• 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.
    • 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)
    • 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)
    • 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.
    • 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)
    • 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.
    • 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)
    • A Polychaete’s Powerful Punch: Venom Gland Transcriptomics of Glycera Reveals a Complex Cocktail of Toxin Homologs

      von Reumont, BM; Campbell, LI; Richter, S; Hering, L; Sykes, D; Hetmank, J; Jenner, RA; Bleidorn, C (2014-09)
    • Pooling as a strategy for the timely diagnosis of soil-transmitted helminths in stool: value and reproducibility

      PAPAIAKOVOU, MARINA; Wright, J; Pilotte, N; Chooneea, D; Schär, F; Truscott, JE; Dunn, JC; Gardiner, I; Walson, JL; Williams, SA; et al. (Springer Science and Business Media LLC, 2019-09-16)
      Background The strategy of pooling stool specimens has been extensively used in the field of parasitology in order to facilitate the screening of large numbers of samples whilst minimizing the prohibitive cost of single sample analysis. The aim of this study was to develop a standardized reproducible pooling protocol for stool samples, validated between two different laboratories, without jeopardizing the sensitivity of the quantitative polymerase chain reaction (qPCR) assays employed for the detection of soil-transmitted helminths (STHs). Two distinct experimental phases were recruited. First, the sensitivity and specificity of the established protocol was assessed by real-time PCR for each one of the STHs. Secondly, agreement and reproducibility of the protocol between the two different laboratories were tested. The need for multiple stool sampling to avoid false negative results was also assessed. Finally, a cost exercise was conducted which included labour cost in low- and high-wage settings, consumable cost, prevalence of a single STH species, and a simple distribution pattern of the positive samples in pools to estimate time and money savings suggested by the strategy. Results The sensitivity of the pooling method was variable among the STH species but consistent between the two laboratories. Estimates of specificity indicate a ‘pooling approach’ can yield a low frequency of ‘missed’ infections. There were no significant differences regarding the execution of the protocol and the subsequent STH detection between the two laboratories, which suggests in most cases the protocol is reproducible by adequately trained staff. Finally, given the high degree of agreement, there appears to be little or no need for multiple sampling of either individuals or pools. Conclusions Our results suggest that the pooling protocol developed herein is a robust and efficient strategy for the detection of STHs in ‘pools-of-five’. There is notable complexity of the pool preparation to ensure even distribution of helminth DNA throughout. Therefore, at a given setting, cost of labour among other logistical and epidemiological factors, is the more concerning and determining factor when choosing pooling strategies, rather than losing sensitivity and/or specificity of the molecular assay or the method.