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Remarks on the types of the New Guinea endemic Otidiphaps Gould, 1870
Get PDFWe detail the types and some other early specimens of the four taxa currently usually treated as subspecies of the New Guinea endemic, Pheasant Pigeon Otidiphaps nobilis. This material has been subject to a number of erroneous statements in the previous literature. In chronological order of description, O. n. nobilis Gould, 1870, was based on a single specimen of unknown provenance and collector, now at the Natural History Museum, Tring; O. n. cervicalis E. P. Ramsay, 1880, and its objective junior synonym O. n. regalis Salvin & Godman, 1880, were based on multiple syntypes taken in 1879 (several of them the same specimens), all held in Tring (despite being previously reported as such, two specimens in Sydney appear to have no name-bearing status); O. n. insularis Salvin and Godman, 1883, is known from the two syntypes, collected in 1882 and held in Tring, and just one other specimen, taken in 1896 and held in the American Museum of Natural History, New York; and O. n. aruensis Rothschild, 1928, was based on a specimen collected in June 1914, now in New York, although there is a significantly earlier
specimen of this taxon in the Museum Heineanum Halberstadt.opyright © 2023 The Authors; This is an open‐access article distributed under the terms of the Creative Commons Attribution-NonCommercial Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
A revision of the type locality of Black-throated Accentor Prunella atrogularis huttoni (Moore)
Get PDFWe examine the type locality of Black-throated Accentor Prunella atrogularis huttoni that is listed as ‘ranges above Simla’ and propose a revision of the same to ‘Afghanistan’COPYRIGHT: © 2025 Praveen & van Grouw. This is an article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. The attached file is the published version of the article.NHM Repositor
Late pleistocene exploitation of Ephedra in a funerary context in Morocco
Get PDFThe active compounds found in many plants have been widely used in traditional medicine and ritual activities. However, archaeological evidence for the use of such plants, especially in the Palaeolithic period, is limited due to the poor preservation and fragility of seed, fruit, and other botanical macro-remains. In this study, we investigate the presence and possible uses of Ephedra during the Late Pleistocene based on the analysis of exceptionally preserved plant macrofossils recovered from c. 15 ka year-old archaeological deposits at Grotte des Pigeons in northeastern Morocco. This cave has yielded the earliest carbonized plant macrofossils of Ephedra, which were found concentrated in a human burial deposit along with other special finds. Ephedra is a plant known to produce high amounts of alkaloids, primarily ephedrine and pseudoephedrine, which have been utilized in traditional medicine. Direct radiocarbon dates on both Ephedra and the human remains indicate that they were contemporaneous. To understand the uses of Ephedra by people at the site, we discuss the different pathways through which plant remains could have arrived. We suggest that the charred cone bracts of Ephedra likely represent residues of the processing and consumption of the plant's fleshy cones, which may have been valued for both their nutritional and therapeutic properties. Furthermore, we interpret the presence of Ephedra and its deposition in the burial area as evidence that this plant played a significant role during the funerary activities.Copyright © The Author(s) 2024. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives
4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in
any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide
a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have
permission under this licence to share adapted material derived from this article or parts of it. The images or
other third party material in this article are included in the article’s Creative Commons licence, unless indicated
otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and
your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain
permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/
licenses/by-nc-nd/4.0/. The attached file is the published version of the article.NHM Repositor
Magma recharge and mush rejuvenation drive paroxysmal activity at Stromboli volcano
Get PDFAbstract - Open-conduit basaltic volcanoes can be characterised by sudden large explosive events (paroxysms) that interrupt normal effusive and mild explosive activity. In June-August 2019, one major explosion and two paroxysms occurred at Stromboli volcano (Italy) within only 64 days. Here, via a multifaceted approach using clinopyroxene, we show arrival of mafic recharges up to a few days before the onset of these events and their effects on the eruption pattern at Stromboli, as a prime example of a persistently active, open-conduit basaltic volcano. Our data indicate a rejuvenated Stromboli plumbing system where the extant crystal mush is efficiently permeated by recharge magmas with minimum remobilisation promoting a direct linkage between the deeper and the shallow reservoirs that sustains the currently observed larger variability of eruptive behaviour. Our approach provides vital insights into magma dynamics and their effects on monitoring signals demonstrating the power of petrological studies in interpreting patterns of surficial activity.Copyright © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended
use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The attached file is the published version of the article.NHM Repositor
Assessing the effectiveness of MARPOL Annex V at reducing marine debris on Australian beaches
Get PDFSource info: MPB-D-22-02521To mitigate marine debris and promote sustainable marine industries, legislation and regulations surrounding the management of marine debris have been adopted worldwide. One of the most well-known and important agreements is the International Convention for the Prevention of Pollution from Ships (MARPOL), which focuses on reducing all types of ship-sourced marine pollution. MARPOL Annex V, which deals with the disposal of solid waste, came into force on 31 December 1988. However, was only amended to include a complete ban on waste disposal as of 1 January 2013. Assessing the effectiveness of key regulations is fundamental for supporting evidence-based decisions regarding the management of our oceans. Here, we evaluated whether MARPOL Annex V translated into a decrease in the incidence of shipping- and commercial fishing-sourced debris on remote beaches in Australia using 14 years of standardised, community-driven data. From 2006 to 2020 there was a significant change over time in the density of fishing and shipping debris on Australian beaches; debris density increased up to 2013 followed by a decrease until mid-2017. Although the new regulation started in January 2013, the decrease in density was not recorded until one year later. The decline was only observed for 4 years, reinforcing the existence of lags between the implementation of international agreements and the corresponding potential reduction in debris in the environment. This provides compelling evidence that international agreements and policies by themselves are not enough to solve the debris problem, with improved implementation and enforcement also required. We discuss future perspectives and solutions to reduce ocean-sourced litter inputs into the ocean and highlight the urgent need for action.Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/bync-nd/4.0/). The attached file is the published version of the article.NHM Repositor
Publisher Correction: Evolution of sexual size dimorphism in tetrapods is driven by varying patterns of sex-specific selection on size
No full textCorrection to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-024-02600-8. Published online 23 December 2024.Copyright © The Author(s) 2025. The linked document is the published version of the article.NHM Repositor
A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections
Get PDFABSTRACT - Low coverage ‘genome‐skims’ are often used to assemble organelle genomes and ribosomal gene sequences for cost‐effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction‐based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome‐skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low‐coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.Copyright © 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article.NHM Repositor
Bioacoustic and Ecoacoustic Data in Audiovisual Core
Get PDFAudiovisual Core (Audiovisual Core Maintenance Group 2023), is the TDWG standard for metadata related to biodiversity multimedia. The Audiovisual Core Maintenance Group has been working to expand the standard to provide the terms necessary for handling sound recordings. Audiovisual Core can now handle acoustic metadata related to biodiversity from single species (bioacoustics) to the ecosystem scale (ecoacoustics).
Bioacoustics
The Natural History Museum, London has a significant collection of recorded insect sounds (Ragge and Reynolds 1998) that are often directly linked to museum specimens (Fig. 1). The sound collection has previously been digitised and made available electronically through the BioAcoustica project (Baker et al. 2015). The BioAcoustica platform allows for annotation of audio files with tags including "Call" for deliberate sound made by an organism, "Voice Introduction" for metadata, and "Extraneous Noise." These boundaries are defined by their start and end times (in seconds) relative to the start of the file (Fig. 2).
Ecoacoustics
Ecoacoustics deals with the sounds present within an entire soundscape or ecosystem. The calls of individual species form the biological part of the soundscape (biophony) alongside sounds produced by non-living natural sources (geophony) and humans (anthropophony). Individual components are often defined by date and time boundaries, and sometimes by upper and lower frequency limits (Fig. 3).
Regions of Interest
The recently added concept of a "Region of Interest" (ROI) allows for the annotation of sound files, identifying multiple regions within a single recording with time and/or frequency bounds. However, the vocabulary of ROI*1 is not just intended for sounds. Equivalent terms also allow for regions to be specified with images and videos.
The use of well-defined annotations has the potential to generate large amounts of training data for machine learning models and provide a standard for generating observation records from these models (e.g., BirdNet, see Kahl et al. 2021), which can be verified by linking them to audio segments within a much larger recording.
The development of a metadata standard for regions of interest has several interesting possibilities, including linking multiple observation records to a single soundscape recording (the recording acts similarly to a voucher specimen) and aggregating regions across multiple datasets to create larger corpora for training machine learning models.Copyright © Baker E. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are
credited. The attached file is the published version of the article.NHM Repositor
Baseline patterns of infection in regions of Benin, Malawi and India seeking to interrupt transmission of soil transmitted helminths (STH) in the DeWorm3 trial
Get PDFGlobal efforts to control morbidity associated with soil-transmitted helminth infections (STH) have focused largely on the targeted treatment of high-risk groups, including children and pregnant women. However, it is not clear when such programs can be discontinued and there are concerns about the sustainability of current STH control programs. The DeWorm3 project is a large multi-country community cluster randomized trial in Benin, India and Malawi designed to determine the feasibility of interrupting the transmission of STH using community-wide delivery of mass drug administration (MDA) with anthelmintics over multiple rounds. Here, we present baseline data and estimate key epidemiological parameters important in determining the likelihood of transmission interruption in the DeWorm3 trial. A baseline census was conducted in October-December 2017 in India, November-December 2017 in Malawi and in January-February 2018 in Benin. The baseline census enumerated all members of each household and collected demographic data and information on occupation, assets, and access to water, sanitation and hygiene (WASH). Each study site was divided into 40 clusters of at least 1,650 individuals per cluster. Clusters were randomized to receive twice yearly community-wide MDA with albendazole (GSK) targeting eligible individuals of all ages (20 clusters), or to receive the standard-of-care deworming program targeting children provided in each country. In each site, a randomly selected group of 150 individuals per cluster (6,000 total per site) was selected from the baseline census using stratified random sampling, and each individual provided a single stool sample for analysis of STH infection using the Kato-Katz technique. Study site, household and individual characteristics were summarized as appropriate. We estimated key epidemiological parameters including the force of infection and the degree of parasite aggregation within the population. The DeWorm3 sites range in population from 94,969 to 140,932. The population age distribution varied significantly by site, with the highest proportion of infants and young children in Malawi and the highest proportion of adults in India. The baseline age- and cluster-weighted prevalence, as measured by Kato-Katz, varied across sites and by species, Baseline hookworm prevalence in India was 21.4% (95% CI: 20.4–22.4%), while prevalence ofAscarisandTrichurisby Kato-Katz was low (0.1% and 0.3% overall). In Malawi, the overall age- and cluster-weighted STH prevalence was 7.7% (95% CI: 7.1–8.4%) predominantly driven by hookworm infections (7.4%) whileAscaris(0.1%) andTrichuris(0.3%) infections were rare. In Benin, the overall age- and cluster-weighted prevalence was significantly lower (5.6%, 95% CI: 5.1–6.2%) andAscaris(2.0%, 95% CI: 1.6–2.3%) was more common than in other sites.Ascarisinfections were more likely to be moderate- or heavy-intensity (43.7%, unweighted) compared to hookworm (5.0%). The force of infection for hookworm was highest in adults in India and Malawi but appeared relatively stable across age groups in Benin. These data demonstrate the significant variability between the sites in terms of demography, socio-economic status and environmental characteristics. In addition, the baseline prevalence and intensity data from DeWorm3 suggest that each site has unique epidemiologic characteristics that will be critical in determining correlates of achieving STH transmission interruption in the DeWorm3 trial.Trial registration:The trial was registered at ClinicalTrials.gov (NCT03014167).</jats:p
Development and validation of a high-throughput qPCR platform for the detection of soil-transmitted helminth infections
No full text
Background
Historically, soil-transmitted helminth (STH) control and prevention strategies have relied on mass drug administration efforts targeting preschool and school-aged children. While these efforts have succeeded in reducing morbidity associated with STH infection, recent modeling efforts have suggested that expanding intervention to treatment of the entire community could achieve transmission interruption in some settings. Testing the feasibility of such an approach requires large-scale clinical trials, such as the DeWorm3 cluster randomized trial. In addition, accurate interpretation of trial outcomes requires diagnostic platforms capable of accurately determining infection prevalence (particularly as infection intensity is reduced) at large population scale and with significant throughput. Here, we describe the development and validation of such a high-throughput molecular testing platform.
Methodology/principal findings
Through the development, selection, and validation of appropriate controls, we have successfully created and evaluated the performance of a testing platform capable of the semi-automated, high-throughput detection of four species of STH in human stool samples. Comparison of this platform with singleplex reference assays for the detection of these same pathogens has demonstrated comparable performance metrics, with index assay accuracy measuring at or above 99.5% and 98.1% for each target species at the level of the technical replicate and individual extraction respectively. Through the implementation of a rigorous validation program, we have developed a diagnostic platform capable of providing the necessary throughput and performance required to meet the needs of the DeWorm3 cluster randomized trial and other large-scale operational research efforts for STH.
Conclusions/significance
Resulting from the rigorous developmental approach taken, the platform we describe here provides the needed confidence in testing outcomes when utilized in conjunction with large-scale efforts such as the DeWorm3 trial. Additionally, the successful development of an evaluation and validation strategy provides a template for the creation of similar diagnostic platforms for other neglected tropical diseases.
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