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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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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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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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RBINS Staff Publications 2022 OA
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Production de meules va-et-vient au Hallstatt final – La Tène ancienne au « Camp de Macquenoise » à Saint-Michel (Aisne) et contextes d’utilisation régionaux.
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RBINS Staff Publications 2023
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Pterosaur melanosomes support signalling functions for early feathers
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RBINS Staff Publications 2022
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The ants of the Galápagos Islands (Hymenoptera, Formicidae): a historical overview, checklist, and identification key
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The Galápagos ant fauna has long been understudied, with the last taxonomic summary being published almost a century ago. Here, a comprehensive and updated overview of the known ant species of the Galápagos Islands is provided with updated species distributions. The list is based on an extensive review of literature, the identification of more than 382,000 specimens deposited in different entomological collections, and recent expeditions to the islands. The ant fauna is composed of five subfamilies (Dolichoderinae, Dorylinae, Formicinae, Myrmicinae, and Ponerinae), 22 genera, 50 species, and 25 subspecies, although three species (Crematogaster crinosa Mayr, 1862, Camponotus senex (Smith, 1858), and Solenopsis saevissima (Smith, 1855)) are considered dubious records. Finally, an illustrated identification key of the species found in the archipelago is presented.
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RBINS Staff Publications 2023
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Dispersal capacity underlies scale-dependent changes in species richness patterns under human disturbance
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Changes in the species richness of (meta-)communities emerge from changes in the relative species abundance distribution (SAD), the total density of individuals, and the amount of spatial aggregation of individuals from the same species. Yet, how human disturbance affects these underlying diversity components at different spatial scales and how this interacts with important species traits, like dispersal capacity, remain poorly understood. Using data of carabid beetle communities along a highly replicated urbanization gradient, we reveal that species richness in urban sites was reduced due to a decline in individual density as well as changes in the SAD at both small and large spatial scales. Changes in these components of species richness were linked to differential responses of groups of species that differ in dispersal capacity. The individual density effect on species richness was due to a drastic 90% reduction of low-dispersal individuals in more urban sites. Conversely, the decrease in species richness due to changes in the SAD at large (i.e., loss of species from the regional pool) and small (i.e., decreased evenness) spatial scales were driven by species with intermediate and high dispersal ability, respectively. These patterns coincide with the expected responses of these dispersal-type assemblages toward human disturbance, namely, (i) loss of low-dispersal species by local extinction processes, (ii) loss of higher-dispersal species from the regional species pool due to decreased habitat diversity, and (iii) dominance of a few highly dispersive species resulting in a decreased evenness. Our results demonstrate that dispersal capacity plays an essential role in determining scale-dependent changes in species richness patterns. Incorporating this information improves our mechanistic insight into how environmental change affects species diversity at different spatial scales, allowing us to better forecast how human disturbance will drive local and regional changes in biodiversity patterns.
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RBINS Staff Publications 2023 OA
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QWIP: A Quantitative Metric for Quality Control of Aquatic Reflectance Spectral Shape Using the Apparent Visible Wavelength
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The colors of the ocean and inland waters span clear blue to turbid brown, and the corresponding spectral shapes of the water-leaving signal are diverse depending on the various types and concentrations of phytoplankton, sediment, detritus and colored dissolved organic matter. Here we present a simple metric developed from a global dataset spanning blue, green and brown water types to assess the quality of a measured or derived aquatic spectrum. The Quality Water Index Polynomial (QWIP) is founded on the Apparent Visible Wavelength (AVW), a one-dimensional geophysical metric of color that is inherently correlated to spectral shape calculated as a weighted harmonic mean across visible wavelengths. The QWIP represents a polynomial relationship between the hyperspectral AVW and a Normalized Difference Index (NDI) using red and green wavelengths. The QWIP score represents the difference between a spectrum’s AVW and NDI and the QWIP polynomial. The approach is tested extensively with both raw and quality controlled field data to identify spectra that fall outside the general trends observed in aquatic optics. For example, QWIP scores less than or greater than 0.2 would fail an initial screening and be subject to additional quality control. Common outliers tend to have spectral features related to: 1) incorrect removal of surface reflected skylight or 2) optically shallow water. The approach was applied to hyperspectral imagery from the Hyperspectral Imager for the Coastal Ocean (HICO), as well as to multispectral imagery from the Visual Infrared Imaging Radiometer Suite (VIIRS) using sensor-specific extrapolations to approximate AVW. This simple approach can be rapidly implemented in ocean color processing chains to provide a level of uncertainty about a measured or retrieved spectrum and flag questionable or unusual spectra for further analysis.
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RBINS Staff Publications 2022
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Assessment of PRISMA water reflectance using autonomous hyperspectral radiometry
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Hyperspectral remote sensing reflectance (Rrs) derived from PRISMA in the visible and infrared range was evaluated for two inland and coastal water sites using above-water in situ reflectance measurements from autonomous hyper- and multispectral radiometer systems. We compared the Level 2D (L2D) surface reflectance, a standard product distributed by the Italian Space Agency (ASI), as well as outputs from ACOLITE/DSF, now adapted for processing of PRISMA imagery. Near-coincident Sentinel-3 OLCI (S3/OLCI) observations were also compared as it is a frequent data source for inland and coastal water remote sensing applications, with a strong calibration and validation record. In situ measurements from two optically diverse sites in Italy, equipped with fixed autonomous hyperspectral radiometer systems, were used: the REmote Sensing for Trasimeno lake Observatory (RESTO), positioned in a shallow and turbid lake in Central Italy, and the Acqua Alta Oceanographic Tower (AAOT), located 15 km offshore from the lagoon of Venice in the Adriatic Sea, which is characterised by clear to moderately turbid waters. 20 PRISMA images were available for the match-up analysis across both sites. Good performance of L2D was found for RESTO, with the lowest relative (Mean Absolute Percentage Difference, MAPD 25\%) and absolute errors (Bias 0.002) in the bands between 500 and 680 nm, with similar performance for ACOLITE. The lowest median and interquartile ranges of spectral angle (SA 8°) denoted a more similar shape to the RESTO in situ data, indicating pigment absorption retrievals should be possible. ACOLITE showed better statistical performance at AAOT compared to L2D, providing R2 0.5, Bias 0.0015 and MAPD 35\%, in the range between 470 and 580 nm, i.e. in the spectral range with highest reflectances. The addition of a SWIR based sun-glint correction to the default atmospheric correction implemented in ACOLITE further improved performance at AAOT, with lower uncertainties and closer spectral similarity to the in situ measurements, suggesting that ACOLITE with glint correction was able to best reproduce the spectral shape of in situ data at AAOT. We found good results for PRISMA Rrs retrieval in our study sites, and hence demonstrated the use of PRISMA for aquatic ecosystem mapping. Further studies are needed to analyse performance in other water bodies, over a wider range of optical properties.
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RBINS Staff Publications 2022
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Het meest duurzame materiaal van België. Belgisch Porfier.
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RBINS Staff Publications 2022