• PESI - a taxonomic backbone for Europe

      de Jong, Y; Kouwenberg, J; Boumans, L; Hussey, C; Hyam, R; Nicolson, N; Kirk, P; Paton, A; Michel, E; Guiry, MD; et al. (2015-09-28)
    • Petrographic and chemical studies of the Cretaceous-Paleogene boundary sequence at El Guayal, Tabasco, Mexico: Implications for ejecta plume evolution from the Chicxulub impact crater

      Salge, T; Tagle, Roald; Schmitt, Ralf-Thomas; Hecht, Lutz; Wolf Uwe, Reimold; Chris, Koeberl (Geological Society of America, 2021-06-30)
      A combined petrographic and chemical study of ejecta particles from the Cretaceous-Paleogene boundary sequence of El Guayal, Tabasco, Mexico (520 km SW of Chicxulub crater), was carried out to assess their formation conditions and genetic relation during the impact process. The reaction of silicate ejecta particles with hot volatiles during atmospheric transport may have induced alteration processes, e.g., silicification and cementation, observed in the ejecta deposits. The various microstructures of calcite ejecta particles are interpreted to reflect different thermal histories at postshock conditions. Spherulitic calcite particles may represent carbonate melts that were quenched during ejection. A recrystallized microstructure may indicate short, intense thermal stress. Various aggregates document particle-particle interactions and intermixing of components from lower silicate and upper sedimentary target lithologies. Aggregates of recrystallized calcite with silicate melt indicate the consolidation of a hot suevitic component with sediments at ≳750 °C. Accretionary lapilli formed in a turbulent, steam-condensing environment at ~100 °C by aggregation of solid, ash-sized particles. Concentric zones with smaller grain sizes of accreted particles indicate a recurring exchange with a hotter environment. Our results suggest that during partial ejecta plume collapse, hot silicate components were mixed with the fine fraction of local surface-derived sediments, the latter of which were displaced by the preceding ejecta curtain. These processes sustained a hot, gas-driven, lateral basal transport that was accompanied by a turbulent plume at a higher level. The exothermic back-reaction of CaO from decomposed carbonates and sulfates with CO2 to form CaCO3 may have been responsible for a prolonged release of thermal energy at a late stage of plume evolution.
    • Petrological and geochemical characterisation of the sarsen stones at Stonehenge

      Nash, David J; Ciborowski, T Jake R; Darvill, Timothy; Parker Pearson, Mike; Ullyott, J Stewart; Damaschke, Magret; Evans, Jane A; Goderis, Steven; Greaney, Susan; Huggett, Jennifer M; et al. (Public Library of Science (PLoS), 2021-08-04)
      Little is known of the properties of the sarsen stones (or silcretes) that comprise the main architecture of Stonehenge. The only studies of rock struck from the monument date from the 19th century, while 20th century investigations have focussed on excavated debris without demonstrating a link to specific megaliths. Here, we present the first comprehensive analysis of sarsen samples taken directly from a Stonehenge megalith (Stone 58, in the centrally placed trilithon horseshoe). We apply state-of-the-art petrographic, mineralogical and geochemical techniques to two cores drilled from the stone during conservation work in 1958. Petrographic analyses demonstrate that Stone 58 is a highly indurated, grain-supported, structureless and texturally mature groundwater silcrete, comprising fine-to-medium grained quartz sand cemented by optically-continuous syntaxial quartz overgrowths. In addition to detrital quartz, trace quantities of silica-rich rock fragments, Fe-oxides/hydroxides and other minerals are present. Cathodoluminescence analyses show that the quartz cement developed as an initial <10 μm thick zone of non-luminescing quartz followed by ~16 separate quartz cement growth zones. Late-stage Fe-oxides/hydroxides and Ti-oxides line and/or infill some pores. Automated mineralogical analyses indicate that the sarsen preserves 7.2 to 9.2 area % porosity as a moderately-connected intergranular network. Geochemical data show that the sarsen is chemically pure, comprising 99.7 wt. % SiO2. The major and trace element chemistry is highly consistent within the stone, with the only magnitude variations being observed in Fe content. Non-quartz accessory minerals within the silcrete host sediments impart a trace element signature distinct from standard sedimentary and other crustal materials. 143Nd/144Nd isotope analyses suggest that these host sediments were likely derived from eroded Mesozoic rocks, and that these Mesozoic rocks incorporated much older Mesoproterozoic material. The chemistry of Stone 58 has been identified recently as representative of 50 of the 52 remaining sarsens at Stonehenge. These results are therefore representative of the main stone type used to build what is arguably the most important Late Neolithic monument in Europe.
    • The Phoenix: The Role of Conservation Ethics in the Development of St Pancras Railway Station (London, UK)

      Allington-Jones, L (Ubiquity Press Ltd., 2013-09-02)
      St Pancras Railway Station, London (UK), has recently undergone alterations that have variously been described as conservation, restoration, refurbishment and rejuvenation, to become the new terminal for Eurostar. This article aims to evaluate the recent changes and relate them to current conservation ethics. Observations were made on site, derived from research in published literature and were assessed according to principles of conservation. The article concludes that, in the recent developments, conservation ethics have been drawn upon in an inconsistent fashion, and that the best description for the rebirth of the station is ‘recycling’. Investigation of the ‘conservation’ of significant items of national heritage, like St Pancras, is essential for formulating future standards and evaluating our own perceptions and the diversity of possible interpretations of conservation terminology.
    • Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer

      Undheim, Eivind AB; Jenner, Ronald (Springer Science and Business Media LLC, 2021-02-05)
      Abstract: Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.
    • The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis

      Mwinyi, A; Bailly, X; Bourlat, SJ; Jondelius, U; Littlewood, T; Podsiadlowski, L (Springer Science and Business Media LLC, 2010-10-13)
      Background Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria". Results We describe the first complete mitochondrial genome sequence of a member of the Acoela, Symsagittifera roscoffensis. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of Xenoturbella bocki as sister group to or part of the deuterostomes was also unstable. Conclusions Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.
    • Phylogenetic relationships within Dicrocoeliidae (Platyhelminthes: Digenea) from birds from the Czech Republic using partial 28S rDNA sequences

      Aldhoun, J; Elmahy, R; Littlewood, T (Springerlink, 2018-09-05)
      Partial (D1-D3) 28S rRNA gene sequences from 16 isolates of digenean parasites of the family Dicrocoeliidae recovered from 16 bird species from the Czech Republic were used for phylogenetic reconstruction. Comparison with sequences available from GenBank suggests that the genus Brachylecithum is paraphyletic, requiring further validation and possible systematic revision. Although partial 28S rDNA is relatively conserved, analyses suggest that the following taxa are synonymous: Lutztrema attenuatum = L. monenteron = L. microstomum, Brachylecithum lobatum = B. glareoli. Zonorchis petiolatus is reassigned back to the genus Lyperosomum with L. collurionis as a junior synonym. The study revealed how complicated the systematics of the family Dicrocoeliidae is currently. The morphology of the group is variable, and the current distinguishing characters at species and even generic level are not sufficiently distinctive; it is difficult to identify the specimens correctly and identification of GenBank isolates is not reliable. Extensive sampling of isolates for both molecular and morphological studies is necessary to resolve the relationships within the family.
    • Phylogenetically Widespread Polyembryony in Cyclostome Bryozoans and the Protracted Asynchronous Release of Clonal Brood-Mates

      Jenkins, HL; Waeschenbach, A; Okamura, B; Hughes, RN; Bishop, JDD; Hejnol, A (2017-01-17)
    • Phylogenomics of non-model ciliates based on transcriptomic analyses

      Chen, X; Zhao, X; Liu, X; Warren, A; Zhao, F; Miao, M (2015-05)
    • Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

      Hamilton, CA; St Laurent, RA; Dexter, K; Kitching, I; Breinholt, JW; Zwick, A; Timmermans, MJTN; Barber, JR; Kawahara, AY (BioMed Central, 2019-09-18)
      Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
    • Phylogeny and Historical Biogeography of Asian Pterourus Butterflies (Lepidoptera: Papilionidae): A Case of Intercontinental Dispersal from North America to East Asia

      Wu, L-W; Yen, S-H; Lees, David; Lu, C-C; Yang, P-S; Hsu, Y-F; Boykin, LM (2015-10-20)
      The phylogenetic status of the well-known Asian butterflies often known as Agehana (a species group, often treated as a genus or a subgenus, within Papilio sensu lato) has long remained unresolved. Only two species are included, and one of them especially, Papilio maraho, is not only rare but near-threatened, being monophagous on its vulnerable hostplant, Sassafras randaiense (Lauraceae). Although the natural history and population conservation of “Agehana” has received much attention, the biogeographic origin of this group still remains enigmatic. To clarify these two questions, a total of 86 species representatives within Papilionidae were sampled, and four genes (concatenated length 3842 bp) were used to reconstruct their phylogenetic relationships and historical scenarios. Surprisingly, “Agehana” fell within the American Papilio subgenus Pterourus and not as previously suggested, phylogenetically close to the Asian Papilio subgenus Chilasa. We therefore formally synonymize Agehana with Pterourus. Dating and biogeographic analysis allow us to infer an intercontinental dispersal of an American ancestor of Asian Pterourus in the early Miocene, which was coincident with historical paleo-land bridge connections, resulting in the present “East Asia-America” disjunction distribution. We emphasize that species exchange between East Asia and America seems to be a quite frequent occurrence in butterflies during the Oligocene to Miocene climatic optima.
    • Phylogeny of Lithobiidae Newport, 1844, with emphasis on the megadiverse genus Lithobius Leach, 1814 (Myriapoda, Chilopoda)

      Ganske, Anne‐Sarah; Vahtera, Varpu; Dányi, László; Edgecombe, GD; Akkari, Nesrine (Wiley, 2020-11-04)
      Phylogenetic analyses based on molecular and morphological data were conducted to shed light on relationships within the mostly Palaearctic/Oriental centipede family Lithobiidae, with a particular focus on the Palaearctic genus Lithobius Leach, 1814 (Lithobiidae, Lithobiomorpha), which contains >500 species and subspecies. Previous studies based on morphological data resolved Lithobius as nonmonophyletic, but molecular-based phylogenetic analyses have until now sampled few species. To elucidate species inter-relationships of the genus, test the validity of its classification into subgenera, and infer its relationships with other Lithobiidae, we obtained molecular data (nuclear markers: 18S rRNA, 28S rRNA; mitochondrial markers: 16S rRNA, COI) and 61 morphological characters for 44 species of Lithobius representing four of its eight subgenera and nine other representatives of Lithobiidae. The data were analyzed phylogenetically using maximum-likelihood, parsimony and Bayesian inference. This study suggests that (i) a close relationship between L. giganteus and the pterygotergine Disphaerobius loricatus highlighted in recent morphological analyses is also strongly supported by molecular data, and Pterygoterginae is formally synonymized with Lithobiinae; (ii) the Oriental/Australian genus Australobius is consistently resolved as sister group to all other sampled Lithobiidae by the molecular and combined data; (iii) the subfamily Ethopolyinae may be paraphyletic; (iv) the genus Lithobius is nonmonophyletic; (v) the subgenera Lithobius, Sigibius and Monotarsobius are nonmonophyletic and should not be used in future taxonomic studies; and (vi) there are instances of cryptic species and cases in which subspecies should be elevated to full species status, as identified for some European taxa within Lithobius.
    • Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean

      Xu, D; Sun, P; Zhang, Y; Li, R; Huang, B; Jiao, N; Warren, A; Wang, L (2018-08-29)
    • Pigs vs people: the use of pigs as analogues for humans in forensic entomology and taphonomy research

      Matuszewski, S; Hall, MJR; Moreau, G; Schoenly, KG; Tarone, AM; Villet, MH (Springer Science and Business Media LLC, 2019-06-17)
      Most studies of decomposition in forensic entomology and taphonomy have used non-human cadavers. Following the recommendation of using domestic pig cadavers as analogues for humans in forensic entomology in the 1980s, pigs became the most frequently used model cadavers in forensic sciences. They have shaped our understanding of how large vertebrate cadavers decompose in, for example, various environments, seasons and after various ante- or postmortem cadaver modifications. They have also been used to demonstrate the feasibility of several new or well-established forensic techniques. The advent of outdoor human taphonomy facilities enabled experimental comparisons of decomposition between pig and human cadavers. Recent comparisons challenged the pig-as-analogue claim in entomology and taphonomy research. In this review, we discuss in a broad methodological context the advantages and disadvantages of pig and human cadavers for forensic research and rebut the critique of pigs as analogues for humans. We conclude that experiments using human cadaver analogues (i.e. pig carcasses) are easier to replicate and more practical for controlling confounding factors than studies based solely on humans and, therefore, are likely to remain our primary epistemic source of forensic knowledge for the immediate future. We supplement these considerations with new guidelines for model cadaver choice in forensic science research.