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A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections
Full text linkABSTRACT - 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
Full text linkAudiovisual 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
Revisiting the genus Bolbosoma Porta, 1908 (Acanthocephala: Polymorphidae): host specificity, phylogeny, and species synonymization
Full text linkAbstract
Background: Acanthocephalans of the genus Bolbosoma Porta, 1908 are trophically transmitted parasites that infect marine mammals (mostly cetaceans and less frequently pinnipeds) worldwide. There are 12 species currently considered as valid; however, most records lack information on the maturity stage of the specimens. This, coupled with the scarce phylogenetic information available, hinders a correct understanding of their patterns of host specificity, evolutionary history, and taxonomy. A particularly intriguing case is that of Bolbosoma vasculosum (Rudolphi, 1819), which has been frequently reported in odontocetes but rarely as an adult, having been suggested to be synonymous with Bolbosoma capitatum (von Linstow, 1880).
Methods: We used a comprehensive approach to investigate the concept of Bolbosoma. First, we conducted a bibliographic review of records of Bolbosoma spp. to clarify which are the final hosts for each species. We paid particular attention to B. vasculosum, using morphological and molecular analyses to compare it with B. capitatum. Second, we characterized the complete mitochondrial genome of Bolbosoma balaenae (Gmelin, 1790), Bolbosoma turbinella (Diesing, 1851), B. capitatum, and B. vasculosum. Then, we reconstructed the phylogenetic relationships of Bolbosoma spp. and related taxa using full mitochondrial genomes (or only cox1 when full mitogenomes were unavailable) and nuclear ribosomal genes (18S and 28S).
Results: Bolbosoma spp. exhibit high specificity for cetaceans, with no confirmed records of adult specimens in other host groups. Within this genus, B. vasculosum appears to be conspecific with B. capitatum based on both morphological and molecular evidence. This species shows high affinity to odontocetes, while the remaining species are specific to mysticetes. Phylogenetic analyses showed strong support for the monophyly of Bolbosoma spp., which appeared as sister taxa to Corynosoma spp. and Andracantha spp.. The resulting topology aligns with the patterns of specificity indicated by host records, revealing two distinct clades for species specific to odontocetes and mysticetes, respectively.
Conclusions: The phylogenetic relationships obtained support the hypothesis that the association of Bolbosoma spp. with cetaceans originated through a host-switching event from aquatic birds.Copyright © The Author(s) 2025. Open Access 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 licence, and indicate if changes were made. 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/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco
mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. The attached file is the published version of the article
Bone retouchers and technological continuity in the Middle Stone Age of North Africa
Full text linkEvidence for specialised bone tools has recently been reported for the Middle Stone Age of North Africa [one], which complements similar finds of slightly younger age in South Africa [two, three]. However, until now scant reference has been made to lesser known tools also made of bone ('bone retouchers') that were employed specifically as intermediaries for working or refining stone artefacts, that are sometimes present in these assemblages. In this paper we describe 20 bone retouchers from the cave of Grotte des Pigeons at Taforalt in north-east Morocco. This is the largest stratified assemblage of bone retouchers from a North African MSA site, and the biggest single collection so far from the African Continent. A total of 18 bone retouchers was recovered in securely dated archaeological levels spanning a period from ~ 84.5 ka to 24 ka cal BP. A further two bone retouchers were found in a layer at the base of the deposits in association with Aterian artefacts dating to around 85,000 BP and so far represent the earliest evidence of this type of tool at Taforalt. In this paper we present a first, detailed description of the finds and trace the stages of their production, use and discard (chaîne opératoire). At the same time, we assess if there were diachronic changes in their form and function and, finally, explore their presence in relation to stone tools from the same occupation layers of the cave.Copyright: © 2020 Turner et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, 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
New insights into the Devonian sea spiders of the Hunsrück Slate (Arthropoda: Pycnogonida)
Full text linkBackground
The sea spiders (Pycnogonida Latreille, 1810) of the Hunsrück Slate (Lower Devonian, ~400 million years ago) are iconic in their abundance, exquisite pyritic preservation, and in their distinctive body plan compared to extant sea spiders (Pantopoda Gerstäcker, 1863). Consequently, the Hunsrück sea spiders are important in understanding the deep evolutionary history of Pycnogonida, yet they remain poorly characterised, impacting upon attempts to establish a time-calibrated phylogeny of sea spiders.
Methods
Here, we investigated previously described and new material representing four of the five Hunsrück pycnogonids: Flagellopantopus blocki Poschmann & Dunlop, 2006; Palaeoisopus problematicus Broili, 1928; Palaeopantopus maucheri Broili, 1929; and Pentapantopus vogteli Kühl, Poschmann & Rust, 2013; as well as a few unidentified specimens. Using X-ray microtomography and Reflectance Transformation Imaging, we describe new fossils, provide evidence for newly revealed anatomical features, and interpret these data in comparison to extant species. We also reinterpret the previously published illustration of the (probably lost) holotype of Palaeothea devonica Bergström, Stürmer & Winter, 1980.
Results
We provide the first detailed description of the cephalic appendages of Palaeoisopus problematicus and revise the interpretation of the organisation of its ocular tubercle. Furthermore, we provide new insights into the structure of the legs and the proboscis of Palaeopantopus maucheri, the first description of the body of Flagellopantopus blocki and describe a new specimen of Pentapantopus vogteli, demonstrating that it had eight legs, in contrast to previous interpretations. We argue that, contrary to previous suggestions, Palaeothea devonica probably had a different body plan from extant pantopods. We discuss the ecological traits of the Hunsrück pycnogonids based on their morphological adaptations, and conclude that there is no compelling evidence of Pantopoda in the Devonian. Through comparative interpretation of the legs as well as general morphology, we can divide the Hunsrück pycnogonids into two morphological groups, while Pantopoda constitutes a third morphological group.Copyright © 2024 Sabroux et al. Distributed under Creative Commons CC-BY 4.0. The attached file is the published version of the article.NHM Repositor
XX International Botanical Congress, Madrid 2024: Report of Congress action on nomenclature proposals
Full text linkCopyright © 2024 International Association for Plant Taxonomy. The attached file is the published version of the article.NHM Repositor
NEW AND POORLY-KNOWN TAXA OF LAGRIINAE LATREILLE, 1825 (COLEOPTERA: TENEBRIONIDAE) FROM THE COLLECTIONS OF THE NATURKUNDEMUSEUM ERFURT. 2
Full text linkIn the second paper of the series devoted to the study of lagriine material deposited at the Naturkundemuseum Erfurt, the following three species from the subtribe Lagriina Latreille, 1825, are described and illustrated: Lagria (s. str.) arfaka sp. nov., L. (s. str.) hatam sp. nov., L. (s. str.) undulata sp. nov. (all from New Guinea).The linked file is the published version of the article.NHM Repositor
Spatial controls on the generation of low-δ18O basalts on São Miguel, Azores
No full textVolcanism in the Azores is generally accepted to result from the decompression melting in the upper mantle associated with the Azorean plume. Basalts on the island of Sao ˜ Miguel have been previously recognised as having δ18O values lower than MORB with different authors ascribing this low-δ18O signature to either a component within the plume itself or as the result of assimilation of crustal materials at shallow level. Here we assess these contrasting models by using a suite of samples that are both geographically and temporally spread. We find that while low-δ18O mafic magmas (reaching 4.98 ‰) do occur on S˜
ao Miguel, they are spatially restricted to the Picos fissure system, between the central volcanoes of Sete Cidades and Fogo. Basalts of similar age from outside this restricted region return δ18O values that are similar to MORB. This spatial constraint argues that the source of the observed low-δ18O signature is within the crust rather than a component of the plume.
Previous studies on mafic to intermediate rocks of the Picos fissure system have identified the assimilation of broadly syenitic lithologies, which were found as co-erupted lithic clasts at the Fogo volcano and may have δ18O values as low as 2.6 ‰. However, trace element geochemistry indicates that these lithologies have not been assimilated within our low-δ18O samples, a more likely assimilant is altered oceanic crust or mafic lavas within the island edifice.Copyright © 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The linked file is the published version of the article.NHM Repositor
The explosive-effusive transition within the Miocene Fataga suite, Gran Canaria
No full textMany volcanoes show transitions between explosive and effusive eruptive styles both through the history of the volcano as a whole and occasionally within the course of a single eruption. These differing eruptive styles have vastly different implications for hazard assessments in surrounding regions and so understanding such changes is important. Here, we investigate the intercalated lavas and ignimbrites of the Miocene Fataga Group on the island of Gran Canaria, Spain. Ignimbrites reflect the products of explosive events from the Tejeda caldera, while lavas found within the pyroclastic succession were erupted from extra-caldera sources some 5–10 km from the caldera margin. The ignimbrites exhibit textural complexity containing both crystal-poor juvenile pyroclasts and late-erupted crystal-rich juvenile clasts interpreted to reflect interaction between cumulates and recharge magmas. The lavas meanwhile are almost phenocryst-free, with the exception of few large (cm-scale), unzoned sanidine crystals. Despite their textural differences, the lavas are geochemically similar (in terms of bulk rock and feldspar compositions) to the crystal-poor juveniles in the ignimbrites. Oxygen and lead isotopic compositions of the lavas and surrounding ignimbrites reveal that the magmas shared a deeper source and that petrographic variability is imprinted upon the magmas at shallow levels. We interpret the lavas as originating from peripheral magmatic pockets, on the edges of the main caldera-feeding reservoir. These peripheral magma chambers felt the effects of recharge only as slight thermal fluctuations that fostered the production of the large sanidine crystals. Our findings highlight the potential for storage of magmas aside from the main magmatic system that may represent an underappreciated hazard at volcanoes worldwide.Copyright © 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The linked file is the published version of the article.NHM Repositor
Geochemistry of the Pepom tephra deposits: The most recent intracaldera volcanism of Sete Cidades volcano, São Miguel, Azores
Full text linkMany volcanoes have the ability to impact human infrastructure with explosive activity and understanding the processes of magma generation and conditions of storage in these systems remains a priority. The Sete Cidades volcano on the island of São Miguel, Azores archipelago is exactly such a volcano lying only 12 km from the island's capital city of Ponta Delgada and has been repeatedly active during the Holocene. Sete Cidades is the westernmost central volcano of São Miguel and its most recent explosive volcanism produced the Pepom series of 17 trachytic pumice deposits that were erupted from vents within the caldera. These variably magmatic and phreatomagmatic eruptions involved trachytic magmas that represent the end point of a magmatic evolution dominated by crystal fractionation processes. The magmas contain a mineral assemblage dominated by feldspar, with biotite, clinopyroxene, Fesingle bondTi oxides, amphibole, and trace apatite. Mineral thermometry and hygrometry reveal that the Pepom magmas were stored at temperatures of 789 ± 23 °C to 894 ± 20 °C under volatile-rich conditions (mostly >5 wt% water). Intercalated within the trachytic pyroclastic succession are mafic products that were erupted from vents on the flanks of the volcano suggesting that the evolved, shallow magmatic system may be acting as a barrier to ascending mafic magmas. The Pepom tephra deposits represent trachytic magmas that show limited evidence for the involvement of feldspar-dominated cumulates as has been observed in other settings whereas the preceding, caldera-forming, Santa Bárbara eruption suggests such involvement. Despite the predominant role of fractionation in petrogenesis, the Pepom tephras formed from mildly low-δ18O magmas (4.1 to 5.6‰ for trachyte) and as such require the addition of hydrothermally altered material. The cause of the low-δ18O values remains unknown, but low-δ18O, hydrothermally altered syenitic clasts found within deposits from the nearby Fogo volcano may be potentially analogues.Copyright © 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article.NHM Repositor