• The type specimens and type localities of the orangutans, genus Pongo Lacépède, 1799 (Primates: Hominidae)

      Brandon-Jones, D; Groves, CP; Jenkins, Paulina (Taylor and Francis, 2016-07-20)
      Uncertain type localities undermine orangutan nomenclature. Bequeathed to the British Museum, the holotype of Pongo pygmaeus, according to Hans Sloane’s catalogue, came from Borneo and died in China. The historical evidence makes Banjarmasin its most probable type locality. William Montgomerie, Assistant Surgeon at Singapore from 1819-1827, and Senior Surgeon from 1832, supplied the holotype of Simia morio. In 1836 an adult female orangutan reached Singapore alive from Pontianak, Borneo. The holotypes of S. morio, S. hendrikzii, S. straussii and P[ithecus] owenii probably had the same origin, as pirate attacks endangered visits to other Bornean coasts. Absent from Brunei and north Sarawak, Malaysia, throughout the Holocene, orangutans occur there only as Pleistocene subfossils at Niah. Pan vetus (the Piltdown mandible) probably came from Paku, Sarawak. We identify Pongo borneo Lacépède, 1799 as an objective senior synonym of P. wurmbii Tiedemann, 1808, correcting its type locality from Sukadana to near Pontianak. This is the earliest name for the western subspecies (previously thought nominotypical) unless Pithecus curtus, probably from the Sadong River, Sarawak, represents a separate subspecies. If so, the name Pongo borneo would transfer to the southern population west of the Kahayan River, genetically distinguished at species level from the Sumatran orangutan, P. abelii.
    • Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea, Eulophidae)

      Kenyon, SG; Buerki, S; Hansson, C; Alvarez, N; Benrey, B; Ballhorn, D (2015-09-09)
    • Uncovering the sub-lethal impacts of plastic ingestion by shearwaters using fatty acid analysis.

      Puskic, PS; Lavers, JL; Adams, LR; Grünenwald, M; Hutton, I; Bond, AL (Oxford Academic, 2019-05-16)
      Marine plastic pollution is increasing exponentially, impacting an expanding number of taxa each year across all trophic levels. Of all bird groups, seabirds display the highest plastic ingestion rates and are regarded as sentinels of pollution within their foraging regions. The consumption of plastic contributes to sub-lethal impacts (i.e. morbidity, starvation) in a handful of species. Additional data on these sub-lethal effects are needed urgently to better understand the scope and severity of the plastics issue. Here we explore the application of fatty acid (FA) analysis as a novel tool to investigate sub-lethal impacts of plastic ingestion on seabird body condition and health. Using gas chromatography-mass spectrometry, we identified 37 individual FAs within the adipose, breast muscle and liver of flesh-footed (Ardenna carneipes) and short-tailed (Ardenna tenuirostris) shearwaters. We found high amounts of FA 16:0, 18:0, 20:5n3 (eicosapentaenoic acid), 22:6n3 (docosahexaenoic acid) and 18:1n9 in both species; however, the overall FA composition of the two species differed significantly. In flesh-footed shearwaters, high amounts of saturated and mono-unsaturated FAs (needed for fast and slow release energy, respectively) in the adipose and muscle tissues were related to greater bird body mass. While total FAs were not related to the amount of plastic ingested in either species, these data are a valuable contribution to the limited literature on FAs in seabirds. We encourage studies to explore other analytical tools to detect these sub-lethal impacts of plastic.
    • Understanding the microscale spatial distribution and mineralogical residency of Re in pyrite: Examples from carbonate-hosted Zn-Pb ores and implications for pyrite Re-Os geochronology

      Hnatyshin, D; Creaser, RA; Meffre, S; Stern, RA; Wilkinson, JJ; Turner, EC (Elsevier BV, 2019-11-26)
      Accurate and precise geochronology using the Re-Os isotopic system in pyrite is an invaluable tool for developing and confirming genetic models of ore systems. However, as a bulk method, the results produced by pyrite Re-Os geochronology are commonly complex, and many imprecise isochrons exist in the literature. Using LA-ICPMS methods it is now possible to map and quantify Re distribution at the ppb level, allowing an unprecedented look into the Re-Os systematics of pyrite-bearing ore. Two samples from the Lisheen Zn-Pb ore deposit in Ireland showing disparate Re-Os isotopic behavior were investigated. In-situ sulfur isotope measurements using SIMS, an analytical technique not previously attempted on the Irish deposits, was used to supplement the Re-Os dataset. A massive pyrite sample from the Main Zone produced a precise, low-scatter isochron (346.6 ± 3.0 Ma, MSWD = 1.6). The Re distribution in this sample is relatively homogeneous, with the Re budget dominated by pyrite containing 1–5 ppb Re, but the δ34S varies significantly from −45.2‰ to 8.2‰. A second, more paragenetically complex, sample from the Derryville Zone produced a younger age with high scatter (322 ± 11 Ma, MSWD = 206) and this also displays a large variation in δ34S (−53‰ to +4‰). The cores of grains of main-stage iron sulfide are depleted in trace elements and show low Re abundances (<10 ppb) but have been altered in an irregular fashion leading to Re-enriched domains that exceed 100 ppb. Additionally, micron-scale molybdenite crystals, found in close association with altered sulfides, contain Re at levels that locally exceed 10 ppm. The highly scattered (MSWD = 206) and younger age (322 Ma), produced by the Derryville Zone sample are interpreted to result from mixing of different generations of sulfide, potentially involving fluids associated with Variscan deformation (<310 Ma). Therefore, the Re-Os data produced from the Derryville Zone sample does not reflect the timing of iron sulfide mineralization, even though a relatively precise age was obtained. A second Re-Os dataset from Zn-Pb mineralization at Hawker Creek, Nunavut, Canada was produced from massive pyrite that displays low Re concentrations (<1 ppb). However, on grain boundaries and in fractures, silicate-rich material contains Re at levels that can locally exceed 500 ppb. Analyses of fracture-free pyrite produced by bulk separation using magnetic separation yielded the oldest model age (1083 Ma), whereas mineral separates containing the highest fracture density produced the youngest age (413 Ma). In general, therefore, the complexities of pyrite Re-Os geochronology can result from impurities in mineral separates. Attempts to eliminate impurities through different mineral separation techniques (e.g. crushing, heavy liquid separation, magnetic separation, acid leaching) are frequently only partially successful and therefore full characterization of any resulting mineral separates is extremely important. We conclude that LA-ICPMS mapping of Re and Mo distributions is essential for the identification of such impurities. Although other trace element LA-ICPMS maps, in-situ sulfur isotope measurements, and petrographic evidence were of limited use in assessing the Re budget of a sample, they are invaluable in linking the documented Re distribution obtained through LA-ICPMS to Re-Os geochronological results.
    • UniEuk : Time to Speak a Common Language in Protistology!

      Berney, C; Ciuprina, A; Bender, S; Brodie, J; Edgcomb, V; Kim, E; Rajan, J; Parfrey, LW; Adl, S; Audic, S; et al. (Wiley, 2017-03-24)
      Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
    • Unifying European Biodiversity Informatics (BioUnify)

      Koureas, D; Hardisty, A; Vos, R; Agosti, D; Arvanitidis, C; Bogatencov, P; Buttigieg, PL; de Jong, Y; Horvath, F; Gkoutos, G; et al. (2016-01-19)
    • A unique CO-like micrometeorite hosting an exotic Al-Cu-Fe-bearing assemblage – close affinities with the Khatyrka meteorite

      Suttle, MD; Twegar, K; Nava, J; Spiess, R; Spratt, J; Campanale, F; Folco, L (Springer Science and Business Media LLC, 2019-08-27)
      We report the discovery of a unique micrometeorite, containing an exotic Al-Cu-Fe alloy composed of two intermixed phases: khatyrkite (CuAl2) and stolperite (CuAl) and both containing minor Fe (<1.4 wt%). These phases are dendritic and rapidly co-crystallized at the binary system’s peritectic (~550 °C). The host micrometeorite is an otherwise typical S-type micro-porphyritic cosmic spherule containing relict olivine (Fo76–90, Cr2O3: 0.01–0.56 wt%, MnO: 0.03–0.32 wt% and CaO: 0.09–0.22 wt%) and a cumulate layered texture. These properties suggest the micrometeorite is derived from a carbonaceous chondrite (best matched to a CO chondrite) and entered the atmosphere a high speed (~16 kms−1), implying an origin from a highly eccentric orbit. This particle represents the second independent discovery of naturally occurring intermetallic Al-Cu-Fe alloys and is thus similar to the previously reported Khatyrka meteorite - a CV chondrite containing near-identical alloys and the only known natural quasicrystals. We did not observe quasicrystalline phases in this micrometeorite, likely due to the low amounts of Fe in the alloy, insufficient to stabilize quasicrystals. Our discovery confirms the existence of Al-Cu-Fe intermetallic alloys on chondritic parent bodies. These unusual phases require a currently unexplained formation process, we tentatively suggest this could represent the delivery of exotic interstellar material to the inner solar system via impact.
    • The unknown planktonic foraminiferal pioneer Henry A. Buckley and his collection at The Natural History Museum, London

      Rillo, MC; Whittaker, J; Ezard, THG; Purvis, A; Henderson, AS; Stukins, S; Giles Miller, C (2016-12-22)
    • Unusual coloration of a Hairy woodpecker from Oregon

      Helm, SR; Stemmer, R; van Grouw, Hein (Society for Northwestern Vertebrate Biology, 2011-03-01)
    • An updated checklist of the Culicidae (Diptera) of Morocco, with notes on species of historical and current medical importance

      Trari, B; Dakki, M; Harbach, RE (Society for Vector Ecology, 2017-06)
      An updated checklist of the mosquito species (Diptera: Culicidae) recorded in Morocco from 1916 to 2016 is provided, including synonyms and synonymous usage for each species. Forty‐three species belonging to seven genera are recorded so far: Anopheles (9), Aedes (12) Coquillettidia (2), Culex (12), Culiseta (5), Orthopodomyia (1) and Uranotaenia (2). Traditional and equivalent names in the polyphyletic concept of Aedes are provided for the aedine species. The historical importance and current potential threat of mosquitoes to human health in Morocco is reviewed.
    • An urban Blitz with a twist: rapid biodiversity assessment using aquatic environmental DNA

      Hupało, K; Majaneva, M; Czachur, MV; Sire, L; Marquina, D; Lijtmaer, DA; Ivanov, V; Leidenberger, S; Čiampor, F; Čiamporová‐Zaťovičová, Z; et al. (Wiley, 2020-10-24)
      As global biodiversity declines, there is an increasing need to create an educated and engaged society. Having people of all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we explore whether sampling eDNA and sequencing it can be used as a means of rapidly surveying urban biodiversity for educational purposes. We sampled 2 × 1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine, and brackish habitats. DNA was extracted, amplified in triplicate targeting the barcoding fragment of COI gene, and sequenced. The obtained data were analyzed on the novel mBRAVE platform, an online open‐access software and computing resource. The water samples were collected in 2 days by two people, and the laboratory analysis was completed in 5 days by one person. Overall, we detected the presence of 506 BINs identified as belonging to 435 taxa, representing at least 265 putative species. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to the geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota. Here we propose a new form of BioBlitz, where with noninvasive sampling effort combined with swift processing and straightforward online analyses, hundreds of species can be detected. Thus, using eDNA analysis of water is useful for rapid biodiversity surveys and valuable for educational purposes. We show that rapid eDNA surveys, combined with openly available services and software, can be used as an educational tool to raise awareness about the importance of biodiversity.
    • Urogenital schistosomiasis and soil-transmitted helminthiasis (STH) in Cameroon: An epidemiological update at Barombi Mbo and Barombi Kotto crater lakes assessing prospects for intensified control interventions

      Campbell, SJ; Stothard, JR; O’Halloran, F; Sankey, D; Durant, T; Ombede, DE; Chuinteu, GD; Webster, BL; Cunningham, L; LaCourse, EJ; et al. (2017-02-27)
    • Urogenital schistosomiasis transmission on Unguja Island, Zanzibar: characterisation of persistent hot-spots

      Pennance, T; Person, B; Muhsin, MA; Khamis, AN; Muhsin, J; Khamis, IS; Mohammed, KA; Kabole, F; Rollinson, D; Knopp, S (2016-12)
    • The use of anthropogenic marine debris as a nesting material by brown boobies (Sula leucogaster)

      Grant, ML; Lavers, JL; Stuckenbrock, S; Sharp, PB; Bond, AL (Elsevier, 2018-10-11)
      Marine debris is pervasive worldwide, and affects biota negatively. We compared the characteristics of debris incorporated within brown booby (Sula leucogaster) nests throughout their pantropical distribution by assessing the type, colour and mass of debris items within nests and in beach transects at 18 sites, to determine if nests are indicators of the amount of debris in local marine environments. Debris was present in 14.4% of nests surveyed, with the proportion of nests with debris varying among sites (range: 0–100%). There was minimal overlap between the type or colour of debris found in nests and on adjacent beaches at individual sites. This suggests that brown boobies do not select debris uniformly across their distribution. We propose that the nests of brown boobies can be used as a sentinel of marine debris pollution of their local environment.
    • Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda)

      Jex, AR; Hu, M; Littlewood, T; Waeschenbach, A; Gasser, RB (Springer Science and Business Media LLC, 2008-01-11)
      Background: Mitochondrial (mt) genomes represent a rich source of molecular markers for a range of applications, including population genetics, systematics, epidemiology and ecology. In the present study, we used 454 technology (or the GS20, massively parallel picolitre reactor platform) to determine the complete mt genome of Haemonchus contortus (Nematoda: Trichostrongylidae), a parasite of substantial agricultural, veterinary and economic significance. We validate this approach by comparison with mt sequences from publicly available expressed sequence tag (EST) and genomic survey sequence (GSS) data sets. Results: The complete mt genome of Haemonchus contortus was sequenced directly from longPCR amplified template utilizing genomic DNA (~20–40 ng) from a single adult male using 454 technology. A single contig was assembled and compared against mt sequences mined from publicly available EST (NemBLAST) and GSS datasets. The comparison demonstrated that the 454 technology platform is reliable for the sequencing of AT-rich mt genomes from nematodes. The mt genome sequenced for Haemonchus contortus was 14,055 bp in length and was highly AT-rich (78.1%). In accordance with other chromadorean nematodes studied to date, the mt genome of H. contortus contained 36 genes (12 protein coding, 22 tRNAs, rrnL and rrnS) and was similar in structure, size and gene arrangement to those characterized previously for members of the Strongylida. Conclusion: The present study demonstrates the utility of 454 technology for the rapid determination of mt genome sequences from tiny amounts of DNA and reveals a wealth of mt genomic data in current databases available for mining. This approach provides a novel platform for high-throughput sequencing of mt genomes from nematodes and other organisms.
    • Using natural history collections to investigate changes in pangolin (Pholidota: Manidae) geographic ranges through time

      Buckingham, Emily; Curry, Jake; Emogor, Charles; Tomsett, Louise; Cooper, N (PeerJ, 2021-02-11)
      Pangolins, often considered the world’s most trafficked wild mammals, have continued to experience rapid declines across Asia and Africa. All eight species are classed as either Vulnerable, Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN) Red List. Alongside habitat loss, they are threatened mainly by poaching and/or legal hunting to meet the growing consumer demand for their meat and keratinous scales. Species threat assessments heavily rely on changes in species distributions which are usually expensive and difficult to monitor, especially for rare and cryptic species like pangolins. Furthermore, recent assessments of the threats to pangolins focus on characterising their trade using seizure data which provide limited insights into the true extent of global pangolin declines. As the consequences of habitat modifications and poaching/hunting on species continues to become apparent, it is crucial that we frequently update our understanding of how species distributions change through time to allow effective identification of geographic regions that are in need of urgent conservation actions. Here we show how georeferencing pangolin specimens from natural history collections can reveal how their distributions are changing over time, by comparing overlap between specimen localities and current area of habitat maps derived from IUCN range maps. We found significant correlations in percentage area overlap between species, continent, IUCN Red List status and collection year, but not ecology (terrestrial or arboreal/semi-arboreal). Human population density (widely considered to be an indication of trafficking pressure) and changes in primary forest cover, were weakly correlated with percentage overlap. Our results do not suggest a single mechanism for differences among historical distributions and present-day ranges, but rather show that multiple explanatory factors must be considered when researching pangolin population declines as variations among species influence range fluctuations. We also demonstrate how natural history collections can provide temporal information on distributions and discuss the limitations of collecting and using historical data.