An ecological framework for the development of a national MPA network

Isolated marine protected areas (MPAs) may not be enough to sustain viable populations of marine species, particularly the many small coastal MPAs which resulted due to social, economic and political constraints. Properly designed MPA networks can circumvent such limitations due to their potential synergistic positive effects, but this crucial step is frequently obstructed by lack of baseline ecological information. In this paper, we use systematic conservation planning on European Nature Information System coastal habitat information available for Portugal to demonstrate how an ecologically coherent nation-wide MPA network can be designed. We used the software Marxan to obtain near optimal solutions for each of three pre-determined conservation targets (10%, 30% and 50% protection) while maintaining the cost of including conservation units as low as possible. Marxan solutions were subsequently optimized with MinPatch by keeping each MPA above a minimum size that reflects the existing information on habitat use by some key marine fishes. Results show that 10% protection for all habitats would only require a relativelly small increase in the number (from 6 to 10) and area (from 479 km(2) to 509 km(2)) of already existing MPAs in mainland Portugal whereas substantial increases would be required to achieve the 50% target. This rather simple approach offers the added benefit of allowing design improvement as more relevant ecological information becomes available, including deeper habitat mapping across the whole continental shelf, allowing a coherent, adaptive and inclusive optimal MPA network to be designed.info:eu-repo/semantics/publishedVersio

A fine-tuned global distribution dataset of marine forests

Species distribution records are a prerequisite to follow climate-induced range shifts across space and time. However, synthesizing information from various sources such as peer-reviewed literature, herbaria, digital repositories and citizen science initiatives is not only costly and time consuming, but also challenging, as data may contain thematic and taxonomic errors and generally lack standardized formats. We address this gap for important marine ecosystem-structuring species of large brown algae and seagrasses. We gathered distribution records from various sources and provide a fine-tuned dataset with ~2.8 million dereplicated records, taxonomically standardized for 682 species, and considering important physiological and biogeographical traits. Specifically, a flagging system was implemented to signal potentially incorrect records reported on land, in regions with limiting light conditions for photosynthesis, and outside the known distribution of species, as inferred from the most recent published literature. We document the procedure and provide a dataset in tabular format based on Darwin Core Standard (DwC), alongside with a set of functions in R language for data management and visualization.FCT: (SFRH/BPD/111003/2015) / (SFRH/BSAB/150485/2019) / (SFRH/BD/144878/2019)(PTDC/MAREST/6053/2014) / MARFOR (BIODIVERSA/004/2015) / UIDB/04326/2020info:eu-repo/semantics/publishedVersio

Small coastal marine protected areas offer recurring, seasonal protection to the common stingray (Dasyatis pastinaca)

Marine protected areas (MPAs) are a crucial tool in safeguarding marine biodiversity. However, elasmobranchs are often not the primary protection target of MPAs, and their contribution to protect these species remains to be better understood. In this study we examine the movement patterns of common stingrays in the Professor Luiz Saldanha marine park, a Portuguese temperate coastal MPA. Using acoustic telemetry, we tagged 31 common stingrays and analyzed their spatial and temporal distribution within the MPA and adjacent areas using a long-term data set. Our findings indicate that this species exhibits seasonal site fidelity, with greater presence during the colder months and reduced presence during warmer months. Space use areas did not exceed the size of the fully protected area, and nocturnal and crepuscular activity was significantly higher than during daytime. Additionally, we observed that most individuals seasonally migrated between this MPA and the nearby Sado estuary, likely to reproduce in the latter. These results demonstrate the site fidelity of common stingrays to an area within the marine park, however the protection provided is only seasonal. Seasonal protection of the movement corridor between the marine park and the estuary would improve the management of this species.La Caixa FoundationLCF/BQ/DI20/11780001, Fundacao para a Ciencia e a Tecnologia (FCT) POSEUR-03-2215-FC-000047info:eu-repo/semantics/publishedVersio

Diel and seasonal changes in the spatial behaviour of a soft-sediment fish (Solea senegalensis) inside a marine reserve

The protection provided by marine reserves directly depends on the short and long-term movement patterns of local organisms. Although there has been an increase in research assessing the behavioural patterns of fishes in reef-based habitats, there is still a paucity of studies addressing the benefits of marine protected areas (MPAs) for soft-sediment species. Here, we investigated both diel and seasonal shifts in spatial behaviour of the Senegalese sole, Solea senegalensis, within a recently-established marine reserve using long-term passive acoustic telemetry. Results showed variable levels of site attachment, with nearly half of the fish (n = 8) disappearing from the monitored area within 30 days, and the remaining (n = 9) being detected for periods up to 293 days and spending 95% of their time within an average area of 0.88 ± 0.46 km2. Although detection frequency was higher during daytime periods, the larger home range areas and greater movement observed during nighttime periods are consistent with a nocturnal activity regime, which might increase the vulnerability of S. senegalensis to illegal fishing. Additionally, patterns observed during the spawning season suggest the existence of shifts in habitat use linked with reproductive activity, opening the door to further research on soles' fine-scale interaction dynamics. Overall, this study provides novel insights into the ecology of a flatfish species and suggests that small no-take areas encompassing suitable soft-sediment habitats can offer adequate protection to at least part of the Senegalese sole population.EU LIFEBIOMARES Project (LIFE06 NAT/P/000192)info:eu-repo/semantics/publishedVersio

Multiple loci within the major histocompatibility complex confer risk of psoriasis

Psoriasis is a common inflammatory skin disease characterized by thickened scaly red plaques. Previously we have performed a genome-wide association study (GWAS) on psoriasis with 1,359 cases and 1,400 controls, which were genotyped for 447,249 SNPs. The most significant finding was for SNP rs12191877, which is in tight linkage disequilibrium with HLA-Cw*0602, the consensus risk allele for psoriasis. However, it is not known whether there are other psoriasis loci within the MHC in addition to HLA-C. In the present study, we searched for additional susceptibility loci within the human leukocyte antigen (HLA) region through in-depth analyses of the GWAS data; then, we followed up our findings in an independent Han Chinese 1,139 psoriasis cases and 1,132 controls. Using the phased CEPH dataset as a reference, we imputed the HLA-Cw*0602 in all samples with high accuracy. The association of the imputed HLA-Cw*0602 dosage with disease was much stronger than that of the most significantly associated SNP, rs12191877. Adjusting for HLA-Cw*0602, there were two remaining association signals: one demonstrated by rs2073048 (p = 2×10(−6), OR = 0.66), located within c6orf10, a potential downstream effecter of TNF-alpha, and one indicated by rs13437088 (p = 9×10(−6), OR = 1.3), located 30 kb centromeric of HLA-B and 16 kb telomeric of MICA. When HLA-Cw*0602, rs2073048, and rs13437088 were all included in a logistic regression model, each of them was significantly associated with disease (p = 3×10(−47), 6×10(−8), and 3×10(−7), respectively). Both putative loci were also significantly associated in the Han Chinese samples after controlling for the imputed HLA-Cw*0602. A detailed analysis of HLA-B in both populations demonstrated that HLA-B*57 was associated with an increased risk of psoriasis and HLA-B*40 a decreased risk, independently of HLA-Cw*0602 and the C6orf10 locus, suggesting the potential pathogenic involvement of HLA-B. These results demonstrate that there are at least two additional loci within the MHC conferring risk of psoriasis

Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants

Establishing the age of each mutation segregating in contemporary human populations is important to fully understand our evolutionary history1,2 and will help facilitate the development of new approaches for disease gene discovery3. Large-scale surveys of human genetic variation have reported signatures of recent explosive population growth4-6, notable for an excess of rare genetic variants, qualitatively suggesting that many mutations arose recently. To more quantitatively assess the distribution of mutation ages, we resequenced 15,336 genes in 6,515 individuals of European (n=4,298) and African (n=2,217) American ancestry and inferred the age of 1,146,401 autosomal single nucleotide variants (SNVs). We estimate that ~73% of all protein-coding SNVs and ~86% of SNVs predicted to be deleterious arose in the past 5,000-10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs compared to other genes. Furthermore, European Americans had an excess of deleterious variants in essential and Mendelian disease genes compared to African Americans, consistent with weaker purifying selection due to the out-of-Africa dispersal. Our results better delimit the historical details of human protein-coding variation, illustrate the profound effect recent human history has had on the burden of deleterious SNVs segregating in contemporary populations, and provides important practical information that can be used to prioritize variants in disease gene discovery

Biologically meaningful distribution models highlight the benefits of the Paris Agreement for demersal fishing targets in the North Atlantic Ocean

Aim: With climate change challenging marine biodiversity and resource management, it is crucial to anticipate future latitudinal and depth shifts under contrasting global change scenarios to support policy-relevant biodiversity impact assessments [e.g., Intergovernmental Panel on Climate Change (IPCC)]. We aim to demonstrate the benefits of complying with the Paris Agreement (United Nations Framework Convention on Climate Change) and limiting environmental changes, by assessing future distributional shifts of 10 commercially important demersal fish species. Location: Northern Atlantic Ocean. Time period: Analyses of distributional shifts compared near present-day conditions (2000–2017) with two Representative Concentration Pathway (RCP) scenarios of future climate changes (2090–2100): one following the Paris Agreement climate forcing (RCP2.6) and another without stringent mitigation measures (RCP8.5). Major taxa studied: Demersal fish. Methods: We use machine learning distribution models coupled with biologically meaningful predictors to project future latitudinal and depth shifts. Structuring projections with information beyond temperature-based predictors allowed us to encompass the physiological limitations of species better. Results: Our models highlighted the additional roles of temperature, primary productivity and dissolved oxygen in shaping fish distributions (average relative contribution to the models of 32.12 ± 10.24, 15.6 ± 7.5 and 12.1 ± 6.1%, respectively). We anticipated a generalized trend of poleward shifts in both future scenarios, with aggravated changes in suitable area with RCP8.5 (average area loss with RCP2.6 = 13.3 ± 4.1%; RCP8.5 = 40.9 ± 13.3%). Shifts to deeper waters were also predicted to be of greater magnitude with RCP8.5 (average depth gain = 25.4 ± 21.5 m) than with RCP2.6 (average depth gain = 10.4 ± 7.9 m). Habitat losses were projected mostly in the Mediterranean, Celtic and Irish Seas, the southern areas of the North Sea and along the NE coast of North America. Main conclusions: Inclusion of biologically meaningful predictors beyond temperature in species distribution modelling can improve predictive performances. Limiting future climate changes by complying with the Paris Agreement can translate into reduced distributional shifts, supporting biodiversity conservation and resource management.MAR2020; European Maritime and Fisheries Fund; Fundação para a Ciência e a Tecnologiainfo:eu-repo/semantics/submittedVersio

Biophysical modelling and graph theory identify key connectivity hubs in the Mediterranean marine reserve network

Connectivity plays a key role in the effectiveness of MPA networks ensuring metapopulation resilience through gene flow and recruitment effect. Yet, despite its recognized importance for proper MPA network functioning, connectivity is not often assessed and is very seldomly used in marine spatial planning. Here, we combined biophysical modelling with graph theory to identify Mediterranean marine reserves that support connectivity between different ecoregions through stepping-stone processes, thus preventing network fragmentation, and those that have an important role as propagule source areas contributing to the recruitment and rescue effects. We identified 19 reserves that play a key role towards the functioning of the network, serving either as stepping-stones or as propagule sources, yet with distinct patterns between ecological groups with contrasting propagule duration (PD). The Cote D'Azur marine reserves are important both as stepping-stones and propagule sources for several ecological groups. Also, key is the Capo Rizzuto and Plemmirio marine reserves due to their role as stepping stones between different marine ecoregions, particularly for species with longer PD (Pisces, Crustacea and Echinodermata). These results provide stakeholders and managers with crucial information for the implementation and management of an efficient marine reserve network in the Mediterranean.info:eu-repo/semantics/publishedVersio

Genetic prediction of complex traits: integrating infinitesimal and marked genetic effects

Genetic prediction for complex traits is usually based on models including individual (infinitesimal) or marker effects. Here, we concentrate on models including both the individual and the marker effects. In particular, we develop a ''Mendelian segregation'' model combining infinitesimal effects for base individuals and realized Mendelian sampling in descendants described by the available DNA data. The model is illustrated with an example and the analyses of a public simulated data file. Further, the potential contribution of such models is assessed by simulation. Accuracy, measured as the correlation between true (simulated) and predicted genetic values, was similar for all models compared under different genetic backgrounds. As expected, the segregation model is worthwhile when markers capture a low fraction of total genetic variance. (Résumé d'auteur