scholarly journals The Genome Sequence of the Octocoral Paramuricea clavata – A Key Resource To Study the Impact of Climate Change in the Mediterranean

2020 ◽  
Vol 10 (9) ◽  
pp. 2941-2952
Author(s):  
Jean-Baptiste Ledoux ◽  
Fernando Cruz ◽  
Jèssica Gómez-Garrido ◽  
Regina Antoni ◽  
Julie Blanc ◽  
...  
Keyword(s):  
Evolutionary Ecology ◽  
De Novo ◽  
Western Mediterranean ◽  
De Novo Genome Assembly ◽  
Protein Coding ◽  
The North ◽  
Paramuricea Clavata ◽  
The Mediterranean ◽  
Differential Responses ◽  
The Impact

Abstract The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change.

scholarly journals The genome sequence of the octocoral Paramuricea clavata – a key resource to study the impact of climate change in the Mediterranean

2019 ◽  
Author(s):  
Jean-Baptiste Ledoux ◽  
Fernando Cruz ◽  
Jèssica Gomez-Garrido ◽  
Regina Antoni ◽  
Julie Blanc ◽  
...  
Keyword(s):  
Evolutionary Ecology ◽  
De Novo ◽  
Western Mediterranean ◽  
Protein Coding ◽  
The North ◽  
Paramuricea Clavata ◽  
Long Read ◽  
The Mediterranean ◽  
Differential Responses ◽  
The Impact

AbstractThe octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e. varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes and genetic factors contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo hybrid assembly accounting for 712.4 Mb and 107,682 scaffolds. The contig and scaffold N50 are 15.85 Kb and 17.01 Kb, respectively. Despite of the low contiguity of the assembly, the gene completeness was relatively high, including 86% of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 76,508 protein-coding genes and 85,763 transcripts have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, the genome of P. clavata will help to understand various aspects of its evolutionary ecology and to elaborate effective conservation plans such as active restoration actions to overcome the threats of global change.

scholarly journals Impact of air–sea coupling on the climate change signal over the Iberian Peninsula

2021 ◽  
Author(s):  
Alba de la Vara ◽  
William Cabos ◽  
Dmitry V. Sein ◽  
Claas Teichmann ◽  
Daniela Jacob
Keyword(s):  
Climate Change ◽  
Iberian Peninsula ◽  
Mediterranean Sea ◽  
Large Scale ◽  
Regional Distribution ◽  
Coupled Model ◽  
Climate Change Signal ◽  
The North ◽  
The Mediterranean ◽  
The Impact

AbstractIn this work we use a regional atmosphere–ocean coupled model (RAOCM) and its stand-alone atmospheric component to gain insight into the impact of atmosphere–ocean coupling on the climate change signal over the Iberian Peninsula (IP). The IP climate is influenced by both the Atlantic Ocean and the Mediterranean sea. Complex interactions with the orography take place there and high-resolution models are required to realistically reproduce its current and future climate. We find that under the RCP8.5 scenario, the generalized 2-m air temperature (T2M) increase by the end of the twenty-first century (2070–2099) in the atmospheric-only simulation is tempered by the coupling. The impact of coupling is specially seen in summer, when the warming is stronger. Precipitation shows regionally-dependent changes in winter, whilst a drier climate is found in summer. The coupling generally reduces the magnitude of the changes. Differences in T2M and precipitation between the coupled and uncoupled simulations are caused by changes in the Atlantic large-scale circulation and in the Mediterranean Sea. Additionally, the differences in projected changes of T2M and precipitation with the RAOCM under the RCP8.5 and RCP4.5 scenarios are tackled. Results show that in winter and summer T2M increases less and precipitation changes are of a smaller magnitude with the RCP4.5. Whilst in summer changes present a similar regional distribution in both runs, in winter there are some differences in the NW of the IP due to differences in the North Atlantic circulation. The differences in the climate change signal from the RAOCM and the driving Global Coupled Model show that regionalization has an effect in terms of higher resolution over the land and ocean.

scholarly journals Further spreading of the non-indigenous bryozoan Celleporaria brunnea in the Mediterranean Sea: port to port morphological variations

2015 ◽  
Author(s):  
Jasmine Ferrario ◽  
Agnese Marchini ◽  
Martina Marić ◽  
Dan Minchin ◽  
Anna Occhipinti-Ambrogi
Keyword(s):  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Indigenous Species ◽  
Large Variability ◽  
Morphometric Characters ◽  
Morphological Variations ◽  
The North ◽  
Western Mediterranean Sea ◽  
The Pacific ◽  
The Mediterranean

The Pacific cheilostome bryozoan Celleporaria brunnea (Hincks, 1884), a non-indigenous species already known for the Mediterranean Sea, was recorded in 2013-2014 from nine Italian port localities (Genoa, Santa Margherita Ligure, La Spezia, Leghorn, Viareggio, Olbia, Porto Rotondo, Porto Torres and Castelsardo) in the North-western Mediterranean Sea; in 2014 it was also found for the first time in the Adriatic Sea, in the marina “Kornati”, Biograd na Moru (Croatia). In Italy, specimens of C. brunnea were found in 44 out of 105 samples (48% from harbour sites ad 52% from marinas). These data confirm and update the distribution of C. brunnea in the Mediterranean Sea, and provide evidence that recreational boating is a vector responsible for the successful spread of this species. Previous literature data have shown the existence of differences in orifice and interzooidal avicularia length and width among different localities of the invaded range of C. brunnea. Therefore, measurements of orifice and avicularia were assessed for respectively 30 zooids and 8 to 30 interzooidal avicularia for both Italian and Croatian localities, and compared with literature data, in order to verify the existence of differences in the populations of C. brunnea that could reflect the geographic pattern of its invasion range. Our data show high variability of orifice measures among and within localities: zooids with broader than long orifice coexisted with others displaying longer than broad orifice, or similar values for both length and width. The morphological variation of C. brunnea in these localities, and above all the large variability of samples within single localities or even within colonies poses questions on the reliability of such morphometric characters for inter and intraspecific evaluations.

scholarly journals Contribution of retrotransposition to developmental disorders

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Eugene J. Gardner ◽  
Elena Prigmore ◽  
Giuseppe Gallone ◽  
Petr Danecek ◽  
Kaitlin E. Samocha ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Protein Coding ◽  
Genome Wide ◽  
De Novo Gene ◽  
The Impact ◽  
Transcribed Sequences

Abstract Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

Trade and stowaways: molecular evidence for human-mediated translocation of eastern skinks into the western Mediterranean

2020 ◽  
Vol 41 (1) ◽  
pp. 49-62
Author(s):  
Josep Francesc Bisbal-Chinesta ◽  
Karin Tamar ◽  
Ángel Gálvez ◽  
Luís Albero ◽  
Pablo Vicent-Castelló ◽  
...  
Keyword(s):  
Iberian Peninsula ◽  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Molecular Evidence ◽  
Long Distance ◽  
Human Movements ◽  
Allochthonous Species ◽  
The Mediterranean ◽  
Chalcides Ocellatus ◽  
The Impact

Abstract Human movements in the regions surrounding the Mediterranean Sea have caused a great impact in the composition of terrestrial fauna due to the introductions of several allochthonous species, intentionally or not. Reptiles are one of the groups where this anthropic impact is most evident, owing to the extensive intra-Mediterranean dispersals of recent chronologies. Chalcides ocellatus is a widespread skink with a natural distribution that covers almost the entire Mediterranean Basin. Two hypotheses have been proposed to explain its origin: natural dispersions and human translocations. Previous molecular data suggest the occurrence of a recent dispersal phenomenon across the Mediterranean Sea. In this study we present the first record of this species in the Iberian Peninsula, in Serra del Molar (South-east Spain). We combined molecular analyses and archaeological records to study the origin of this population. The molecular results indicate that the population is phylogenetically closely related to specimens from north-eastern Egypt and southern Red Sea. We suggest that the species arrived at the Iberian Peninsula most likely through human-mediated dispersal by using the trade routes. Between the Iron to Middle Ages, even now, the region surrounding Serra del Molar has been the destination of human groups and commercial goods of Egyptian origins, in which Chalcides ocellatus could have arrived as stowaways. The regional geomorphological evolution would have restricted its expansion out of Serra del Molar. These findings provide new data about the impact of human movements on faunal introductions and present new information relating to mechanisms of long-distance translocations.

Coastal climatology of the North-Western Mediterranean area for long-term and short-term risk assessment.

2020 ◽  
Author(s):  
Carlo Brandini ◽  
Stefano Taddei ◽  
Valentina Vannucchi ◽  
Michele Bendoni ◽  
Bartolomeo Doronzo ◽  
...  
Keyword(s):  
Risk Assessment ◽  
High Resolution ◽  
Mediterranean Area ◽  
Western Mediterranean ◽  
Climate Trends ◽  
Short Term ◽  
The North ◽  
The Mediterranean ◽  
North Western

<p>In this work we present the results obtained through a dynamic downscaling of the ERA5 reanalysis dataset (hindcast) of ECMWF, using high-resolution meteorological and wave models defined on unstructured computation grids along the Mediterranean coasts, with a particular focus on the North-Western Mediterranean area. Downscaling of the ERA5 meteorological data is obtained through the BOLAM and MOLOCH models (up to a resolution of 2.5 km) which force an unstructured WW3 model with a resolution of up to 500 m along the coast. Models were validated through available meteorological stations, wave buoy data and X-band wave radars, the latter for the purposes of wave spectra validation.</p><p>On the one hand, this allowed, by extracting the time series of some attack parameters of the waves along the coast, and according to the type of coast (rocky coasts, sandy coasts, coastal structures etc.), to compute the return periods and to characterize the impact of any individual storm. On the other hand, it is possible to highlight some trends observed in the last 30 years, during which recent research is showing an increasing evidence  of some changes in global circulation at regional to local scales. These changes also include effects of wind rotation, wave regimes, storm surges, wave-induced coastal currents and coastal morphodynamics. For example, in the North-Western Mediterranean extreme events belonging to cyclonic weather-types circulation with stronger S-SE components (like the storm of October 28-30th 2018 and many others), rather than events associated with perturbations of Atlantic origin and zonal circulation, are becoming more frequent. These long-term wind/wave climate trends can have consequences not only in the assessment of long-term risk due to main morphodynamic variations (ie. coastal erosion), but also in the short-term risk assessment.</p><p>This work was funded by the EU MAREGOT project (2017-2020) and ECMWF Special Project spitbran  “Evaluation of coastal climate trends in the Mediterranean area by means of high-resolution and multi-model downscaling of ERA5 reanalysis” (2018-2020).</p>

Two live sightings of Sowerby's beaked whale (Mesoplodon bidens) from the western Mediterranean (Tyrrhenian Sea)

2017 ◽  
Vol 98 (5) ◽  
pp. 1003-1009 ◽  
Author(s):  
Luca Bittau ◽  
Mattia Leone ◽  
Adrien Gannier ◽  
Alexandre Gannier ◽  
Renata Manconi
Keyword(s):  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Tyrrhenian Sea ◽  
Beaked Whale ◽  
Long Distance ◽  
The North ◽  
Western Mediterranean Sea ◽  
Beaked Whales ◽  
Species Groups ◽  
The Mediterranean

Sowerby's beaked whale (Mesoplodon bidens) was previously known in the Mediterranean Sea from a single live stranding of two individuals in the French Riviera. We report here on two live sightings in the western Mediterranean, central-western Tyrrhenian Sea off eastern Corsica (Montecristo Trough) and off eastern Sardinia (Caprera Canyon) in 2010 and 2012, respectively. In both cases single individuals, possibly the same individual, occurred within groups of Cuvier's beaked whales (Ziphius cavirostris) suggesting inter-specific interactions. Based on our close observations of mixed-species groups of Sowerby's and Cuvier's beaked whales, we hypothesize that some previous long-distance sightings of beaked whales in the Mediterranean may not be reliably attributed to Z. cavirostris. The present sightings and previous live stranding indicate that the western Mediterranean Sea is the easternmost marginal area of M. bidens within the North Atlantic geographic range. Notes on behaviour are also provided.

Age-related trends in otolith chemistry of Merluccius merluccius from the north-eastern Atlantic Ocean and the western Mediterranean Sea

2005 ◽  
Vol 56 (5) ◽  
pp. 599 ◽  
Author(s):  
B. Morales-Nin ◽  
S. C. Swan ◽  
J. D. M. Gordon ◽  
M. Palmer ◽  
A. J. Geffen ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Western Mediterranean ◽  
Elemental Concentrations ◽  
The Core ◽  
The North ◽  
Western Mediterranean Sea ◽  
Growth Increments ◽  
Age Related ◽  
North Eastern ◽  
The Mediterranean

Sagittal otoliths of European hake obtained from five geographic locations in the north-eastern Atlantic and western Mediterranean were examined using laser ablation and inductively coupled plasma mass spectrometry. Otolith sections were analysed for the isotopes 24Mg, 55Mn, 66Zn, 85Rb, 86Sr, 138Ba and 208Pb, measured relative to 43Ca counts. These analyses considered only age 0 (core area) and ages 1 to 3. Age-related trends in otolith elemental composition were observed in hake from all areas, but were masked by variability between locations. Elemental concentrations generally decreased outside the core, with some increase at age 3. The composition of the otolith core was very distinct from that of the other growth increments. In the Mediterranean, part of this differentiation was a result of Mn, which was present in the core at high concentrations compared with the rest of the otolith. Mediterranean otoliths also had higher concentrations of Sr, Zn and Ba in the core. For most samples a similar trend was observed, although samples from one of the Mediterranean areas showed some differences, mainly in the concentrations of Mg and Sr. These results provide new empirical evidence of the variation in elemental concentrations across hake otoliths with age, at least throughout the first 3 years of life.

scholarly journals Determining the impact of putative loss-of-function variants in protein-coding genes

2017 ◽  
Author(s):  
Suganthi Balasubramanian ◽  
Yao Fu ◽  
Mayur Pawashe ◽  
Patrick McGillivray ◽  
Mike Jin ◽  
...  
Keyword(s):  
De Novo ◽  
Mendelian Disease ◽  
Loss Of Function ◽  
Homozygous State ◽  
Driver Genes ◽  
Protein Coding ◽  
Disease Gene Discovery ◽  
Human Genes ◽  
Using Data ◽  
The Impact

AbstractVariants predicted to result in the loss of function (LoF) of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (Annotation of Loss-of-Function Transcripts), a method to annotate and predict the disease-causing potential of LoF variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between LoF variants deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied to de novo pLoF variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in > 6,500 cancer exomes shows that pLoF variants predicted to be deleterious by ALoFT are enriched in known driver genes.

scholarly journals Assimilation of wind data from airborne Doppler cloud-profiling radar in a kilometre-scale NWP system

2018 ◽  
Author(s):  
Mary Borderies ◽  
Olivier Caumont ◽  
Julien Delanoë ◽  
Véronique Ducrocq ◽  
Nadia Fourrié
Keyword(s):  
Positive Impact ◽  
Heavy Precipitation ◽  
Mediterranean Area ◽  
Western Mediterranean ◽  
Wind Data ◽  
Heavy Rainfall Event ◽  
Rain Gauges ◽  
The North ◽  
W Band ◽  
The Impact

Abstract. The article reports on the impact of the assimilation of wind vertical profile data in a kilometre-scale NWP system on predicting heavy precipitation events in the north-western Mediterranean area. The data collected in diverse conditions by the airborne W-band radar RASTA (Radar Airborne System Tool for Atmosphere) during a 45-day period are assimilated in the 3-h 3DVar assimilation system of AROME. The impact of the length of the assimilation window is investigated. The data assimilation experiments are performed for a heavy rainfall event, which occurred over south-eastern France on 26 September 2012 (IOP7a), and over a 45-day cycled period. During IOP7a, results indicate that the quality of the rainfall accumulation forecasts increases with the length of the assimilation window. By contrast, on the 45-day period, the best scores against rain gauges measurements are reached with a 1 hour assimilation window, which recommends to use observations with a small period centred on the assimilation time. The positive impact of the assimilation of RASTA wind data is particularly evidenced for the IOP7a case since results indicate an improvement in the predicted wind at short term ranges (2 hours and 3 hours) and in the 12-hour precipitation forecasts. However, on the 45-day cycled period, the comparison against other assimilated observations shows an overall neutral impact. Results are still encouraging since a slight positive improvement in the 6-, 9- and 12-hour precipitation forecasts of heavier rainfall was demonstrated.

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