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Twenty years of big plant genera
Get PDFIn 2004, David Frodin published a landmark review of the history and concepts of big plant genera. Two decades of taxonomic activity have taken place since, coinciding with a revolution in phylogenetics and taxonomic bioinformatics. Here we use data from the World Flora Online (WFO) to provide an updated list of big (more than 500 species) and megadiverse (more than 1000 species) flowering plant genera and highlight changes since 2004. The number of big genera has increased from 57 to 86; today one of every four plant species is classified as a member of a big genus, with 14% in just 28 megadiverse genera. Most (71%) of the growth in big genera since 2000 is the result of new species description, not generic re-circumscription. More than 15% of all currently accepted flowering plant species described in the last two decades are in big genera, suggesting that groups previously considered intractable are now being actively studied taxonomically. Despite this rapid growth in big genera, they remain a significant yet understudied proportion of plant diversity. They represent a significant proportion of global plant diversity and should remain a priority not only for taxonomy but for understanding global diversity patterns and plant evolution in general.</jats:p
Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)
No full textThe ability to identify and quantify the constituent plant species that make up a mixed‐species sample of pollen has important applications in ecology, conservation, and agriculture. Recently, metabarcoding protocols have been developed for pollen that can identify constituent plant species, but there are strong reasons to doubt that metabarcoding can accurately quantify their relative abundances. A PCR‐free, shotgun metagenomics approach has greater potential for accurately quantifying species relative abundances, but applying metagenomics to eukaryotes is challenging due to low numbers of reference genomes.
We have developed a pipeline, RevMet (Reverse Metagenomics) that allows reliable and semi‐quantitative characterization of the species composition of mixed‐species eukaryote samples, such as bee‐collected pollen, without requiring reference genomes. Instead, reference species are represented only by ‘genome skims’: low‐cost, low‐coverage, short‐read sequence datasets. The skims are mapped to individual long reads sequenced from mixed‐species samples using the MinION, a portable nanopore sequencing device, and each long read is uniquely assigned to a plant species.
We genome‐skimmed 49 wild UK plant species, validated our pipeline with mock DNA mixtures of known composition, and then applied RevMet to pollen loads collected from wild bees. We demonstrate that RevMet can identify plant species present in mixed‐species samples at proportions of DNA ≥ 1%, with few false positives and false negatives, and reliably differentiate species represented by high versus low amounts of DNA in a sample.
RevMet could readily be adapted to generate semi‐quantitative datasets for a wide range of mixed eukaryote samples. Our per‐sample costs were £90 per genome skim and £60 per pollen sample, and new versions of sequencers available now will further reduce these costs.Copyright © 2019 The Authors. Methods in Ecology and Evolution © 2019 British Ecological Society. The linked file is the published version of the article.NHM Repositor
The evolutionary history and timeline of mites in ancient soils
Get PDFAcariform mites play a crucial role as primary soil decomposers, impacting the carbon cycle. However, the timing of their diversification is uncertain, with estimated dates ranging from the Precambrian (no land plants) to the Carboniferous (diverse terrestrial ecosystems). One factor affecting these time estimates is an uncertain phylogenetic position of the earliest unequivocal fossil mites from the Devonian Rhynie Chert, which have been classified in five modern families and three suborders. Here, we thoroughly examine these specimens, assign them to a single species Protacarus crani (family Protoacaridae, fam. nov., suborder Endeostigmata) and integrate this information into a time-calibrated phylogenetic analysis. Our phylogeny suggests a Cambrian basal divergence of Acariformes (508-486 Ma), coinciding with the land colonization by bryophytes. At this time, the mites' ecological niches were probably diversified beyond the upper soil. Our study provides temporal context, improves the accuracy of fossil dating, and underscores the importance of mites' diverse habitats and their potential roles in soil food webs.Copyright © The Author(s) 2025. 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://creativecommo
ns.org/licenses/by-nc-nd/4.0/. The attached file is the published version of the article.NHM Repositor
Subfossil cyclostome bryozoans from Daidokutsu submarine cave, Okinawa, Japan
Get PDFA sediment core (Core 19) taken in Daidokutsu cave on Ie Island, Okinawa, spans the last 7,000 years. The sampling of multiple taxa from this submarine cave has been aimed at understanding the Holocene history of biodiversity and ecological dynamics. The results have already been published for ostracods, molluscs, foraminifera and cheilostome bryozoans. The current study focuses on the cyclostome bryozoan fauna, establishing a taxonomic foundation that will contribute to an understanding of responses by the bryozoan community in this cave habitat to environmental and climate changes through the Holocene. Very little has been published on modern and Quaternary fossil cyclostomes from Japan, and nearly all publications predate the routine use of scanning electron microscopy in cyclostome taxonomy. Fifteen cyclostome species are described here from Daidokutsu. Eight of these are new species, the remaining seven were identified only to the genus level. The high proportion of new species may not only reflect the uniqueness of the Daidokutsu cyclostome fauna but also the scarcity of studies on Japanese cyclostomes and the inadequacy of descriptions and figures in older publications, which make it difficult or impossible to interpret the species they describe. Unlike cyclostome cave faunas from the Mediterranean, erect cyclostomes strongly outnumber species with encrusting colonies. In addition, the secondary homonymy of Parasmittina ligulata, used for both a new species from Daidokutsu Cave and a Western Atlantic species, is resolved by renaming the Japanese species Parasmittina vieirai nom. nov.Copyright: July 2025 Palaeontological Association.
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.
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The genome sequence of the banded centipede, Lithobius variegatus Leach, 1814.
Get PDFWe present a genome assembly from a female specimen of Lithobius variegatus (banded centipede; Arthropoda; Chilopoda; Lithobiomorpha; Lithobiidae). The assembly contains two haplotypes with total lengths of 1,766.49 megabases and 1,768.00 megabases. Most of haplotype 1 (97.68%) is scaffolded into 23 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.44 kilobases.Copyright: © 2025 Edgecombe GD 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 work is properly cited. The attached file is the published version of the article.NHM Repositor
The genome sequence of a longhorn beetle, Rhagium mordax (Degeer, 1775)
Get PDFWe present a genome assembly from an individual female specimen of Rhagium mordax (longhorn beetle; Arthropoda; Insecta; Coleoptera; Cerambycidae). The genome sequence has a total length of 775.60 megabases. Most of the assembly (99.53%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.68 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,937 protein-coding genes.Copyright: © 2025 Barclay MVL 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 work is properly cited. The attached file is the published version of the article.NHM Repositor
Recognising type specimens in a dispersed collection. The Macaronesian land Mollusca described by R. T. Lowe
Get PDFA catalogue of the dispersed collection of the land snails of the Macaronesian Islands described by and attributed to R. T. Lowe is presented. The provenance of the material which relates primarily to T. V. Wollaston, his wife Edith Shepherd, Col. L. Worthington-Wilmer and H. B. Preston is discussed. Parts of the dispersed collection have been located in fifteen institutions in the United Kingdom, Ireland, The Netherlands, Germany, Belgium, Israel and the United States of America. The list (Appendix 1) comprises 216 nominal taxa attributable to Lowe of which 9 are infra-subspecific, introduced as subvarieties. In addition 8 manuscript names have been included. Possible type material of all but 21 have been located, these comprising 17 varieties and 4 subvarieties. A total of 9537 specimens have been located. The verification of the type status is discussed and a ranking of the type resources is attempted. Evidence is lacking to either corroborate or dismiss the syntype status of the majority of the material but past nomenclatural acts have selected lectotypes from many parts. Furthermore many museums consider the co-types distributed by H. B. Preston to be of syntype status. Only the shells stated to be figured in the 1831 and 1860 papers can be considered as figured syntypes, and these are figured in Appendix 2.The attached file is the published version of the article.NHM Repositor
HELIX INCRASSATA KLEIN, 1853 (MAY) IS NOT A JUNIOR PRIMARY HOMONYM OF HELIX INCRASSATA REEVE, 1853 (FEBRUARY) (GASTROPODA: HELICOIDEA)
Get PDFThe name of a well-known Miocene land snail species, Helix incrassata Klein, 1853 (May) (currently Pseudochloritis incrassata) is not a junior primary homonym of the name Helix incrassata Reeve, 1853 (February), because the latter is unavailable as it is a subsequent erroneous spelling of the name Helix incrustata Poey, 1852 (currently Thysanophora incrustata). Reeve gave Poey as author of incrassata; possibly as a lapsus for the similar word incrustata.Copyright © The Author(s). The attached file is the published version of the article.NHM Repositor
Centipedes (Myriapoda, Chilopoda) of Aldabra Atoll (Seychelles)
Get PDFCentipedes collected during Royal Society surveys of the arthropod fauna of the Aldabra Atoll in 1968–1975 are identified, described, and illustrated to provide the first checklist to the Aldabran centipede fauna, comprising 12 species. These newly include the lithobiomorph Lamyctes tristani (Pocock, 1893), the scolopendromorphs Scolopendra morsitansLinnaeus 1758, Cryptops cf. japonicus Takakuwa, 1934, Cryptops mauritianus Verhoeff, 1939, and Cryptops nigropictus Takakuwa, 1936, and the geophilomorphs Ityphilus cf. taeniaformis (Lawrence, 1960), Mecistocephalus angusticeps (Ribaut, 1914), Mecistocephalus lohmanderi Verhoeff, 1939, Orphnaeus dekanius Verhoeff, 1938, Ribautia cf. paucipes Attems, 1952, and Tuoba sydneyensis (Pocock, 1891). The geophilomorph genera Hovanyx Lawrence, 1960, syn. nov., and Mixophilus Silvestri, 1929, syn. nov., are revised in light of the examined material and hereby designated junior subjective synonyms of Tuoba Chamberlin, 1920 with the species Geophilus lemuricus Verhoeff, 1939, syn. nov., and Hovanyx waterloti Lawrence, 1960, syn. nov., designated as junior subjective synonyms of T. sydneyensis. The oryid genus Nycternyssa Crabill, 1959, syn. nov., is revised and designated a junior subjective synonym of Orphnaeus Meinert, 1870. New data on intraspecific morphological variation are presented for C. nigropictus, with the validity of Cryptops daszaki Lewis, 2002 being questioned following examination of its type material. The affinities and possible origins of the Aldabran centipede fauna are found to be mainly East African, with several species occurring across other islands in the Western Indian Ocean.Copyright: © George Popovici & Gregory D. Edgecombe. This is an open access article distributed under terms of the Creative Commons Attribution License (Attribution 4.0 International – CC BY 4.0). The attached file is the published version of the article.NHM Repositor
The old, unique C1 chondrite Flensburg – Insight into the first processes of aqueous alteration, brecciation, and the diversity of water-bearing parent bodies and lithologies
Get PDFOn September 12, 2019 at 12:49:48 (UT) a bolide was observed by hundreds of eye-witnesses from the Netherlands, Germany, Belgium, Denmark and the UK. One day later a small meteorite stone was found by accident in Flensburg. The presence of short-lived cosmogenic radionuclides with half-lives as short as 16 days proves the recent exposure of the found object to cosmic rays in space linking it clearly to the bolide event. An exceptionally short exposure time of ∼5000 years was determined. The 24.5 g stone has a fresh black fusion crust, a low density of <2 g/cm3, and a magnetic susceptibility of logχ = 4.35 (χ in 10−9 m3/kg). The rock consists of relict chondrules and clusters of sulfide and magnetite grains set in a fine-grained matrix. The most abundant phases are phyllosilicates. Carbonates (∼3.9 vol.%) occur as calcites, dolomites, and a Na-rich phase. The relict chondrules (often surrounded by sulfide laths) are free of anhydrous silicates and contain abundant serpentine. Lithic clasts are also surrounded by similar sulfide laths partly intergrown with carbonates. 53Mn-53Cr ages of carbonates in Flensburg indicate that brecciation and contemporaneous formation of the pyrrhotite-carbonate intergrowths by hydrothermal activities occurred no later than 4564.6 ± 1.0 Ma (using the angrite D'Orbigny as the Mn-Cr age anchor). This corresponds to 2.6 ± 1.0 or 3.4 ± 1.0 Ma after formation of CAIs, depending on the exact absolute age of CAIs. This is the oldest dated evidence for brecciation and carbonate formation, which likely occurred during parent body growth and incipient heating due to decay of 26Al.
In the three oxygen isotope diagram, Flensburg plots at the 16O-rich end of the CM chondrite field and in the transition field to CV-CK-CR chondrites. The mass-dependent Te isotopic composition of Flensburg is slightly different from mean CM chondrites and is most similar to those of the ungrouped C2 chondrite Tagish Lake. On the other hand, 50Ti and 54Cr isotope anomalies indicate that Flensburg is similar to CM chondrites, as do the ∼10 wt.% H2O of the bulk material. Yet, the bulk Zn, Cu, and Pb concentrations are about 30% lower than those of mean CM chondrites. The He, Ne, and Ar isotopes of Flensburg show no solar wind contribution; its trapped noble gas signature is similar to that of CMs with a slightly lower concentration of 20Netr.
Based on the bulk H, C, and N elemental abundances and isotopic compositions, Flensburg is unique among chondrites, because it has the lightest bulk H and N isotopic compositions of any type 1 or 2 chondrite investigated so far. Moreover, the number of soluble organic compounds in Flensburg is even lower than that of the brecciated CI chondrite Orgueil.
The extraordinary significance of Flensburg is evident from the observation that it represents the oldest chondrite sample in which the contemporaneous episodes of aqueous alteration and brecciation have been preserved. The characterization of a large variety of carbonaceous chondrites with different alteration histories is important for interpreting returned samples from the OSIRIS-REx and Hayabusa 2 missions.Copyright © 2020 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). The attached file is the published version of the article.NHM Repositor