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  • 1
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    Classification of a high latitude bog using multispectral drone imagery (2023)
    In:  EPIC3
    Details
    Publication Date: 2024-04-27
    Description: Peatlands store and emit large amounts of greenhouse gases. With the climate changing due to global warming, measuring these emissions helps to get a better understanding of the role of peatlands in the global carbon cycle. Measurements at a bog site of the Siikaneva peatland show that the emissions vary along the different microtopographies shaped by their vegetation and ground water level. To upscale these measurements, a supervised classification of the study area was implemented in this study by testing a method that uses high-resolution multispectral aerial imagery, captured by a UAV (Uncrewed Aerial Vehicle), and a Random Forest classifier. A cohesive orthomosaic of the study area was produced, training data were generated to adjust the Random Forest model, and the study area was classified. The results show that the applied methods were successful in generating a multispectral orthomosaic as well as a classified raster of the study area. A mean classification accuracy of 75.7 % was achieved, which can be considered as a good result. Misclassification rates of neighboring microtopographies with similar vegetation could be mitigated by utilizing a LiDAR (Light Detection and Ranging) sensor in further studies.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Thesis , notRev
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  • 2
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    Boletín CTN Diocean No. 3 / 2023 (2024)
    Comisión Colombiana del Océano | Bogotá D.C., Colombia
    Details
    Publication Date: 2024-04-27
    Description: Hace tres años atrás el Comité Técnico Nacional de Coordinación de Datos e Información Oceánicos (CTN Diocean) de la Comisión Colombiana del Océano (CCO), estableció un plan de trabajo que abarca cinco años de actividades institucionales para fortalecer la gestión de estos importantes activos del país. Para entonces se tuvieron en cuenta diferentes estrategias como línea base para definir las tareas a desarrollar, y en la actualidad es gratificante para miembros e invitados permanentes confirmar, que lo planeado sigue vigente y acorde con los desafíos del ‘Decenio de las Ciencias Oceánicas para el Desarrollo Sostenible’, las necesidades de la comunidad y los recientes lineamientos de política nacionales e internacionales. En el presente número del Boletín CTN Diocean, se destacan entre otros, dos reconocimientos logrados en el nivel internacional por parte de instituciones que hacen parte del comité y que le aportan al fortalecimiento de la gestión de datos oceánicos de Colombia: el primero, los datos abiertos oceanográficos como una actividad del ‘Decenio de las Ciencias Oceánicas para el Desarrollo Sostenible’ de la Comisión Oceanográfica Intergubernamental (COI); y el segundo, la copresidencia para el periodo entre sesiones 2023-2025 del programa para el Intercambio Internacional de Datos Oceanográficos (COI-IODE) junto con Suecia, en el marco de la cual se inició la asesoría con nuestros hermanos panameños en la materia.
    Description: Published
    Description: Not Known
    Keywords: Acceso abierto ; Usuario de información ; Gestión de la información ; Base de datos ; Sistema de información ; Organización y gestión ; ASFA_2015::G::Geographic information systems ; ASFA_2015::I::Information centres ; ASFA_2015::D::Databases ; ASFA_2015::I::Information handling
    Repository Name: AquaDocs
    Type: Book/Monograph/Conference Proceedings
    Format: 29
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  • 3
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    Efeitos de ações antrópicas sobre as interações bióticas entre os peixes de uma planície de inundação Neotropical: alterações nos padrões de coocorrência de espécies. (2024)
    Universidade Estadual de Maringá. Departamento de Biologia. Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais
    Details
    Publication Date: 2024-04-27
    Description: The freshwater ichthyofauna is largely threatened by the anthropogenic impacts in these ecosystems. The climatic changes caused by human actions and dams’ constructions concerningly affects the freshwater fishes, including its biotic interactions network. Thus, this work aimed at evaluating the Upper Paraná River floodplain’s (UPRF) ichthyofauna under the impacts caused by climate changes, years of extreme drought an extreme flood, and under the impacts caused by the construction of an upstream dam, the Sérgio Motta Hydroelectric Power Plant, Brazil. The sampled years were classified in extreme drought, neutral and extreme flood, according to the predominant characteristics of its hydrological regime, and in pré-damming years, before the upstream hydroelectric power plant construction and reservoir’s flooding, and post-damming years. The abiotic and hydrometric variables were concurrently sampled with the abundance of fish species, allowing to exclude the environmental variables’ effects over the species’ cooccurrence, using multivariate generalized linear models with latent variables. The force of the interspecific biotic interactions was obtained through cooccurrence values for each pair of species, visualized through negative, neutral, and positive values. Regarding the results involving the hydrological regime influence, it was observed differences between drought, neutral and flood years, with stronger cooccurrence values between the UPRF’s ichthyofauna in drought years (for positive and negative values). Regarding the results involving the construction of the UPRF’s upstream dam, it was observed differences comparing the pré-damming and post-damming years cooccurrence patters, with predominantly positive values in post-damming years, and predominantly neutral cooccurrences in pré-damming years. These work results indicate the increment of the cooccurrence values between a floodplain’s fish species due to extreme droughts and upstream dams’ constructions, once the cooccurrence values were more intense under these conditions. Stands out the importance of biotic interactions for the elaboration of management plans and freshwater species conservation in response to anthropogenic actions.
    Description: A ictiofauna de ambientes de água doce se encontra amplamente ameaçada por ações antrópicas. As mudanças climáticas e a construção de barragens afetam os peixes de água doce e suas redes de interações bióticas. Neste contexto, este estudo avaliou a ictiofauna da planície de inundação do alto rio Paraná (PIARP) sob os impactos de mudanças climáticas, épocas de secas e cheias extremas, e sob os impactos causados pela construção de uma barragem a montante, a Usina Hidrelétrica Sérgio Motta, Brasil. Os anos amostrados foram classificados em anos de seca extrema, neutros e de cheia extrema, de acordo com as condições predominantes de seu regime hidrológico, e em anos de pré-barramento, antes da construção e inundação do reservatório da usina hidrelétrica a montante, e pós-barramento. As variáveis abióticas e variáveis hidrométricas foram amostradas concomitantemente com a abundância das espécies de peixe, permitindo excluir o efeito das variáveis ambientais sobre a ocorrência das espécies, com o uso de modelos lineares generalizados multivariados de variáveis latentes. Obteve-se a força das interações bióticas interespecíficas pelos valores de coocorrência, positivos ou negativos, entre cada par de espécies. Com relação aos resultados envolvendo a influência dos regimes hidrológicos, foram encontradas diferenças nos valores médios de coocorrência entre anos de seca extrema, anos neutros e anos de cheia extrema, indicando que os valores de coocorrência são mais fortes entre a ictiofauna da PIARP (tanto interações positivas quanto negativas) em anos de seca. Para os efeitos da construção da barragem a montante da PIARP, observou-se diferenças entre os padrões de coocorrência de espécies antes e após a sua construção, indicando valores de coocorrência predominantemente positivos no período pós-barramento, e coocorrências predominantemente neutras no período pré-barramento. Os resultados indicam incremento nos padrões de coocorrência entre as espécies de peixes da planície de inundação frente secas extremas e construção de barragens a montante, uma vez que os valores de coocorrência foram mais intensos sob essas condições. Destaca-se a importância das interações bióticas em resposta às ações antrópicas para a elaboração de planos de manejo e para a conservação das espécies de peixes de água doce.
    Description: PhD
    Keywords: Peixes de água doce ; Comunidades, Ecologia de ; Interações bióticas ; Ações antrópicas ; Coocorrência de espécies ; Variáveis ambientais ; Variáveis hidrométricas ; Generalized linear latent variable models (GLLVM) ; ASFA_2015::F::Freshwater ecology ; ASFA_2015::F::Freshwater fish ; ASFA_2015::C::Communities (ecological) ; ASFA_2015::I::Interactions ; ASFA_2015::A::Anthropogenic factors ; ASFA_2015::S::Species diversity ; ASFA_2015::E::Environmental factors ; ASFA_2015::H::Hydrometers
    Repository Name: AquaDocs
    Type: Thesis/Dissertation
    Format: 71pp.
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  • 4
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    Dieback and decline pathogens of olive trees in South Africa (2020)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 196-220
    Details
    Publication Date: 2024-04-27
    Description: Trunk disease fungal pathogens reduce olive production globally by causing cankers, dieback, and other decline-related symptoms on olive trees. Very few fungi have been reported in association with olive dieback and decline in South Africa. Many of the fungal species reported from symptomatic olive trees in other countries have broad host ranges and are known to occur on other woody host plants in the Western Cape province, the main olive production region of South Africa. This survey investigated the diversity of fungi and symptoms associated with olive dieback and decline in South Africa. Isolations were made from internal wood symptoms of 145 European and 42 wild olive trees sampled in 10 and 9 districts, respectively. A total of 99 taxa were identified among 440 fungal isolates using combinations of morphological and molecular techniques. A new species of Pseudophaeomoniella, P. globosa, had the highest incidence, being recovered from 42.8 % of European and 54.8 % of wild olive samples. This species was recovered from 9 of the 10 districts where European olive trees were sampled and from all districts where wild olive trees were sampled. Members of the Phaeomoniellales (mainly P. globosa) were the most prevalent fungi in five of the seven symptom types considered, the only exceptions being twig dieback, where members of the Botryosphaeriaceae were more common, and soft/white rot where only Basidiomycota were recovered. Several of the species identified are known as pathogens of olives or other woody crops either in South Africa or elsewhere in the world, including species of Neofusicoccum, Phaeoacremonium, and Pleurostoma richardsiae. However, 81 of the 99 taxa identified have not previously been recorded on olive trees and have unknown interactions with this host. These taxa include one new genus and several putative new species, of which four are formally described as Celerioriella umnquma sp. nov., Pseudophaeomoniella globosa sp. nov., Vredendaliella oleae gen. & sp. nov., and Xenocylindrosporium margaritarum sp. nov.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Celerioriella ; five new taxa ; Olea europaea subsp. cuspidata ; Olea europaea subsp. europaea ; phylogenetics ; Pseudophaeomoniella ; taxonomy ; Vredendaliella ; Xenocylindrosporium
    Repository Name: National Museum of Natural History, Netherlands
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  • 5
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    Amazonia through time: Andean uplift, climate change, landscape evolution and biodiversity (2010)
    In:  Science vol. 330 no. 6006, pp. 927-931
    Details
    Publication Date: 2024-04-26
    Description: The Amazonian rainforest is arguably the most species-rich terrestrial ecosystem in the world, yet the timing of the origin and volutionary causes of this diversity are a matter of debate. We review the geologic and phylogenetic evidence from Amazonia and compare it with uplift records from the Andes. This uplift and its effect on regional climate fundamentally changed the Amazonian landscape by reconfiguring drainage patterns and creating a vast influx of sediments into the basin. On this “Andean” substrate, a region-wide edaphic mosaic developed that became extremely rich in species, particularly in Western Amazonia. We show that Andean uplift was crucial for the evolution of Amazonian landscapes and ecosystems, and that current biodiversity patterns are rooted deep in the pre-Quaternary.
    Keywords: Amazonia ; evolution ; biodiversity
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
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    Shifts in dominance of benthic communities along a gradient of water temperature and turbidity in tropical coastal ecosystems (2024)
    In:  PeerJ vol. 12 no. e17132
    Details
    Publication Date: 2024-04-26
    Description: Tropical coastal benthic communities will change in species composition and relative dominance due to global (e.g., increasing water temperature) and local (e.g., increasing terrestrial influence due to land-based activity) stressors. This study aimed to gain insight into possible trajectories of coastal benthic assemblages in Raja Ampat, Indonesia, by studying coral reefs at varying distances from human activities and marine lakes with high turbidity in three temperature categories (〈31 °C, 31–32 °C, and 〉32 °C). The benthic community diversity and relative coverage of major benthic groups were quantified via replicate photo transects. The composition of benthic assemblages varied significantly among the reef and marine lake habitats. The marine lakes 〈31 °C contained hard coral, crustose coralline algae (CCA), and turf algae with coverages similar to those found in the coral reefs (17.4–18.8% hard coral, 3.5–26.3% CCA, and 15–15.5% turf algae, respectively), while the higher temperature marine lakes (31–32 °C and 〉32 °C) did not harbor hard coral or CCA. Benthic composition in the reefs was significantly influenced by geographic distance among sites but not by human activity or depth. Benthic composition in the marine lakes appeared to be structured by temperature, salinity, and degree of connection to the adjacent sea. Our results suggest that beyond a certain temperature (〉31 °C), benthic communities shift away from coral dominance, but new outcomes of assemblages can be highly distinct, with a possible varied dominance of macroalgae, benthic cyanobacterial mats, or filter feeders such as bivalves and tubeworms. This study illustrates the possible use of marine lake model systems to gain insight into shifts in the benthic community structure of tropical coastal ecosystems if hard corals are no longer dominant.
    Keywords: Benthic cover ; Biodiversity ; Coral reef ; Marine lake ; Anthropogenic pressures ; Raja ; Ampat (Indonesia)
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial (2024)
    In:  Antonie van Leeuwenhoek vol. 117 no. 1
    Details
    Publication Date: 2024-04-26
    Description: Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confrmed a spatial specifcity amongst samples at diferent longitudinal scales. Results from this additional spatial analysis confrmed that diferences in prokaryotic communities might frst be explained by environmental changes (mainly temperature and salinity), while no signifcant efect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative infuence of sponge translocation during in situ aquaculture.
    Keywords: Holobiont ; Marine sponges ; Microbiome ; Farming trials ; Biogeography ; French Polynesia
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    Diachronic quantification of the local marine reservoir effect (MRE) using Loripes orbiculatus shells from Late Holocene lagoonal deposits at Puntone di Scarlino (Central Tuscany, Italy): Proposed roles of microbial diagenesis and sedimentation rates (2024)
    In:  Quaternary Geochronology vol. 81 no. 101505
    Details
    Publication Date: 2024-04-26
    Description: With the aim of dating the early salt production at Puntone di Scarlino (Central Tuscany, Italy) and establishing the environmental history of this coastal site, a sediment core was studied, taken from the lagoon next to the archaeological site. Diachronic radiocarbon dating of terrestrial plant macro remains and Loripes orbiculatus (Poli, 1795) shells, a burrowing lucinid bivalve occurring throughout the sediment cored, revealed a Marine Reservoir Effect (MRE) that varied markedly over time. Between ca. 4000 and 2500 cal BP, the △R values ranged between −50 and + 500 14C years, thus rendering the Loripes shells truly unsuited for independent radiocarbon dating. Extensive geochemical and palaeoecological study of the core and its environment showed that none of the ubiquitous explanations for this highly variable MRE, such as ‘hard water’ or ‘upwelling old seawater’, can be valid. We attribute the phenomenon to the uptake by this lucinid mollusc of ‘old carbon’ from the sediment column into which it had burrowed, released by diagenetic microbial decomposition processes such as methanogenesis. The age of this inorganic carbon varied, being linked to the sedimentation rate: with decreasing sedimentation rate its impact will increase, whereas at high sedimentation rates its impact will likely be minimal. Our results raise serious doubts about the suitability for radiocarbon dating of benthic fauna from shallow coastal environments and point at these diagenetic processes as potentially important sources of ‘old carbon’.
    Keywords: Holocene ; Paleoceanography ; Europe ; Radiogenic isotopes ; Marine reservoir effect ; Loripes orbiculatus ; Diagenetic carbon flux
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
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    Illuminating type collections of nectriaceous fungi in Saccardo's fungarium (2020)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 221-249
    Details
    Publication Date: 2024-04-26
    Description: Specimens of Nectria spp. and Nectriella rufofusca were obtained from the fungarium of Pier Andrea Saccardo, and investigated via a morphological and molecular approach based on MiSeq technology. ITS1 and ITS2 sequences were successfully obtained from 24 specimens identified as ‘Nectria’ sensu Saccardo (including 20 types) and from the type specimen of Nectriella rufofusca. For Nectria ambigua, N. radians and N. tjibodensis only the ITS1 sequence was recovered. On the basis of morphological and molecular analyses new nomenclatural combinations for Nectria albofimbriata, N. ambigua, N. ambigua var. pallens, N. granuligera, N. peziza subsp. reyesiana, N. radians, N. squamuligera, N. tjibodensis and new synonymies for N. congesta, N. flageoletiana, N. phyllostachydis, N. sordescens and N. tjibodensis var. crebrior are proposed. Furthermore, the current classification is confirmed for Nectria coronata, N. cyanostoma, N. dolichospora, N. illudens, N. leucotricha, N. mantuana, N. raripila and Nectriella rufofusca. This is the first time that these more than 100-yr-old specimens are subjected to molecular analysis, thereby providing important new DNA sequence data authentic for these names.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; ancient DNA ; Ascomycota ; Hypocreales ; Illumina ; ribosomal sequences ; Sordariomycetes
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 10
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    Fungal Planet description sheets: 1112–1181 (2020)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 251-409
    Details
    Publication Date: 2024-04-26
    Description: Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; ITS nrDNA barcodes ; LSU ; new taxa ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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