Now showing items 1-20 of 1290

    • The northernmost known observation of Myrmecophilus acervorum and the first records of Myrmecophilidae (Orthoptera, Ensifera) from Latvia

      Balodis, Aleksandrs; Starka, Rūta; Telnov, Dmitry (Pensoft, 2025-04-25)
      The first observations of myrmecophilous ant cricket Myrmecophilus acervorum (Panzer, 1799) and the family Myrmecophilidae from Latvia are presented. The observations were made in two locations subject to flooding in springtime. Adult and juvenile female individuals were observed. The discussed records appear to be the northernmost known distribution limit of this species.
    • The evolutionary history and timeline of mites in ancient soils

      Klimov, Pavel B; Kolesnikov, Vasiliy B; Vorontsov, Dmitry D; Ball, Alexander D; Bolton, Samuel J; Mellish, Claire; Edgecombe, GD; Pepato, Almir R; Chetverikov, Philipp E; He, Qixin; et al. (Springer Science and Business Media LLC, 2025-04-19)
      Acariform 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.
    • Gregarious behaviour in Carboniferous cyclidan crustaceans

      Bicknell, Russell DC; Klompmaker, Adiël A; Edgecombe, GD; McCoy, Victoria E; Young, Andrew; Lauer, Bruce; Lauer, René; Cuomo, Carmela (The Royal Society, 2025-03-19)
      Gregarious behaviours in modern and fossil arthropods are commonly associated with defensive strategies, mass moulting and synchronous reproduction. Such behaviour is scarcely documented in the crustacean fossil record. Identifying clusters in extinct Pancrustacea is, therefore, important for understanding the evolutionary history and origin of crustacean gregariousness. Cyclida, an order of extinct, enigmatic pancrustaceans that have been subject to limited palaeoecological examination, represents an ideal group for testing the presence of gregarious behaviour. Here, we report a cluster of 50 <jats:italic>Schramine montanaensis</jats:italic> individuals from the Serpukhovian-aged Bear Gulch Limestone of Montana, USA, expanding the exceptionally rare record of cyclidan aggregations. The presence of articulated specimens with appendages and possible gill preservation supports the interpretation of carcasses that were preserved during a rapid burial event. We propose that this cluster records either a mass moulting event or clustering for shelter, representing one of the oldest records of crustacean gregariousness. These findings provide important insights into cyclidan life modes and ecological interactions in Carboniferous marine environments.
    • Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

      Peel, Ned; Dicks, Lynn V; Clark, Matthew D; Heavens, Darren; Percival‐Alwyn, Lawrence; Cooper, Chris; Davies, Richard G; Leggett, Richard M; Yu, Douglas W; Freckleton, Robert (Wiley, 2019-07-08)
      The 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.
    • Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

      Martin, Samuel; Heavens, Darren; Lan, Yuxuan; Horsfield, Samuel; Clark, Matthew D; Leggett, Richard M (Springer Science and Business Media LLC, 2022-01-24)
      Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic mock community and construct sequencing libraries with a range of mean read lengths. Enrichment is up to 13.87-fold for the least abundant species in the longest read length library; factoring in reduced yields from rejecting molecules the calculated efficiency raises this to 4.93-fold. Finally, we introduce a mathematical model of enrichment based on molecule length and relative abundance, whose predictions correlate strongly with mock and complex real-world microbial communities.
    • Publisher Correction: Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods

      Marsh, William A; Hall, Andie; Barnes, I; Price, Ben (Springer Science and Business Media LLC, 2025-03-19)
    • Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods

      Marsh, William A; Hall, Andie; Barnes, I; Price, Ben (Springer Science and Business Media LLC, 2025-02-19)
      While DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output. Several DNA extraction and library build methods that are designed to work with degraded DNA have been developed, although the ability to implement these methods at scale and at low cost has yet to be formally addressed. Here, the performance of widely used DNA extraction and library build methods are compared using museum specimens. We find that while our selected DNA extraction methods do not significantly differ in DNA yield, the Santa Cruz Reaction (SCR) library build method is not only the most effective at retrieving degraded DNA from museum specimens but also easily implemented at high throughput for low cost. Results highlight the importance of lab protocol on data yield. An optimised “sample to sequencing” high-throughput protocol which incorporates SCR is included to allow for easy uptake by the wider scientific community.
    • A new euarthropod from the Soom Shale (Ordovician) Konservat‐Lagerstätte, South Africa, with exceptional preservation of the connective endoskeleton and myoanatomy

      Gabbott, Sarah E; Edgecombe, GD; Theron, Johannes N; Aldridge, Richard J (Wiley, 2025-03-26)
      A new exceptionally preserved euarthropod, Keurbos susanae gen. et sp. nov. from the Upper Ordovician Soom Shale Konservat‐Lagerstätte of South Africa, is described herein. Two specimens exhibit an unusual preservation style such that the cuticular exoskeleton is preserved in low relief but retains high‐fidelity details, whereas the internal anatomy is preserved in three dimensions and includes myoanatomy and aspects of the connective inter‐ and intrasegmental endoskeleton. The trunk has 46 homonomous segments and tapers towards the posterior. The dorsal surface comprises the posterior margins of tergites that form rounded paratergal folds at their lateral margins. Sternal morphology is seen from an internal view of the fossils and includes axial sternites and associated ovoid plates, both with fringing setae along their posterior margins. Patchy, incomplete preservation of the appendages is consistent with the ‘reversed’ taphonomy of these fossils in which sclerotized elements that project beyond the body margin, such as lamellae with vascular channels and pits, are preserved, whereas those inside the body margins are absent or poorly expressed. Euarthropod characters include an arthrodized tergal and sternal exoskeleton, and a segmental connective endoskeleton. Recent depopulation of the euarthropod stem group has witnessed conspicuously arthrodized fossils formerly placed in the stem group being shifted into the crown, increasing the likelihood that <jats:italic>Keurbos</jats:italic> is likewise a crown‐group euarthropod. Comparison with a phylogenetically disparate suite of similarly homonomous, multisegmented taxa indicates no convincing synapomorphies. The grouping of relevant middle Palaeozoic exemplars as ‘enantiopod’ pancrustaceans could suggest that Keurbos might be allied.
    • The problems of resolving historical specimen data, focusing on a specimen of Myotis austroriparius (Mammalia, Chiroptera, Vespertilionidae) collected by Thomas Drummond

      Jenkins, Paulina; Sealy, Spencer G (Canadian Science Publishing, 2022-03-15)
      The geographical itineraries of Thomas Drummond’s two separate expeditions to Canada (1825–1827) and the United States of America (1831–1835) are used to provide historical context for the specimens collected and their localities. The coordinates for these locations are estimated and their geographical positions mapped. The difficulties of resolving various problems with historical specimens are explored and several examples are provided, including the contentious origin and identification of a southeastern myotis, Myotis austroriparius (Rhoads, 1897) (NHMUK 1837.4.8.127). Information about type specimens is discussed and the geographical position of several type localities of rodents and a mustelid in the Rocky Mountains and a lagomorph in the USA are refined.
    • Secrets of a Silent Miniaturist: Findings from a Technical Study of Miniatures Attributed to Isaac Oliver

      Kimbriel, Christine Slottved; Ricciardi, Paola (Paul Mellon Centre for Studies in British Art, 2020-09-30)
      An evidently accomplished draughtsman, Isaac Oliver (circa 1565–1617) remains an enigmatic artist in many respects. While Nicholas Hilliard’s treatise on the art of limning provides considerable insight into his material use, techniques, and self-perception, no equivalent documentary evidence survives from Oliver’s hand, and many questions regarding his training, approach, and oeuvre have yet to be answered. This article presents key findings from the collaborative and technically focused research project “Secrets of a Silent Miniaturist: Technical Analysis of Isaac Oliver’s Miniatures”, undertaken by the Fitzwilliam Museum and the Hamilton Kerr Institute in Cambridge (UK). The project aims to shed light on Oliver’s artistic practice through the detailed, technical study of a representative selection of his surviving miniatures, investigated through an up-to-date, non-invasive analytical and technical lens. The article discusses the discovery of near-invisible changes to compositions implemented during the initial execution, differences in execution and later history between two versions of a portrait of Henry Frederick Prince of Wales, the first identification in a miniature of a rare mercury-based white pigment whose deterioration led to later campaigns of repainting, and the use of a hitherto unacknowledged range of pigments and media in Oliver’s landscape miniatures that raises further questions about Oliver’s connection with artistic traditions on the Continent.
    • New evidence for the intentional use of calomel as a white pigment

      Crippa, Mila; Legnaioli, Stefano; Kimbriel, Christine; Ricciardi, Paola (Wiley, 2021-01-14)
      In this work, we report the results of the in situ application of micro‐Raman spectroscopy to the analysis of two historic painted objects: a 15th‐century illuminated manuscript and a late 16th‐century portrait miniature. Both objects were unexpectedly found to contain calomel (Hg<jats:sub>2</jats:sub>Cl<jats:sub>2</jats:sub>), intentionally used as a white pigment. Calomel was a widespread and popular medicine until it fell out of use at the end of the 19th century due to its toxicity, and a material called ‘mercury white’ is referred to in 16th‐century technical literature on painting. However, although calomel has been recognised in the past as a degradation product of cinnabar in both wall and easel paintings, its deliberate use as a pigment on cultural heritage objects has only been documented recently in white areas painted on 17th‐century South American objects. The present study describes the first ever verified use of calomel as a white pigment on European works of art, both of which predate its documented use in South America.
    • Non-Invasive Technical Investigation of English Portrait Miniatures Attributed to Nicholas Hilliard and Isaac Oliver

      Fiorillo, Flavia; Burgio, Lucia; Kimbriel, Christine Slottved; Ricciardi, Paola (MDPI AG, 2021-07-09)
      This study presents the results of the technical investigation carried out on several English portrait miniatures painted in the 16th and 17th century by Nicholas Hilliard and Isaac Oliver, two of the most famous limners working at the Tudor and Stuart courts. The 23 objects chosen for the analysis, spanning almost the entire career of the two artists, belong to the collections of the Victoria and Albert Museum (London) and the Fitzwilliam Museum (Cambridge). A non-invasive scientific methodology, comprising of stereo and optical microscopies, Raman microscopy, and X-ray fluorescence spectroscopy, was required for the investigation of these small-scale and fragile objects. The palettes and working techniques of the two artists were characterised, focusing in particular on the examination of flesh tones, mouths, and eyes. These findings were also compared to the information written in the treatises on miniature painting circulating during the artists’ lifetime. By identifying the materials and techniques most widely employed by the two artists, this study provides information about similarities and differences in their working methods, which can help to understand their artistic practice as well as contribute to matters of attribution.
    • Use of standard analytical tools to detect small amounts of smalt in the presence of ultramarine as observed in 15th-century Venetian illuminated manuscripts

      Ricciardi, Paola; Dooley, Kathryn A; MacLennan, Douglas; Bertolotti, Giulia; Gabrieli, Francesca; Patterson, Catherine Schmidt; Delaney, John K (Springer Science and Business Media LLC, 2022-03-21)
      A previous preliminary study of 15th-century Venetian manuscript fragments by the Master of the Murano Gradual identified the presence of cobalt in many ultramarine blue areas, suggesting the presence of smalt. This would represent an early use of this glassy pigment in Venetian illuminated manuscripts. Whereas sampling has been used to identify smalt in 15th century paintings, only non-invasive methods can be used on manuscripts due to their small size and fragile nature. Here we investigated four non-invasive analysis techniques to identify small amounts of smalt in the presence of ultramarine, including single-point and scanning XRF spectroscopy, UV–vis-NIR-SWIR reflectance spectroscopy (FORS), Raman spectroscopy, and external reflection FT-IR spectroscopy. This was done by studying paint mock-ups of ultramarine and smalt mixtures with and without the presence of a white pigment on parchment. The results showed molecular spectroscopy techniques (reflectance, Raman, and FTIR) require at least ~ 30–40% smalt by percent mass when in the presence of ultramarine in order to detect its presence, whereas elemental XRF spectroscopy can detect cobalt (and thus infer the presence of smalt) at the ~ 1% level. To further explore the inference of smalt by XRF, additional XRF analysis was conducted to specifically look for elements associated with cobalt minerals (i.e. nickel, arsenic, bismuth, etc.). High spatial resolution XRF scanning (60–100 μm X-ray spot size) was used to look for cobalt in smalt particles which are typically larger than those of ultramarine. These two XRF analysis approaches worked well with the mock-up paint samples, and were subsequently applied to the manuscripts for which molecular spectroscopy methods yielded no unambiguous evidence for smalt. The data underscore the challenges of conclusively identifying smalt in complex paint systems when samples are not available, but do suggest that the Master of the Murano illuminated manuscript fragments contain smalt, but perhaps not in a form or amount researchers are used to seeing in paintings.
    • A revision of the type locality of Black-throated Accentor Prunella atrogularis huttoni (Moore)

      van Grouw, Hein; J., Praveen (The Trust for Avian Systematics, 2025-02-26)
      We 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’
    • First evidence of attached juveniles in the solutan echinoderm Pahvanticystis from the middle Cambrian Weeks Formation (Utah, USA)

      Savage, Harry; Rahman, Imran (Polska Akademia Nauk Instytut Paleobiologii (Institute of Paleobiology, Polish Academy of Sciences), 2025)
      The fossil record of the Palaeozoic echinoderm class Soluta suggests they originated in the Miaolingian (middle Cambrian) of Laurentia as permanently attached suspension feeders, demonstrating a stepwise shift towards vagility in successive strata. Here, we report a new specimen of Pahvanticystis cf. utahensis associated with three putative juveniles interpreted as belonging to the same species. We interpret this as evidence of facultative attachment in juveniles of Pahvanticystis, which had not previously been reported in this taxon, but is known in the earlier genus Castericystis. Our findings indicate that attachment as a juvenile was more widespread in solutans than previously thought.
    • Geology and fossils of Chatham Island, New Zealand

      Taylor, Paul (Deposits Magazine, 2023-04-23)
    • Trabecular bone structure of the proximal capitate in extant hominids and fossil hominins with implications for midcarpal joint loading and the dart‐thrower's motion

      Bird, Emma Elizabeth; Kivell, Tracy L; Dunmore, Christopher J; Tocheri, Matthew W; Skinner, Matthew M (Wiley, 2024-02-16)
      Objectives This research examines whether the distribution of trabecular bone in the proximal capitates of extant hominids, as well as several fossil hominin taxa, is associated with the oblique path of the midcarpal joint known as the dart‐thrower's motion (DTM). Materials and Methods We analyzed proximal capitates from extant (<jats:italic>Pongo n</jats:italic> = 12; <jats:italic>Gorilla n</jats:italic> = 11; <jats:italic>Pan n</jats:italic> = 10; fossil and recent <jats:italic>Homo sapiens n</jats:italic> = 29) and extinct (<jats:italic>Australopithecus sediba n</jats:italic> = 2; <jats:italic>Homo naledi n</jats:italic> = 1<jats:italic>; Homo floresiensis n</jats:italic> = 2; Neandertals <jats:italic>n</jats:italic> = 3) hominids using a new canonical holistic morphometric analysis, which quantifies and visualizes the distribution of trabecular bone using relative bone volume as a fraction of total volume (rBV/TV). Results Homo sapiens and Neandertals had a continuous band of high rBV/TV that extended across the scaphoid, lunate, and hamate subarticular regions, but other fossil hominins and extant great apes did not. <jats:italic>A. sediba</jats:italic> expressed a distinct combination of human‐like and <jats:italic>Pan</jats:italic>‐like rBV/TV distribution. Both <jats:italic>H. floresiensis</jats:italic> and <jats:italic>H. naledi</jats:italic> had high rBV/TV on the ulnar‐side of the capitate but low rBV/TV on the radial‐side. Conclusion The proximal capitates of <jats:italic>H. sapiens</jats:italic> and Neandertals share a distinctive distribution of trabecular bone that suggests that these two species of <jats:italic>Homo</jats:italic> regularly load(ed) their midcarpal joints along the full extent of the oblique path of the DTM. The observed pattern in <jats:italic>A. sediba</jats:italic> suggests that human‐like stress at the capito‐scaphoid articular surface was combined with <jats:italic>Pan</jats:italic>‐like wrist postures, whereas the patterns in <jats:italic>H. floresiensis</jats:italic> and <jats:italic>H. naledi</jats:italic> suggest their midcarpal joints were loaded differently from that of <jats:italic>H. sapiens</jats:italic> and Neandertals.
    • Bryozoa from the Maastrichtian Korojon Formation, Western Australia

      Håkansson, Eckart; Gordon, Dennis P; Taylor, PD (Scandinavian University Press, 2024-06-14)
      The first Australian Cretaceous bryozoan fauna is described from the Upper Campanian – Lower Maastrichtian Korojon Formation from the Giralia Anticline in north-western Western Australia. Bryozoans are the numerically dominant element in a sclerobiont community dependent on the abundant large inoceramids, utilizing both valves in life position as well as reworked shell fragments. A total of 68 species-level taxa are described (22 cyclostomes and 46 cheilostomes); 50 of these are new (12 cyclos-tomes and 38 cheilostomes) and the remaining 18 taxa are left at various levels of open nomenclature. They are referred to 47 genera (14 cyclostome and 33 cheilostome genera, 11 of which are new), with a total of 10 taxa left in open nomenclature. One new family, Cardabiellidae, is introduced. The total Late Cretaceous bryozoan fauna known from the Southern Hemisphere remnants of the Gondwana supercontinent – South America, Africa, India, Antarctica, Australia, Zealandia – is significantly less diverse than that known from the Northern Hemisphere, where the European Chalk Sea fauna constitutes the diversity hotspot. The addition of the Korojon fauna described here expands our knowledge of the Cretaceous bryozoan fauna from the Southern Hemisphere considerably, particularly with respect to the youngest bryozoan order, the Cheilostomata. And importantly, the Korojon fauna, more than doubles the proportion of Late Cretaceous cheilostome genera endemic to the Southern Hemisphere from 12.5% to more than 25% of the total number of Late Cretaceous genera presently known from this realm. We suggest that this significant expansion may well warrant a reassessment of the role of Southern Hemisphere bryozoan faunas in the recovery from the Cretaceous-Paleogene biotic turnover.
    • Convergent evolution of plant prickles by repeated gene co-option over deep time

      Satterlee, James W; Alonso, David; Gramazio, Pietro; Jenike, Katharine M; He, Jia; Arrones, Andrea; Villanueva, Gloria; Plazas, Mariola; Ramakrishnan, Srividya; Benoit, Matthias; et al. (American Association for the Advancement of Science (AAAS), 2024-08-02)
      An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles—sharp epidermal projections—that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus <jats:italic>Solanum</jats:italic> . Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new <jats:italic>Solanum</jats:italic> genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.
    • A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant (Azure Tit Cyanistes cyanus (Pallas, 1770))

      Irestedt, Martin; Thörn, Filip; Ericson, Per GP; van Grouw, Hein; Red'kin, Yaroslav A; Hellquist, Alexander; Johansson, Frank; Nylander, Johan AA (Elsevier BV, 2023-08-26)
      The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus (Pallas, 1770) and European Blue Tit Cyanistes caeruleus (Linnaeus, 1758), by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying plumages. The project was funded by crowdsourcing and initiated when two presumed Azure Tits, observed by hundreds of Swedish birdwatchers, were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue Tit. The results confirm that hybrids with intermediate plumages, so called Pleske’s Tits, are first generation hybrids (F1 hybrids). Individuals, whose plumages are similar to Azure Tits, but assessed as hybrids based on minor plumage deviations, are all backcrosses but vary in their degree of hybrid content. However, some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid content. The results indicate that: (1) hybrid content may be widespread in Azure Tits in the western part of its habitat distribution; (2) plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin; and (3) all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid origin. We therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation backcrosses. We argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.