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  • Articles  (22,751,244)
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  • 1
    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
    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
    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
    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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    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 221-249
    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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