• 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.
    • Solanum medusae (Solanaceae), a new wolf-fruit from Brazil, and a key to the extra-Amazonian Brazilian Androceras/Crinitum Clade species

      Gouvea, YF; Stehmann, JR; Knapp, S (Pensoft, 2019-02-27)
      Solanum medusae sp. nov. is described from the Cerrado biome in the Serra da Canastra region, southwestern Minas Gerais State, Brazil. The new species is morphologically similar to the common S. lycocarpum A.St.-Hil. (known as lobeira or wolf-fruit), but differs from it in habit and pubescence characters. We here describe this new taxon and discuss its morphology, some aspects of its ecology, affinities and distribution. Full specimen citations are provided, as well as illustrations, distribution map and a preliminary conservation assessment of the species. A key to all of the known extra-Amazonian Brazilian species of the Androceras/Crinitum clade is also provided to aid in their identification.
    • Species‐level image classification with convolutional neural network enables insect identification from habitus images

      Hansen, OLP; Svenning, J; Olsen, K; Dupont, Steen; garner, beulah; Iosifidis, A; Price, BW; Høye, TT (Wiley, 2019-12-24)
      1. Changes in insect biomass, abundance, and diversity are challenging to track at sufficient spatial, temporal, and taxonomic resolution. Camera traps can capture habitus images of ground-dwelling insects. However, currently sampling involves manually detecting and identifying specimens. Here, we test whether a convolutional neural network (CNN) can classify habitus images of ground beetles to species level, and estimate how correct classification relates to body size, number of species inside genera, and species identity. 2. We created an image database of 65,841 museum specimens comprising 361 carabid beetle species from the British Isles and fine-tuned the parameters of a pretrained CNN from a training dataset. By summing up class confidence values within genus, tribe, and subfamily and setting a confidence threshold, we trade-off between classification accuracy, precision, and recall and taxonomic resolution. 3. The CNN classified 51.9% of 19,164 test images correctly to species level and 74.9% to genus level. Average classification recall on species level was 50.7%. Applying a threshold of 0.5 increased the average classification recall to 74.6% at the expense of taxonomic resolution. Higher top value from the output layer and larger sized species were more often classified correctly, as were images of species in genera with few species. 4. Fine-tuning enabled us to classify images with a high mean recall for the whole test dataset to species or higher taxonomic levels, however, with high variability. This indicates that some species are more difficult to identify because of properties such as their body size or the number of related species. 5. Together, species-level image classification of arthropods from museum collections and ecological monitoring can substantially increase the amount of occurrence data that can feasibly be collected. These tools thus provide new opportunities in understanding and predicting ecological responses to environmental change.
    • The Spotted green pigeon Caloenas maculata: as dead as a Dodo, but what else do we know about it?

      van Grouw, Hein (British Ornithologists' Club, 2014-12-01)
      Described in 1783 and since then re-examined by many notable ornithologists, the single specimen known as the ‘Spotted Green Pigeon’ Caloenas maculata in the collections of the World Museum, Liverpool, has always been a mystery. No-one has ever doubted that it is a pigeon, and many researchers were convinced it was a distinct species. Although its taxonomic status remained unclear, it was officially declared extinct by BirdLife International in early 2008. Recent DNA analysis has now revealed that Spotted Green Pigeon can indeed be considered a distinct species within the extended Dodo Raphus cucullatus clade of morphologically very diverse pigeon species. Most members of this clade exhibit terrestrial or semi-terrestrial habits. Further morphological research into this unique specimen, initiated by the World Museum, demonstrates that Spotted Green Pigeon, in contrast to its fellow clade members, may have possessed strongly arboreal habits.