Food for Thought Integrating population genomics and biophysical models towards evolutionary-based fisheries management

Overfishing and rapid environmental shifts pose severe challenges to the resilience and viability of marine fish populations. To develop and implement measures that enhance species’ adaptive potential to cope with those pressures while, at the same time, ensuring sustainable exploitation rates is part of the central goal of fisheries management. Here, we argue that a combination of biophysical modelling and population genomic assessments offer ideal management tools to define stocks, their physical connectivity and ultimately, their short-term adaptive potential. To date, biophysical modelling has often been confined to fisheries ecology whereas evolutionary hypotheses remain rarely considered. When identified, connectivity patterns are seldom explored to understand the evolution and distribution of adaptive genetic variation, a proxy for species’ evolutionary potential. Here, we describe a framework that expands on the conventional seascape genetics approach by using biophysical modelling and population genomics. The goals are to identify connectivity patterns and selective pressures, as well as putative adaptive variants directly responding to the selective pressures and, ultimately, link both to define testable hypotheses over species response to shifting ecological conditions and overexploitation

Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases

Hydrogenases are efficient biocatalysts for H2 production and oxidation with various potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both production and oxidation processes—albeit primarily biased to the latter—but suffer from being sensitive to O2.[NiFeSe] hydrogenases are a subclass of [NiFe] hydrogenases with, usually, an increased insensitivity to aerobic environments. In this study we aim to understand the structural causes of the low sensitivity of a [NiFeSe]-hydrogenase, when compared with a [NiFe] class enzyme, by studying the diffusion of O2. To unravel the differences between the two enzymes, we used computational methods comprising Molecular Dynamics simulations with explicit O2 and Implicit Ligand Sampling methodologies. With the latter, we were able to map the free energy landscapes for O2 permeation in both enzymes. We derived pathways from these energy landscapes and selected the kinetically more relevant ones with reactive flux analysis using transition path theory. These studies evidence the existence of quite different pathways in both enzymes and predict a lower permeation efficiency for O2 in the case of the [NiFeSe]-hydrogenase when compared with the [NiFe] enzyme. These differences can explain the experimentally observed lower inhibition by O2 on [NiFeSe]-hydrogenases, when compared with [NiFe]-hydrogenases. A comprehensive map of the residues lining the most important O2 pathways in both enzymes is also presented.publishersversionpublishe

Linking epigenetics and biological conservation: Towards a conservation epigenetics perspective

International audience1. Biodiversity conservation is a global issue where the challenge is to integrate all levels of biodiversity to ensure the long-term evolutionary potential and resilience of biological systems. Genetic approaches have largely contributed to conservation biology by defining "conservation entities" accounting for their evolutionary history and adaptive potential, the so-called evolutionary significant units (ESUs). Yet, these approaches only loosely integrate the short-term ecological history of organisms. 2. Here, we argue that epigenetic variation, and more particularly DNA methylation, represents a molecular component of biodiversity that directly links the genome to the environment. As such, it provides the required information on the ecological background of organisms for an integrative field of conservation biology. 3. We synthesize knowledge about the importance of epigenetic mechanisms in (a) orchestrating fundamental development alternatives in organisms, (b) enabling individuals to respond in real-time to selection pressures and (c) improving ecosystem stability and functioning. 4. Using practical examples in conservation biology, we illustrate the relevance of DNA methylation (a) as biomarkers of past and present environmental stress events as well as biomarkers of physiological conditions of individuals; (b) for documenting the ecological structuring/clustering of wild populations and hence for better integrating ecology into ESUs; (c) for improving conservation transloca-tions; and (d) for studying landscape functional connectivity. 5. We conclude that an epigenetic conservation perspective will provide environmental managers the possibility to refine ESUs, to set conservation plans taking into account the capacity of organisms to rapidly cope with environmental changes, and hence to improve the conservation of wild populations. K E Y W O R D S conservation, DNA methylation, ecological timescales, epigenetic, evolutionary significant unit

Forecasting shifts in habitat suitability across the distribution range of a temperate small pelagic fish under different scenarios of climate change

Climate change often leads to shifts in the distribution of small pelagic fish, likely by changing the match-mismatch dynamics between these sensitive species within their environmental optima. Using present-day habitat suitability, we projected how different scenarios of climate change (IPCC Representative Concentration Pathways 2.6, 4.5 and 8.5) may alter the large scale distribution of European sardine Sardina pilchardus (a model species) by 2050 and 2100. We evaluated the variability of species-specific environmental optima allowing a comparison between present-day and future scenarios. Regardless of the scenario, sea surface temperature and salinity and the interaction between current velocity and distance to the nearest coast were the main descriptors responsible for the main effects on sardine's distribution. Present-day and future potential “hotspots” for sardine were neritic zones ( 20 (PSU), on average. Most variability in projected shifts among climatic scenarios was in habitats with moderate to low suitability. By the end of this century, habitat suitability was projected to increase in the Canary Islands, Iberian Peninsula, central North Sea, northern Mediterranean, and eastern Black Sea and to decrease in the Atlantic African coast, southwest Mediterranean, English Channel, northern North Sea and Western U.K. A gradual poleward-eastward shift in sardine distribution was also projected among scenarios. This shift was most pronounced in 2100 under RCP 8.5. In that scenario, sardines had a 9.6% range expansion which included waters along the entire coast of Norway up and into the White Sea. As habitat suitability is mediated by the synergic effects of climate variability and change on species fitness, it is critical to apply models with robust underlying species-habitat data that integrate knowledge on the full range of processes shaping species productivity and distribution.Preprin

Distribution of genetic diversity reveals colonization patterns and philopatry of the loggerhead sea turtles across geographic scales.

Understanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species' evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species' evolutionary potential

Optimization of iron-ZIF-8 catalysts for degradation of tartrazine in water by Fenton-like reaction

Optimization of iron zeolitic imidazole framework-8 (FeZIF-8) nanoparticles, as heterogeneous catalysts, were synthesized and evaluated by the Fenton-like reaction for to degrade tartrazine (Tar) in aqueous environment. To achieve this, ZIF-8 nanoparticles were modified with different iron species (Fe2+ or Fe3O4), and subsequently assessed through the Fenton-like oxidation. The effect of different parameters such as the concentration of hydrogen peroxide, the mass of catalyst and the contact time of reaction on the degradation of Tar by Fenton-like oxidation was studied by using the Box-Behnken design (BBD). The BBD model indicated that the optimum catalytic conditions for Fenton-like reaction with an initial pollutant concentration of 30ppm at pH 3.0 were T=40°C and 12mM of H2O2, 2g/L of catalyst and 4h of reaction. The maximum Tar conversion value achieved with the best catalyst, Fe1ZIF-8, was 66.5% with high mineralization (in terms of decrease of total organic carbon TOC), 44.2%. To assess phytotoxicity, the germination success of corn kernels was used as an indicator in the laboratory. The results show that the catalytic oxidation by Fenton-like reaction using heterogeneous iron ZIF-8 catalysts is a viable alternative for treating contaminated effluents with organic pollutants and highlighted the importance of the validation of the optimized experimental conditions by mathematical models.O.A. thanks to ERASMUS + Program for the mobility Ph.D. grant and A.R.B. thanks to Fundação para Ciência e Tecnologia, FCT (Portugal) for her Ph.D. grant (SFRH/BD/141058/2018). This research work has been funded by national funds funded through FCT/MCTES (PIDDAC) over the projects: LA/P/0045/2020 (ALiCE), UIDB/50020/2020 and UIDP/50020/2020 (LSRE-LCM), Centre of Chemistry (UID/QUI/0686/2020), CEB (UIDB/04469/2020) and project BioTecNorte (operation NORTE-01-0145-FEDER-000004), supported by the Northern Portugal Regional Operational Program (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).info:eu-repo/semantics/publishedVersio

Portuguese propolis: a source of valuable bioactivities

To FEDER/COMPETE/POCI– Operational Competitiveness and Internationalization Programme, under Project POCI-01-0145-FEDER-006958 and FCT - Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013

Population genetics and demography of the endemic mouse species of Cyprus, Mus cypriacus

Mus cypriacus is one of three small palaeoendemic mammals that have survived the Mediterranean islands’ anthropization. This species, endemic to Cyprus, was described in 2006 and stands out as one of the last mammal species to have been discovered in Europe. Despite scarce data on its genetics, ecology, and life-history traits, Mus cypriacus is assessed as Least Concern LC in the IUCN Red List, partly due to its morphological similarity with the sympatric house mouse that prevented earlier identification. Our study uses mitochondrial and microsatellite markers to investigate this small rodent's population genetic structure and diversity. Our analysis did not identify any population genetic structure and suggested a high genetic diversity across Cyprus. When inferring habitat preference using sample locations, it appeared that M. cypriacus utilizes a diverse variety of habitats, covering more than 80% of the island. Although these results are encouraging for the conservation status of the species, they still need to be cautiously applied as potential threats may arise due to increasing habitat destruction and changes in land use. Consequently, our encouraging results should be applied judiciously. Additional ecological data are urgently needed to gain a more comprehensive understanding of this inconspicuous endemic species