• Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science

      Smith, V; Rycroft, S; Brake, I; Scott, B; Baker, E; Livermore, L; Blagoderov, V; Roberts, D (Pensoft, 2011-11-28)
      The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project’s operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.
    • Seasonal ingestion of anthropogenic debris in an urban population of gulls

      Stewart, LG; Lavers, JL; Grant, ML; Puskic, PS; Bond, AL (Elsevier BV, 2020-08-15)
      Gulls are generalist seabirds, increasingly drawn to urban environments where many species take advantage of abundant food sources, such as landfill sites. Despite this, data on items ingested at these locations, including human refuse, is limited. Here we investigate ingestion of prey and anthropogenic debris items in boluses (regurgitated pellets) from Pacific Gulls (Larus pacificus). A total of 374 boluses were collected between 2018 and 2020 in Tasmania. Debris was present in 92.51% of boluses (n = 346), with plastic (86.63%, n = 324) and glass (64.71%, n = 242) being the most prominent types. An abundance of intact, household items (e.g., dental floss, food wrappers) suggest the gulls regularly feed at landfill sites. In addition, the boluses are deposited at a roosting site located within an important wetland, thus we propose that the gulls may be functioning as a previously unrecognised vector of anthropogenic debris from urban centres to aquatic environments.
    • Sensitivity and Specificity of a Urine Circulating Anodic Antigen Test for the Diagnosis of Schistosoma haematobium in Low Endemic Settings

      Knopp, S; Corstjens, PLAM; Koukounari, A; Cercamondi, CI; Ame, SM; Ali, SM; de Dood, CJ; Mohammed, KA; Utzinger, J; Rollinson, D; et al. (2015-05-14)
    • Sex biases in bird and mammal natural history collections.

      Cooper, N; Bond, AL; Davis, JL; Portela Miguez, R; Tomsett, L; Helgen, Kristofer (Royal Society, 2019-10-23)
      Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.
    • Sexual and geographic dimorphism in northern rockhopper penguins breeding in the South Atlantic Ocean

      Steinfurth, A; Booth, JM; White, J; Bond, AL; McQuaid, CD (Inter-Research Science Center, 2019-08-22)
      The Endangered northern rockhopper penguin Eudyptes moseleyi, like all penguins, is monomorphic, making sex determination of individuals in the field challenging. We examined the degree of sexual size dimorphism of adult birds across the species’ breeding range in the Atlantic Ocean and developed discriminant functions (DF) to predict individuals’ sex using morphometric measurements. We found significant site-specific differences in both bill length and bill depth, with males being the larger sex on each island. Across all islands, bill length contributed 78% to dissimilarity between sexes. Penguins on Gough Island had significantly longer bills, whilst those from Tristan da Cunha had the deepest. Island-specific DFs correctly classified 82-94% of individuals, and all functions performed significantly better than chance. The model for Nightingale Island correctly classified the greatest proportion of individuals (94-95%), while that for Tristan da Cunha performed the poorest (80-82%). A discriminant function derived from all sites accurately sexed 86-88% of northern rockhopper penguins achieving similar accuracy to island-specific functions. While molecular techniques conclusively determine an individual’s sex, morphometric measurements can provide a reliable estimate with close to 90% accuracy using a method that is less invasive and requires little technical expertise. Sexing is an important tool for meaningful interpretation of ecological data. Consideration of sex-specific differences in future studies will aid investigation of a potential sex-dependent vulnerability in this Endangered species.
    • sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

      Chapman, Abbie; Beaulieu, SE; Colaço, A; Gebruk, AV; Hilario, A; KIHARA, TC; Ramirez‐Llodra, E; Sarrazin, J; Tunnicliffe, V; Amon, Diva; et al. (Wiley, 2019-07-30)
      Motivation: Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite grow‐ ing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single re‐ pository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFD‐ vent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent da‐ tabase, describe our approach, and evaluate its scope. Finally, we compare the sFD‐ vent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI. Main types of variable contained: Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Spatial location and grain: Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres. Time period and grain: sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years. Major taxa and level of measurement: Deep‐sea hydrothermal‐vent fauna with spe‐ cies‐level identification present or in progress. Software format: .csv and MS Excel (.xlsx).
    • Shedding light on the ‘dark side’ of phylogenetic comparative methods

      Cooper, N; Thomas, GH; FitzJohn, RG; O'Hara, RB (2016-06)
    • The Shenzhen Declaration on Plant Sciences-Uniting plant sciences and society to build a green, sustainable Earth

      Crane, PR; Ge, S; Hong, D-Y; Huang, H-W; Jiao, G-L; Knapp, S; Kress, WJ; Mooney, H; Raven, PH; Wen, J; et al. (2017-09)
    • Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

      Glenn, TC; Lance, SL; McKee, AM; Webster, BL; Emery, AM; Zerlotini, A; Oliveira, G; Rollinson, D; Faircloth, BC (Springer Nature, 2013)
      Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance.
    • Singing from the Grave: DNA from a 180 Year Old Type Specimen Confirms the Identity of Chrysoperla carnea (Stephens)

      Price, BW; Henry, CS; Hall, AC; Mochizuki, A; Duelli, P; Brooks, SJ; Steinke, D (2015-04-08)
    • Solanaceae endémicas del Perú. In León, B. (ed) Libro Rojo de las plantas endémicas del Perú

      Knapp, S (UNMSM. Facultad de Biología, 2006-12)
      The Solanaceae are among the most diverse families in the Peruvian flora, with about 42 genera and 600 species (Brako & Zarucchi, 1993; Ulloa Ulloa et al., 2004), mostly herbs and shrubs. Here we recognize as endemics 203 species and six varieties in 16 genera. This family ranks 6th among the most diverse families in endemic taxa. Solanum, Nolana and Jaltomata are the genera with more endemic species. Endemic taxa are found in almost all regions, mainly Mesoandean, Very Humid Montane Forests and Subtropical Costal Desert, from sea level 100 to 3800 m elevation. Thirty-six taxa have been recorded within Peru’s protected areas system.
    • Solanum chenopodioides Lam. (Solanaceae) en la ciudad de Madrid

      Martínez Labarga, JM; García Guillén, E; Meliá Vaca, D; Knapp, S (Fotografía y Biodiversidad, 2017-07-23)
      RESUMEN: Se da a conocer la presencia de Solanum chenopodiodes Lam. en Madrid, por primera vez. Supone la única población conocida para el centro de la Península Ibérica. Se aportan fotografías tomadas en el lugar del hallazgo e imágenes de la descripción original y de la primera ilustración que se conoce de la especie. ABSTRACT: The presence of Solanum chenopodiodes Lam. is reported for Madrid for the first time. It seems to be the only known population in the centre of the Iberian Peninsula. Photographs of the record are published and images of the original description and the first known illustration of the species are shown.