ha secuenciado el genoma mitocondrial completo de dos ejemplares del mar Mediterráneo y del suroeste del Pacífico, realizando análisis comparativos con especies próximas, con el fin de aclarar la relación filogenética de ciertas especies estrechamente relacionadas. Los datos revelaron que D. dianthus pertenece filogenéticamente al grupo ‘robusto’ de los escleractínidos, en uno de los clados polifiléticos de Caryophyllidae. Por su parte, su extremadamente alta variabilidad morfológica no ha mostrado patrones ecológicos o geográficos. En cuanto a la estructura genética de sus poblaciones, se ha detectado una cierta diferenciación entre los ejemplares procedentes de los hemisferios norte y sur, con un modelo de flujo génico de aislamiento por distancia. Las corrientes profundas parecen desempeñar un papel clave en la dispersión de las larvas, creando peculiares barreras o, por el contrario, conectividad genética entre las poblaciones de D. dianthus, tal como ocurre con las procedentes de Nueva Zelanda y Chile, cuyas poblaciones presentaron características genéticas propias, o las de Australia y Argentina, entre las que se ha detectado un cierto flujo génico, a pesar de la gran distancia geográfica que existe entre las dos regiones. Por último, se ha encontrado una sorprendente similitud genética, a través de diferentes marcadores moleculares de origen nuclear y mitocondrial caracterizados por diferentes tasas de mutación y niveles de polimorfismo, entre D. dianthus y el principal coral constructor de arrecifes de mares profundos Lophelia pertusa. Como con los objetivos planteados, en esta Tesis se han desarrollado nuevas herramientas moleculares, que han permitido conocer de forma más precisa los procesos que han modulado la historia evolutiva de D. dianthus, y que pueden resultar igualmente útiles para el análisis de especies cercanas.Results of Chapter I adapted from: Addamo AM, Reimer JD, Taviani M, Freiwald A, Machordom A. Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity. PLoS ONE 7(11): e50215 (2012), doi: 10,1371/journal.pone.0050215, handle: http://hdl.handle.net/10261/134186Results of Chapter II adapted from: Addamo AM, Vertino A, Martínez-Baraldés I, López-González PJ, Taviani M, Machordom A. Morphological polymorphism of Desmophyllum dianthus (Anthozoa: Hexacorallia) over a wide ecological and biogeographic range: Stability in deep habitats? Zoologischer Anzeiger - A Journal of Comparative Zoology 259: 113-130 (2015), doi: 10.1016/j.jcz.2015.10.004, http://digital.csic.es/handle/10261/134222Results of Chapter III adapted from: Addamo AM, García Jiménez R, Taviani M, Machordom A. Development of microsatellite markers in the deep-dea cup coral Desmophyllum dianthus by 454 sequencing and cross-species amplifications in Scleractinia Order. Journal of Heredity 106(3): 322-330 (2015). http://dx.doi.org/10.1093/jhered/esv010. http://hdl.handle.net/10261/134279Results of Chapter VI adapted from: Addamo AM, Vertino A, Stolarski J, Garcia R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evolutionary Biology 16(1): 108 (2016), http://hdl.handle.net/10261/134210Peer reviewe

Morphological polymorphism of Desmophyllum dianthus (Anthozoa: Hexacorallia) over a wide ecological and biogeographic range: Stability in deep habitats?

[EN] This adaptation text reproduces chapter II of the dissertation “Results”: Systematics and phylogeography of the deep-sea coral Desmophyllum dianthus (Anthozoa, Hexacorallia): Morphological and molecular evidences, de Anna Maria Addamo (2014), http://hdl.handle.net/10261/134194[ES] Este artículo es una adaptación del capítulo II de “Resultados” de la tesis doctoral: Sistemática y filogeografía del coral de profundidad Desmophyllum dianthus (Anthozoa, Hexacorallia): Indicios morfológicos y moleculares, de Anna Maria Addamo (2014), http://hdl.handle.net/10261/134194Although zooxanthellate corals are well known for their ecophenotypic variations, there is increasing evidence that azooxanthellate species also harbour a high degree of plasticity. Desmophyllum dianthus, a widespread solitary coral, exhibits a high degree of morphological variation in corallum forms that has never been analysed quantitatively. To assess if the clear morphological variation of D. dianthus follows a specific pattern based on environmental (or others) variables, this study combines three different morphometric approaches: (1) classical linear external morphology, (2) use of three-dimensional coordinates landmarks, and (3) linear measurements and counts made of cnidocyst features. Comparative morphological characterization of D. dianthus specimens shows a pattern of intraspecific variation over a wide ecological and biogeographic range. However, additional future studies on this and other proposed cosmopolitan species, including a similar sampling effort in localities and specimens, will be useful to explore the existence of common global patterns of morphological variability. Hypotheses for intraspecific polymorphism are discussed to explain the incongruence between the obtained results and the seemingly high morphological variability observed within D. dianthus.This research was supported by Spanish grants (CGL2011-23306 and CTM2014-57949-R) and EU CoCoNET- “Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential”- from the VII FP of the European Commission. The Spanish projects REN2001-4920-E/ANT and CTM2005-07756-C02-02/MAR supported the participation in Sub-Antarctic and Mediterranean expeditions.Peer reviewe

Development of microsatellite markers in the deep-dea cup coral Desmophyllum dianthus by 454 sequencing and cross-species amplifications in Scleractinia Order

[EN] This adaptation text reproduces chapter III of the dissertation “Results”: Systematics and phylogeography of the deep-sea coral Desmophyllum dianthus (Anthozoa, Hexacorallia): Morphological and molecular evidences, de Anna Maria Addamo (2014), http://hdl.handle.net/10261/134194[ES] Este artículo es una adaptación del capítulo III de los “Resultados” de la tesis doctoral: Sistemática y filogeografía del coral de profundidad Desmophyllum dianthus (Anthozoa, Hexacorallia): Indicios morfológicos y moleculares, de Anna Maria Addamo (2014), http://hdl.handle.net/10261/134194Microsatellite loci were isolated for the first time for the deep-sea coral Desmophyllum dianthus, using 454 GS-FLX Titanium pyrosequencing. We developed conditions for amplifying 24 markers in 10 multiplex reactions. Three to 16 alleles per locus were detected across 25 samples analyzed from Santa Maria di Leuca coral province (Mediterranean Sea). For the 24 polymorphic loci, observed and expected heterozygosities ranged from 0.211 to 0.880 and 0.383 to 0.910, respectively; 3 loci deviated from Hardy-Weinberg equilibrium, after null allele and sequential Holm-Bonferroni corrections. These newly isolated microsatellites are very useful genetic markers that provide data for future conservation strategies. Cross-amplification of these microsatellites, tested in 46 coral species, representing 40 genera, and 10 families of the phylum Cnidaria, produced informative allelic profiles for 1 to 24 loci. The utility of extending analyses to cross-species amplifications is also discussed.Spanish Ministry of Innovation and Competition (CGL2011-23306); EU CoCoNET (287844)—“Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential”—from the VII FP of the European Commission.Peer reviewe