• Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

      Welker, F; Hajdinjak, M; Talamo, S; Jaouen, K; Dannemann, M; David, F; Julien, M; Meyer, M; Kelso, J; Barnes, I; et al. (National Academy of Sciences, 2016-09-16)
      In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this “transitional” assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal–Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.
    • Palladosilicide, Pd2Si, a new mineral from the Kapalagulu Intrusion, Western Tanzania and the Bushveld Complex, South Africa

      Cabri, LJ; McDonald, AM; Rudashevsky, NS; Poirier, G; Wilhelmij, HR; Zhe, W; Rudashevsky, VN; Stanley, Christopher (2015-04)
    • A parakeet specimen held at National Museums Scotland is a unique skin of the extinct Reunion Parakeet Psittacula eques eques: a reply to Cheke and Jansen ()

      Jones, CG; Jackson, HA; McGowan, RY; Hume, JP; Forshaw, JM; Tatayah, V; Winters, R; Groombridge, JJ (Wiley, 2018-11-02)
      Cheke and Jansen (2016) questioned the identity of a parakeet specimen at National Museums Scotland (NMS), Edinburgh, which is considered in a paper by Jackson et al. (2015) to be a specimen of the extinct R eunion Parakeet Psittacula eques eques (Boddaert, 1783). They suggest that with the available information, its provenance cannot be ascribed with any certainty and it is most likely, on the basis of probability, to be from Mauritius, although they do not exclude the possibility that the parakeet comes from R eunion, the neighbouring island of Mauritius. The provenance and identity of this specimen has previously been questioned (Jones 1987, Hume 2007, Hume & Walters 2012), with the possibility that it may be a Mauritius Parakeet Psittacula eques echo. Since these accounts were written, more work conducted on Psittacula parakeets of the Indian Ocean Islands indicates that the Edinburgh specimen is a R eunion Parakeet, and Cheke and Jansen (2016) would have been unaware of some of this work.
    • Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses

      Jenner, RA; von Reumont, BM; Campbell, LI; Undheim, EAB (Oxford University Press (OUP), 2019-08-08)
      Centipedes are among the most ancient groups of venomous predatory arthropods. Extant species belong to five orders, but our understanding of the composition and evolution of centipede venoms is based almost exclusively on one order, Scolopendromorpha. To gain a broader and less biased understanding we performed a comparative proteotranscriptomic analysis of centipede venoms from all five orders, including the first venom profiles for the orders Lithobiomorpha, Craterostigmomorpha, and Geophilomorpha. Our results reveal an astonishing structural diversity of venom components, with 93 phylogenetically distinct protein and peptide families. Proteomically-annotated gene trees of these putative toxin families show that centipede venom composition is highly dynamic across macroevolutionary timescales, with numerous gene duplications as well as functional recruitments and losses of toxin gene families. Strikingly, not a single family is found in the venoms of representatives of all five orders, with 67 families being unique for single orders. Ancestral state reconstructions reveal that centipede venom originated as a simple cocktail comprising just four toxin families, with very little compositional evolution happening during the approximately 50 My before the living orders had diverged. Venom complexity then increased in parallel within the orders, with scolopendromorphs evolving particularly complex venoms. Our results show that even venoms composed of toxins evolving under the strong constraint of negative selection can have striking evolutionary plasticity on the compositional level. We show that the functional recruitments and losses of toxin families that shape centipede venom arsenals are not concentrated early in their evolutionary history, but happen frequently throughout.
    • Parasites lost: using natural history collections to track disease change across deep time

      Harmon, A; Littlewood, DTJ; Wood, CL (Ecological Society of America, 2019-03-04)
      Recent decades have brought countless outbreaks of infectious disease among wildlife. These events appear to be increasing in frequency and magnitude, but to objectively evaluate whether ecosystems are experiencing rising rates of disease, scientists require historical data on disease abundance. Specimens held in natural history collections represent a chronological archive of life on Earth and may, in many cases, be the only available source of data on historical disease patterns. It is possible to extract information on past disease rates by studying trace fossils (indirect fossilized evidence of an organism's presence or activity, including coprolites or feces), sequencing ancient DNA of parasites, and examining sediment samples, mummified remains, study skins (preserved animal skins prepared by taxidermy for research purposes), liquid‐preserved hosts, and hosts preserved in amber. Such use of natural history collections could expand scientific understanding of parasite responses to environmental change across deep time (that is, over the past several centuries), facilitating the development of baselines for managing contemporary wildlife disease.
    • Patterns and drivers of lichen species composition in a NW-European lowland deciduous woodland complex

      Wolseley, PA; Thüs, H; Eggleton, P; Sanderson, N; Carpenter, D (2017-02)
    • Patterns and Risk Factors of Helminthiasis and Anemia in a Rural and a Peri-urban Community in Zanzibar, in the Context of Helminth Control Programs

      Knopp, S; Mohammed, KA; Stothard, JR; Khamis, IS; Rollinson, D; Marti, H; Utzinger, J; Bethony, JM (2010-05-11)
    • Patterns of genetic diversity in three plant lineages endemic to the Cape Verde Islands

      Romeiras, MM; Monteiro, F; Duarte, MC; Schaefer, H; Carine, M (2015)
    • Patterns of magnesium content in Arctic bryozoan skeletons along a depth gradient

      Taylor, PD; Borszcz, Tomasz; Kuklin´ski, Piotr (Springer, 2012-10-14)
      A growing body of evidence suggests that ocean acidification acting synergistically with ocean warming alters carbonate biomineralization in a variety of marine biota. Magnesium often substitutes for Ca in the calcite skeletons of marine invertebrates, increasing their solubility. The spatio-environmental distribution of Mg in marine invertebrates has seldom been studied, despite its importance for assessing vulnerabilities to ocean acidification. Because pH decreases with water depth, it is predicted that levels of Mg in calcite skeletons should also decrease to counteract dissolution. Such a pattern has been suggested by evidence from echinoderms. Data on magnesium content and depth in Arctic bryozoans (52 species, 103 individuals, 150 samples) are here used to test this prediction, aided by comparison with six conceptual models explaining all possible scenarios. Analyses were based on a uniform dataset spanning more than 200 m of coastal water depth. No significant relationship was found between depth and Mg content; indeed, the highest Mg content among the analyzed taxa (8.7 % mol MgCO3) was recorded from the deepest settings (>200 m). Our findings contrast with previously published results from echinoderms in which Mg was found to decrease with depth. The bryozoan results suggest that ocean acidification may have less impact on the studied bryozoans than is generally assumed. In the broad context, our study exemplifies quantitative testing of spatial patterns of skeletal geochemistry for predicting the biological effects of environmental change in the oceans.
    • PCB pollution continues to impact populations of orcas and other dolphins in European waters

      Jepson, PD; Deaville, R; Barber, JL; Aguilar, A; Borrell, A; Murphy, S; Barry, J; Brownlow, A; Barnett, J; Berrow, S; et al. (2016-05)
    • Pentaradial eukaryote suggests expansion of suspension feeding in White Sea-aged Ediacaran communities

      Cracknell, Kelsie; García-Bellido, Diego C; Gehling, James G; Ankor, Martin J; Darroch, Simon AF; Rahman, Imran (Springer Science and Business Media LLC, 2021-12)
      Suspension feeding is a key ecological strategy in modern oceans that provides a link between pelagic and benthic systems. Establishing when suspension feeding first became widespread is thus a crucial research area in ecology and evolution, with implications for understanding the origins of the modern marine biosphere. Here, we use three-dimensional modelling and computational fluid dynamics to establish the feeding mode of the enigmatic Ediacaran pentaradial eukaryote Arkarua. Through comparisons with two Cambrian echinoderms,Cambraster and Stromatocystites, we show that flow patterns around Arkarua strongly support its interpretation as a passive suspension feeder.Arkarua is added to the growing number of Ediacaran benthic suspension feeders, suggesting that the energy link between pelagic and benthic ecosystems was likely expanding in the White Sea assemblage (~ 558–550 Ma). The advent of widespread suspension feeding could therefore have played an important role in the subsequent waves of ecological innovation and escalation that culminated with the Cambrian explosion.
    • People and plants: the unbreakable bond

      Knapp, S (New Phytologist Trust, 2018-12-05)
      Societal Impact Statement Plants are crucial for human survival, providing nutrition, warmth, clothing, and shelter, as well as the air that we breathe. Plants also enhance our environment by making it more beautiful and thereby enriching our lives and increasing our wellbeing. We need to study plants more and better understand their biodiversity so that we can conserve and safeguard their future to create an ecological civilization. Plant scientists must work together with other members of human societies to ensure the survival of these crucial organisms upon which we are reliant. Summary We are losing biodiversity at an unprecedented rate, which will have unknown but potentially devastating consequences for the Earth's planetary systems. Before we can conserve biodiversity, however, we must understand it, both as a concept and by performing an assessment of the diversity of life on our planet. Here, I highlight and explore the relationships between people and plants. Plants perform a diverse array of ecosystem processes, which provide us with a huge number of ecosystem services. We have domesticated a relatively tiny number of plant species to better optimize some of the products they provide us, including food, fiber, and fuel, but our relationships even with these few species are complex. Using the Solanaceae as an example, I explore the cultural, societal, economic, and nutritional aspects of our relationships with crop plants, as well as our use and knowledge of the genetic diversity stored in their wild relatives. Conserving plant biodiversity is vital for ourselves and for the rest of the biosphere, but plant scientists cannot achieve this alone. Highlighting the importance of biodiversity is key to attract public support and collaboration, enabling us to better map diversity and understand the impacts of our local behaviors on a global scale.
    • Perforocycloides nathalieae new genus and species, an unusual Silurian cyclocystoid (Echinodermata) from Anticosti Island, Québec, Canada

      Graham, M; Ewin, TAM; Reich, Mike; Cournoyer, ME; Klug, C (Springer, 2019-08-22)
      Cyclocystoids are a poorly known, rare, extinct class of bi-facially flattened, disc shaped echinoderms, ranging from the Middle Ordovician to the Early Carboniferous. Articulated cyclocystoids are relatively common in the Ordovician but are rarer in younger strata. Here we describe Perforocycloides nathaliae new genus and species, from the early Silurian of Anticosti Island, Québec, Canada, the first articulated cyclocystoid from the Silurian of North America. This taxon is distinguished from other cyclocystoids by the number of variably sized marginal ossicles, the lack of interseptal plates, and the novelty of pores located in the distal part of the sutures between adjacent marginals on the dorsal surface. These dorsal intermarginal sutural pores led to canals which penetrated the contiguous area of the lateral surface of the marginals and emerged on the ventral surface between the cupules of adjacent marginals. These dorsal intermarginal sutural pores/canals appear to be unique to Perforocycloides and whilst their function is speculative, they provided some form of communication between the dorsal disc and the distal side of the ventral marginals/cupules. Perforocycloides most closely resembles the Ordovician–Silurian genus Zygocycloides, suggesting that this genus may have diversified more widely during the Silurian than previously reported. A review of global Silurian cyclocystoid distribution suggests taxa were geographically confined and that greatest diversity appears to have been located within Baltica. However, it also demonstrates our current limited knowledge. No specimens have been recorded from Gondwana (e.g. Africa, Australia, South America), Siberia, and North and South China, nor are any specimens known confidently anywhere from Přidolí strata.
    • Persistence of intense, climate-driven runoff late in Mars history

      Kite, ES; Mayer, DP; Wilson, SA; Lucas, AS; Stucky de Quay, G; Davis, Joel (American Association for the Advancement of Science, 2019-03-27)
      Mars is dry today, but numerous precipitation-fed paleo-rivers are found across the planet’s surface. These rivers’ existence is a challenge to models of planetary climate evolution. We report results indicating that, for a given catchment area, rivers on Mars were wider than rivers on Earth today. We use the scale (width and wavelength) of Mars paleo-rivers as a proxy for past runoff production. Using multiple methods, we infer that intense runoff production of >(3–20) kg/m2 per day persisted until <3 billion years (Ga) ago and probably <1 Ga ago, and was globally distributed. Therefore, the intense runoff production inferred from the results of the Mars Science Laboratory rover was not a short-lived or local anomaly. Rather, precipitation-fed runoff production was globally distributed, was intense, and persisted intermittently over >1 Ga. Our improved history of Mars’ river runoff places new constraints on the unknown mechanism that caused wet climates on Mars.
    • Perspectives in Animal Phylogeny and Evolution: A decade later

      Giribet, G; Edgecombe, GD; Fusco, G (University of Padova PressPadova, 2019-01-15)
      Refinements in phylogenomic methods and novel data have clarified several controversies in animal phylogeny that were intractable with traditional PCR-based approaches or early Next Gen analyses. An alliance between Placozoa and Cnidaria has recently found support. Data from newly discovered species of Xenoturbella contribute to Xenacoelomorpha being placed as sister group of Nephrozoa rather than within the deuterostomes. Molecular data reinforce the monophyly of Gnathifera and ally the longenigmatic chaetognaths with them. Platyzoa was an artefactual grouping, and deep relationships within Spiralia now depict Rouphozoa (= Gastrotricha + Platyhelminthes) as sister group to Lophotrochozoa, and Gnathifera (plus Chaetognatha) their immediate sister group. A “divide and conquer” strategy of subsampling clades to optimize gene selection may be needed to simultaneously resolve the many disparate clades of the animal tree of life
    • 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.