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Quality-control tests for OC4, OC5 and NIR-red satellite chlorophyll-a algorithms applied to coastal waters
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Reliable satellite estimates of chlorophyll-a concentration (Chl-a) are needed in coastal waters for applications such as eutrophication monitoring. However, because of the optical complexity of coastal waters, retrieving accurate Chl-a is still challenging. Many algorithms exist and give quite different performance for different optical conditions but there is no clear definition of the limits of applicability of each algorithm and no clear basis for deciding which algorithm to apply to any given image pixel (reflectance spectrum). Poor quality satellite Chl-a data can easily reach end-users. To remedy this and provide a clear decision on when a specific Chl-a algorithm can be used, we propose simple quality control tests, based on MERIS water leaving reflectance (ρw) bands, to determine on a pixel-by-pixel basis if any of three popular and complementary algorithms can be used. The algorithms being tested are: 1. the OC4 blue-green band ratio algorithm which was designed for open ocean waters; 2. the OC5 algorithm which is based on look-up tables and corrects OC4 overestimation in moderately turbid waters and 3. a near infrared-red (NIR-red) band ratio algorithm designed for eutrophic waters. Using a dataset of 348 in situ Chl-a / MERIS matchups, the conditions for reliable performance of each of the selected algorithms are determined. The approach proposed here looks for the best compromise between the minimization of the relative difference between In situ measurements and satellite estimations and the number of pixels processed. Conditions for a reliable application of OC4 and OC5 depend on ρw412/ρw443 and ρw560, used as proxies of coloured dissolved organic matter and suspended particulate matter (SPM), as compared to ρw560/ρw490, used as a proxy for Chl-a. Conditions for reliable application of the NIR-red band ratio algorithm depend on Chl-a and SPM. These conditions are translated into pixel-based quality control (QC) tests with appropriately chosen thresholds. Results show that by removing data which do not pass QC, the performance of the three selected algorithms is significantly improved. After combining these algorithms, 70\% of the dataset could be processed with a median absolute percent difference of 30.5\%. The QC tests and algorithm merging methodology were then tested on four MERIS images of European waters. The OC5 algorithm was found to be suitable for most pixels, except in very turbid and eutrophic waters along the coasts where the NIR-red band ratio algorithm helps to fill the gap. Finally, a test was performed on an OLCI-S3A image. Although some validations of water reflectance are still needed for the OLCI sensors, results show similar behavior to the MERIS applications which suggests that when applied to OLCI data the present methodology will help to accurately estimate Chl-a in coastal waters for the next decade.
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RBINS Staff Publications 2022
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Sand and Sustainability: 10 strategic recommendations to avert a crisis. GRID-Geneva, United Nations Environment Programme
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RBINS Staff Publications 2022 OA
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Seabed CommUnity Initiative: communicating sustainability challenges of marine sand use in a changing world <Seabed4U>. Final Report.
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RBINS Staff Publications 2022 OA
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Residual currents and transports near the C-Power and Norther wind farms
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RBINS Staff Publications 2022 OA
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Tremadocian and Floian (Ordovician) linguliformean brachiopods from the Stavelot–Venn Massif (Avalonia; Belgium and Germany)
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RBINS Staff Publications 2022
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One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus
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Bacterial endosymbionts of the groups Wolbachia , Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia , ‘Candidatus Tisiphia’ (formerly Torix group Rickettsia ), Cardinium and Rhabdochlamydia . Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host–endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia , ‘Ca. Tisiphia’ and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium , ‘Ca. Tisiphia’ and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary ‘contact-tracing’ tool.
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RBINS Staff Publications 2023
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Ocean acidification modifies behaviour of shelf seabed macrofauna: A laboratory study on two ecosystem engineers, Abra alba and Lanice conchilega
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The feeding activity and burrow ventilation by benthic invertebrates importantly affect the biodiversity and functioning of seafloor sediments. Here we investigated how ocean acidification can modify these behavioural activities in two common and abundant macrofaunal ecosystem engineering species in temperate continental shelf communities: the white furrow shell Abra alba and the sand mason Lanice conchilega. Using time-lapse imagery and sediment porewater hydraulic signatures we show that both species adapt their behaviour in response to predicted future pH conditions (-0.3 units). During a three-week laboratory experiment, A. alba reduced the duration per feeding event when suspension and deposit feeding (by 86 and 53%, respectively), and almost completely ceased suspension feeding under reduced seawater pH in comparison to ambient seawater pH (pH ~ 8.2). This behavioural change reduces the intake of low pH water during feeding and respiration. L. conchilega increased its piston-pumping frequency by 30 and 52%, respectively, after one and two weeks of exposure to future pH conditions (-0.3 units) relative to ambient conditions. This change in irrigation activity suggests higher metabolic demands under low seawater pH, and also extended low water column pH conditions deeper into the seafloor. Because the distribution of other populations depends on the physicochemical setting by our focal species, we argue that the demonstrated behavioural plasticity will likely have cascading effects on seafloor diversity and functioning, highlighting the complexity of how ocean acidification, and climate change in general, will affect seafloor ecology.
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RBINS Staff Publications 2023
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Challenges and a call to action for protecting European red wood ants
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Red wood ants (RWAs) are a group of keystone species widespread in temperate and boreal forests of the Northern Hemisphere. Despite this, there is increasing evidence of local declines and extinctions. We reviewed the current protection status of RWAs throughout Europe and their International Union for the Conservation of Nature (IUCN) threat classification. Only some RWA species have been assessed at a global scale, and not all national red lists of the countries where RWAs are present include these species. Different assessment criteria, inventory approaches, and risk categories are used in different countries, and data deficiency is frequent. Legislative protection is even more complex, with some countries protecting RWAs implicitly together with the wildlife fauna and others explicitly protecting the whole group or particular species. This complexity often occurs within countries, for example, in Italy, where, outside of the Alps, only the introduced species are protected, whereas the native species, which are in decline, are not. Therefore, an international, coordinated framework is needed for the protection of RWAs. This first requires that the conservation target should be defined. Due to the similar morphology, complex taxonomy, and frequent hybridization, protecting the entire RWA group seems a more efficient strategy than protecting single species, although with a distinction between autochthonous and introduced species. Second, an update of the current distribution of RWA species is needed throughout Europe. Third, a protection law cannot be effective without the collaboration of forest managers, whose activity influences RWA habitat. Finally, RWA mounds offer a peculiar microhabitat, hosting a multitude of taxa, some of which are obligate myrmecophilous species on the IUCN Red List. Therefore, RWAs’ role as umbrella species could facilitate their protection if they are considered not only as target species but also as providers of species-rich microhabitats.
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RBINS Staff Publications 2022
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Un crâne de crocodilien du Paléocène inférieur de Chine recule l'apparition des crocodyloïdes en Asie
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Les plus anciens crocodiliens (Crocodylia) d’Asie ne sont représentés jusqu’à présent que par des alligatoroïdes et des planocraniidés. Bien que les crocodyloïdes ne soient pas connus avec certitude avant l’Éocène supérieur, l’hypothèse a été émise que des crocodyloïdes basaux de type Asiatosuchus étaient originaires d’Asie avant la fin du Paléocène. Nous décrivons ici un nouveau crocodyloïde fossile provenant du Paléocène inférieur du Bassin de Qianshan, province d’Anhui, Chine. Le crâne et le fragment de mâchoire inférieure associé présentent plusieurs caractéristiques typiques de crocodiliens juvéniles. Ils présentent également une combinaison de caractères non observés dans aucun autre taxon, ce qui justifie l’érection d’une nouvelle espèce et d’un nouveau genre. Les affinités phylogénétiques sont testées dans des analyses basées sur deux matrices de caractères récentes d’Eusuchia. Pour évaluer l’effet des caractéristiques juvéniles sur le résultat des analyses phylogénétiques, des spécimens juvéniles des crocodiliens actuels Alligator mississippiensis et Crocodylus niloticus ont été analysés de la même manière, montrant que l’effet de leur stade ontogénétique sur leur position dans l’arbre est minime. Nos analyses indiquent que le nouveau taxon de Qianshan occupe une position basale au sein des Crocodyloidea. La présence de ces derniers en Asie est donc reculée au Paléocène inférieur, soit 15 à 20 millions d’années plus tôt que ce que l’on pensait auparavant. De plus, nos résultats corroborent les hypothèses précédentes d’une route de dispersion paléocène des crocodyloïdes de type Asiatosuchus de l’Asie vers l’Europe.
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RBINS Staff Publications 2022 OA
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On a small collection of sea cucumbers from the Mediterranean continental slope with the first record and re-description of Pseudothyone serrifera (Oestergren, 1898) (Holothuroidea: Dendrochirotida), a new species for the Mediterranean Sea
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