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  • 1
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    Complete mitochondrial genome MK992912 of Great Knot (Calidris tenuirostris) is a chimera with DNA from Pacific Golden Plover Pluvialis fulva (Aves: Charadriiformes) (2024)
    In:  Mitochondrial DNA Part B vol. 9 no. 4, pp. 532-535
    Details
    Publication Date: 2024-04-28
    Description: A complete mitochondrial genome of Great Knot (Calidris tenuirostris), MK992912, was published by He and colleagues in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both C. tenuirostris (15,567 bp, 92.8%) and Pacific Golden Plover (Pluvialis fulva, 1208 bp, 7.2%). Detecting such errors is possible before publication if each sequenced fragment is separately analyzed phylogenetically before assembling the fragments into a single mitogenome. This mitogenome has been re-used in at least four phylogenies. The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
    Keywords: Chimerism ; laboratory ; errors ; mitogenome ; sequence artifacts ; shorebirds
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 2
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    A new, unusually large, Clavicornaltica Scherer, 1974 flea beetle from Borneo, described and sequenced in the field by citizen scientists (Coleoptera, Chrysomelidae, Galerucinae) (2024)
    Pensoft Publishers
    In:  Biodiversity Data Journal vol. 12 no. e119481
    Details
    Publication Date: 2024-04-28
    Description: Background: The genus Clavicornaltica Scherer 1974 consists of very small, soil-dwelling flea beetles in South, Southeast and East Asia. Due to their diminutive size and morphological similarities, very little is known about their ecology and taxonomical diversity. It is likely that further studies will reveal this genus to be much more speciose than the 30 species currently recognised. New information: A new species of Clavicornaltica from Brunei Darussalam is described, C. mataikanensis Otani et al., sp. nov. This is the second species of this genus recorded from Ulu Temburong National Park.
    Keywords: Lowland Dipterocarp rainforest ; citizen science ; new species ; humicole beetles ; taxonomy ; tourism
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 3
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    Efficient Speech Detection in Environmental Audio Using Acoustic Recognition and Knowledge Distillation (2024)
    In:  Sensors vol. 24 no. 7, pp. 2046-2046
    Details
    Publication Date: 2024-04-28
    Description: The ongoing biodiversity crisis, driven by factors such as land-use change and global warming, emphasizes the need for effective ecological monitoring methods. Acoustic monitoring of biodiversity has emerged as an important monitoring tool. Detecting human voices in soundscape monitoring projects is useful both for analyzing human disturbance and for privacy filtering. Despite significant strides in deep learning in recent years, the deployment of large neural networks on compact devices poses challenges due to memory and latency constraints. Our approach focuses on leveraging knowledge distillation techniques to design efficient, lightweight student models for speech detection in bioacoustics. In particular, we employed the MobileNetV3-Small-Pi model to create compact yet effective student architectures to compare against the larger EcoVADteacher model, a well-regarded voice detection architecture in eco-acoustic monitoring. The comparative analysis included examining various configurations of the MobileNetV3-Small-Pi-derived student models to identify optimal performance. Additionally, a thorough evaluation of different distillation techniques was conducted to ascertain the most effective method for model selection. Our findings revealed that the distilled models exhibited comparable performance to the EcoVAD teacher model, indicating a promising approach to overcoming computational barriers for real-time ecological monitoring.
    Keywords: passive acoustic monitoring ; eco-acoustics ; deep learning ; knowledge distillation ; bioacoustics ; classification ; transfer learning ; speech detection
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
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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: 2024-04-28
    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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  • 5
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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: 2024-04-28
    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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  • 6
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    The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees (2024)
    Pensoft Publishers
    In:  Biodiversity Data Journal vol. 12 no. e117172
    Details
    Publication Date: 2024-04-28
    Description: Bees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing 514 Iberian species, was constructed. The "InBIO Barcoding Initiative Database: DNA Barcodes of Iberian bees" dataset contains records of 1,059 sequenced specimens. The species of this dataset correspond to about 47% of Iberian bee species diversity and 21% of endemic species diversity. For peninsular Portugal only, the corresponding coverage is 71% and 50%. Specimens were collected between 2014 and 2022 and are deposited in the research collection of Thomas Wood (Naturalis Biodiversity Center, The Netherlands), in the FLOWer Lab collection at the University of Coimbra (Portugal), in the Andreia Penado collection at the Natural History and Science Museum of the University of Porto (MHNC-UP) (Portugal) and in the InBIO Barcoding Initiative (IBI) reference collection (Vairão, Portugal).
    Keywords: Hymenoptera ; occurrence records ; species distributions ; peninsular Portugal ; peninsular ; Spain ; DNA barcode ; cytochrome c oxidase subunit I (COI) ; pollinator
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Cryphonectriaceae on Myrtales in China: phylogeny, host range, and pathogenicity (2020)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 101-131
    Details
    Publication Date: 2024-04-28
    Description: Plantation-grown Eucalyptus (Myrtaceae) and other trees residing in the Myrtales have been widely planted in southern China. These fungal pathogens include species of Cryphonectriaceae that are well-known to cause stem and branch canker disease on Myrtales trees. During recent disease surveys in southern China, sporocarps with typical characteristics of Cryphonectriaceae were observed on the surfaces of cankers on the stems and branches of Myrtales trees. In this study, a total of 164 Cryphonectriaceae isolates were identified based on comparisons of DNA sequences of the partial conserved nuclear large subunit (LSU) ribosomal DNA, internal transcribed spacer (ITS) regions including the 5.8S gene of the ribosomal DNA operon, two regions of the β-tubulin (tub2/tub1) gene, and the translation elongation factor 1-alpha (tef1) gene region, as well as their morphological characteristics. The results showed that eight species reside in four genera of Cryphonectriaceae occurring on the genera Eucalyptus, Melastoma (Melastomataceae), Psidium (Myrtaceae), Syzygium (Myrtaceae), and Terminalia (Combretaceae) in Myrtales. These fungal species include Chrysoporthe deuterocubensis, Celoporthe syzygii, Cel. eucalypti, Cel. guangdongensis, Cel. cerciana, a new genus and two new species, as well as one new species of Aurifilum. These new taxa are hereby described as Parvosmorbus gen. nov., Par. eucalypti sp. nov., Par. guangdongensis sp. nov., and Aurifilum terminali sp. nov. Pathogenicity tests showed that the eight species of Cryphonectriaceae are pathogenic to two Eucalyptus hybrid seedlings, Melastoma sanguineum branches, and Psidium guajava and Syzygium jambos seedlings. The overall data showed that Chr. deuterocubensis is the most aggressive, followed by Par. eucalypti. Significant differences in tolerance were observed between the two tested Eucalyptus hybrid genotypes, suggesting that disease-tolerant genotypes can be selected for disease management in the Eucalyptus industry.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Eucalyptus ; fungal pathogen ; host jump ; Myrtaceae ; new taxa ; plantation forestry
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    RADReef: A global Holocene Reef Rate of Accretion Dataset (2024)
    In:  Scientific Data vol. 11 no. 398
    Details
    Publication Date: 2024-04-28
    Description: Reef cores are a powerful tool for investigating temporal changes in reef communities. Radiometric dating facilitates the determination of vertical accretion rates, which has allowed for examination of local-regional controlling factors, such as subsidence and sea level changes. Coral reefs must grow at sufcient rates to keep up with sea level rise, or risk ‘drowning.’ As sea level is expected to rise signifcantly in the next 100 years and beyond, it is important to understand whether reefs will be able to survive. Historical records of reef accretion rates extracted from cores provide valuable insights into extrinsic controlling factors of reef growth and are instrumental in helping predict if future reefs can accrete at rates needed to overcome predicted sea level changes. While extensive research exists at local and regional scales, limited attention has been given to identifying global patterns and drivers. To address this, we present “RADReef”: A global dataset of dated Holocene reef cores. RADReef serves as a foundation for further research on past, present and future reef accretion.
    Keywords: Biogeochemistry ; Geomorphology ; Palaeoceanography ; Physical oceanography
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
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    Critical transitions in the Amazon forest system (2024)
    In:  Nature vol. 626 no. 7999, pp. 555-564
    Details
    Publication Date: 2024-04-28
    Description: The possibility that the Amazon forest system could soon reach a tipping point, inducing large-scale collapse, has raised global concern. For 65 million years, Amazonian forests remained relatively resilient to climatic variability. Now, the region is increasingly exposed to unprecedented stress from warming temperatures, extreme droughts, deforestation and fires, even in central and remote parts of the system. Long existing feedbacks between the forest and environmental conditions are being replaced by novel feedbacks that modify ecosystem resilience, increasing the risk of critical transition. Here we analyse existing evidence for five major drivers of water stress on Amazonian forests, as well as potential critical thresholds of those drivers that, if crossed, could trigger local, regional or even biome-wide forest collapse. By combining spatial information on various disturbances, we estimate that by 2050, 10% to 47% of Amazonian forests will be exposed to compounding disturbances that may trigger unexpected ecosystem transitions and potentially exacerbate regional climate change. Using examples of disturbed forests across the Amazon, we identify the three most plausible ecosystem trajectories, involving diferent feedbacks and environmental conditions. We discuss how the inherent complexity of the Amazon adds uncertainty about future dynamics, but also reveals opportunities for action. Keeping the Amazon forest resilient in the Anthropocene will depend on a combination of local eforts to end deforestation and degradation and to expand restoration, with global eforts to stop greenhouse gas emissions.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 10
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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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