• 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)
    • 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)
    • 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.