• Colour aberrations in extinct and endangered birds

      Hume, JP; van Grouw, Hein (British Ornithologists' Club, 2014-09-01)
      Several groups of birds have suffered high extinction rates, especially rails, pigeons, parrots and passerines. Some island species that disappeared in the early 19th century, e.g. Lord Howe Gallinule Porphyrio albus, Rodrigues Parakeet Psittacula exsul and Mascarene Parrot Mascarinus mascarinus, are known from only a few skins and illustrations, whereas the Huia Heteralocha acutirostris of New Zealand is known from hundreds of specimens. Furthermore, two North American species—Passenger Pigeon Ectopistes migratorius and Carolina Parakeet Conuropsis carolinensis—which became extinct in the early 20th century, are also represented by hundreds of specimens. Other supposedly extinct bird species are enigmatic. Confusion exists concerning the unique specimens of Sharpe’s Rail Gallirallus sharpei and Townsend’s Bunting Spiza townsendi, paintings of a parrot from the West Indies and an aberrant white Huia, as well as aberrant specimens of the Critically Endangered Kakapo Strigops habroptilus. Much has been written concerning these birds and why they became extinct, or have become extremely rare, but few data are available concerning colour aberrations in certain specimens; the literature is also riddled with incorrect terminology. This paper addresses this shortfall and describes the various colour aberrations in these extinct and endangered birds and why they have occurred.
    • Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants

      Trueman, C; Jackson, A; Chadwick, K; Coombs, Ellen J; Feyrer, L; Magozzi, S; Sabin, R; Cooper, N (PeerJ Inc., 2019-10-18)
      The spatial ecology of rare, migratory oceanic animals is difficult to study directly. Where incremental tissues are available, their chemical composition can provide valuable indirect observations of movement and diet. Interpreting the chemical record in incremental tissues can be highly uncertain, however, as multiple mechanisms interact to produce the observed data. Simulation modeling is one approach for considering alternative hypotheses in ecology and can be used to consider the relative likelihood of obtaining an observed record under different combinations of ecological and environmental processes. Here we show how a simulation modeling approach can help to infer movement behaviour based on stable carbon isotope profiles measured in incremental baleen tissues of a blue whale (Balaenoptera musculus). The life history of this particular specimen, which stranded in 1891 in the UK, was selected as a case study due to its cultural significance as part of a permanent display at the Natural History Museum, London. We specifically tested whether measured variations in stable isotope compositions across the analysed baleen plate were more consistent with residency or latitudinal migrations. The measured isotopic record was most closely reproduced with a period of residency in sub-tropical waters for at least a full year followed by three repeated annual migrations between sub-tropical and high latitude regions. The latitudinal migration cycle was interrupted in the year prior to stranding, potentially implying pregnancy and weaning, but isotopic data alone cannot test this hypothesis. Simulation methods can help reveal movement information coded in the biochemical compositions of incremental tissues such as those archived in historic collections, and provides context and inferences that are useful for retrospective studies of animal movement, especially where other sources of individual movement data are sparse or challenging to validate.
    • Community engagement: The ‘last mile’ challenge for European research e-infrastructures

      Koureas, D; Arvanitidis, C; Belbin, L; Berendsohn, W; Damgaard, C; Groom, Q; Güntsch, A; Hagedorn, G; Hardisty, A; Hobern, D; et al. (2016-07-20)
    • Comparative analyses of glycerotoxin expression unveil a novel structural organization of the bloodworm venom system

      Richter, S; Helm, C; Meunier, FA; Hering, L; Campbell, LI; Drukewitz, SH; Undheim, EAB; Jenner, RA; Schiavo, G; Bleidorn, C (2017-12)
    • Comparative biogeography of Southeast Asia and the West Pacific region

      Ung, V; Zaragueta-Bagils, R; Williams, DM (2016-02)
    • Comparative morphology of immature Trictenotoma formosana Kriesche, 1919 and systematic position of the Trictenotomidae (Coleoptera, Tenebrionoidea)

      Hu, F-S; Pollock, DA; Telnov, Dmitry (Museum National D'Histoire Naturelle, 2020-05-05)
      Detailed description and illustrations of immature Trictenotoma Gray, 1832 (Trictenotomidae Blanchard, 1845) are presented for the first time, based on larvae and pupae of T. formosana Kriesche, 1919. Characters exhibited by the mature larva are similar to those described by Gahan (1908) for T. childreni Gray, 1832, which was based on a single specimen. The phylogenetic position of Trictenotomidae has varied among Scarabaeoidea, Chrysomeloidea and Tenebrionoidea, though recent studies place the family clearly among the latter. Features of the immature stages described here corroborate this placement. Evidence supports placement within or near the “salpingid group” (Pythidae, Salpingidae, Boridae, Pyrochroidae). Distinguishing features of the mature trictenotomid larva include the absence of stemmata, antennal sensorium, urogomphal pit(s) and lip, the presence of paired series of longitudinal ridges on the meso- and metathorax and abdominal tergites 1–8 and sternites 2–8, a paired arcuate row of 12–15 asperities on the anterior margin of sternite 9 and relatively short, upturned urogomphi. The systematic position of trictenotomids within the Tenebrionoidea Latreille, 1802 is confirmed. The phylogenetic relationships among Trictenotomidae and other “salpingid group” members (e.g., Pythidae Solier, 1834 and Salpingidae Leach, 1815) are highlighted and discussed, solving an almost two centuries old puzzle in Coleoptera systematics.
    • Competition matters: Determining the drivers of land snail community assembly among limestone karst areas in northern Vietnam

      von Oheimb, Parm Viktor; von Oheimb, Katharina C. M.; Hirano, T; Do, TV; Luong, HV; Ablett, J; Pham, SV; Naggs, F (Wiley, 2018-03-26)
      The insular limestone karsts of northern Vietnam harbor a very rich biodiversity. Many taxa are strongly associated with these environments, and individual species communities can differ considerably among karst areas. The exact processes that have shaped the biotic composition of these habitats, however, remain largely unknown. In this study, the role of two major processes for the assembly of snail communities on limestone karsts was investigated, interspecific competition and filtering of taxa due to geographical factors. Communities of operculate land snails of the genus Cyclophorus were studied using the dry and fluid‐preserved specimen collections of the Natural History Museum, London. Phylogenetic distances (based on a Bayesian analysis using DNA sequence data) and shell characters (based on 200 semilandmarks) were used as proxies for ecological similarity and were analyzed to reveal patterns of overdispersion (indicating competition) or clustering (indicating filtering) in observed communities compared to random communities. Among the seven studied karst areas, a total of 15 Cyclophorus lineages were found. Unique communities were present in each area. The analyses revealed phylogenetic overdispersion in six and morphological overdispersion in four of seven karst areas. The pattern of frequent phylogenetic overdispersion indicated that competition among lineages is the major process shaping the Cyclophorus communities studied. The Coastal Area, which was phylogenetically overdispersed, showed a clear morphological clustering, which could have been caused by similar ecological adaptations among taxa in this environment. Only the community in the Cuc Phuong Area showed a pattern of phylogenetic clustering, which was partly caused by an absence of a certain, phylogenetically very distinct group in this region. Filtering due to geographical factors could have been involved here. This study shows how museum collections can be used to examine community assembly and contributes to the understanding of the processes that have shaped karst communities in Vietnam.
    • Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

      Li, B; Lopes, JS; Foster, PG; Embley, TM; Cox, CJ (Oxford Academic, 2014-07)
      Archaeplastida (=Kingdom Plantae) are primary plastid-bearing organisms that evolved via the endosymbiotic association of a heterotrophic eukaryote host cell and a cyanobacterial endosymbiont approximately 1,400 Ma. Here, we present analyses of cyanobacterial and plastid genomes that show strongly conflicting phylogenies based on 75 plastid (or nuclear plastid-targeted) protein-coding genes and their direct translations to proteins. The conflict between genes and proteins is largely robust to the use of sophisticated data- and tree-heterogeneous composition models. However, by using nucleotide ambiguity codes to eliminate synonymous substitutions due to codon-degeneracy, we identify a composition bias, and dependent codon-usage bias, resulting from synonymous substitutions at all third codon positions and first codon positions of leucine and arginine, as the main cause for the conflicting phylogenetic signals. We argue that the protein-coding gene data analyses are likely misleading due to artifacts induced by convergent composition biases at first codon positions of leucine and arginine and at all third codon positions. Our analyses corroborate previous studies based on gene sequence analysis that suggest Cyanobacteria evolved by the early paraphyletic splitting of Gloeobacter and a specific Synechococcus strain (JA33Ab), with all other remaining cyanobacterial groups, including both unicellular and filamentous species, forming the sister-group to the Archaeplastida lineage. In addition, our analyses using better-fitting models suggest (but without statistically strong support) an early divergence of Glaucophyta within Archaeplastida, with the Rhodophyta (red algae), and Viridiplantae (green algae and land plants) forming a separate lineage.
    • Conditional persistence and tolerance characterize endoparasite–colonial host interactions

      Fontes, I; Hartikainen, H; Taylor, Nick GH; Okamura, B (2017-07)
    • Confocal laser scanning microscopy as a valuable tool in Diptera larval morphology studies

      Grzywacz, A; Góral, T; Szpila, K; Hall, MJR (Springer Science and Business Media LLC, 2014-09-19)
      Larval morphology of flies is traditionally studied using light microscopy, yet in the case of fine structures compound light microscopy is limited due to problems of resolution, illumination and depth of field, not allowing for precise recognition of sclerites’ edges and interactions. Using larval instars of cyclorrhaphan Diptera, we show the usefulness of confocal laser scanning microscopy (CLSM) for studying the morphological characters of immature stages by taking advantage of the autofluorescent properties of cephaloskeleton structures. We compare data obtained from killed but unprepared larvae with those from larvae prepared by clearing according to two commonly used methods, either with potassium hydroxide or with Hoyer’s medium. We also evaluated the CLSM application for examining already slide-mounted larvae stored in museum collections and those freshly prepared. Our results indicate that CLSM and 3D reconstruction are excellent for visualizing small, compound structures of cylrorrhaphan larvae cephaloskeleton, if appropriate clearing techniques, i.e. the application of KOH, are used. Maximum intensity projection of confocal data sets obtained from material freshly prepared and that stored in museum collection does not differ. Because of this and the fact that KOH is commonly used as a clearing method to examine the cephaloskeleton of Diptera larvae, it is possible, and highly recommended, to use slides already prepared with this method for re-examination by CLSM. We conclude that CLSM application can be an invaluable source of data for studies of larval morphology of Cyclorrhapha by way of taxonomic diagnoses, character identification and improvement in characters homologization.
    • Connectivity and zebra mussel invasion offer short‐term buffering of eutrophication impacts on floodplain lake landscape biodiversity

      Salgado, J; Sayer, CD; Brooks, SJ; Davidson, TA; Baker, AG; Willby, N; Patmore, IR; Goldsmith, B; Bennion, H; Okamura, B (Wiley, 2019-05-16)
      Aim To investigate if connectivity and zebra mussel (Dreissena polymorpha) occurrence can mitigate effects of eutrophication in a lowland lake landscape. Location Upper Lough Erne, Northern Ireland, UK. Methods Data on environment, macrophytes and invertebrates were assembled for three basins of a large central lake and its satellite floodplain lakes via field surveys and palaeolimnological analyses. Space–time interaction analyses of palaeoecological data were compared pre‐1950 and post‐1950. Multivariate analyses examined how connectivity, environment and zebra mussels influenced contemporary lake communities, and explain their divergence from historical communities in the past. Results Pre‐1950, we found high community variation across sites and low within‐lake variation in macrophytes, but progressive eutrophication accentuated within‐lake community variation after 1950. Partitioning analysis showed larger effects of connectivity than nutrient enrichment on contemporary macrophyte composition, while local effects structured invertebrate communities. Three clusters of lakes were revealed according to variation in macrophyte composition, isolation from the central lake and nutrient enrichment: Group 1– the central lake and six nearby lakes were meso‐eutrophic (TP = 66.7 ± 47.6 μg/L; TN = 0.79 ± 0.41 mg/L) and had the highest zebra mussel abundances and organismal biodiversity; Group 2– Eight eutrophic (TP = 112±36.6 μg/L; TN = 1.25 ± 0.5 mg/L) and connected lakes; Group 3– Seven isolated and hypertrophic (TP = 163.2 ± 101.5 μg/L; TN = 1.55 ± 0.3 mg/L) lakes. Pre‐1950 palaeolimnological data for macrophytes and invertebrates for 5 lakes and a basin in the central lake most resembled extant lake communities of Group 1. However, palaeo‐records revealed that macrophytes and invertebrates subsequently converged towards those of Groups 2 and 3. Main conclusions Our study reveals that the central “mother” lake acts as a hub for preserving biodiversity via shared hydrological connectivity with satellite lakes and high zebra mussel abundances. These may buffer the impoverishing effects of eutrophication and sustain unexpectedly high biodiversity in the short term. Such protective buffering, however, cannot be relied upon indefinitely to conserve biodiversity.
    • Conservation in a Barcode Age: A cross-discipline re-storage project for pyritic specimens

      Allington-Jones, L; Trafford, A (International Council of Museums, 2017-01-01)
      The dichotomy of conservation and access has long been recognised within the museum profession. The recent push for digitisation has added a new dimension to this argument: digital records can both increase potential access, due to increased awareness of the existence of objects, and decrease potential handling, since a more thorough awareness of an object creates a more informed decision regarding whether access is actually necessary. The use of barcodes and the creation of digital resources have therefore been incorporated into a re-storage project at the Natural History Museum, London to reduce duplication of work (and handling) by staff and to combat the reduction in access caused by the enclosure of objects within microenvironments, which in turn helps preserve specimens for future access. This project demonstrates how conservation and digitisation can successfully synthesise through the use of barcodes, when working with a cross-discipline team.
    • Contrasting Biogeographic and Diversification Patterns in Two Mediterranean-Type Ecosystems

      Buerki, S; Jose, S; Yadav, SR; Goldblatt, P; Manning, JC; Forest, F; Salamin, N (PLOS, 2012-06-20)
      The five Mediterranean regions of the world comprise almost 50,000 plant species (ca 20% of the known vascular plants) despite accounting for less than 5% of the world’s land surface. The ecology and evolutionary history of two of these regions, the Cape Floristic Region and the Mediterranean Basin, have been extensively investigated, but there have been few studies aimed at understanding the historical relationships between them. Here, we examine the biogeographic and diversification processes that shaped the evolution of plant diversity in the Cape and the Mediterranean Basin using a large plastid data set for the geophyte family Hyacinthaceae (comprising ca. 25% of the total diversity of the group), a group found mainly throughout Africa and Eurasia. Hyacinthaceae is a predominant group in the Cape and the Mediterranean Basin both in terms of number of species and their morphological and ecological variability. Using state-of-the-art methods in biogeography and diversification, we found that the Old World members of the family originated in sub-Saharan Africa at the Paleocene–Eocene boundary and that the two Mediterranean regions both have high diversification rates, but contrasting biogeographic histories. While the Cape diversity has been greatly influenced by its relationship with sub-Saharan Africa throughout the history of the family, the Mediterranean Basin had no connection with the latter after the onset of the Mediterranean climate in the region and the aridification of the Sahara. The Mediterranean Basin subsequently contributed significantly to the diversity of neighbouring areas, especially Northern Europe and the Middle East, whereas the Cape can be seen as a biogeographical cul-de-sac, with only a few dispersals toward sub-Saharan Africa. The understanding of the evolutionary history of these two important repositories of biodiversity would benefit from the application of the framework developed here to other groups of plants present in the two regions.
    • Contributions to conservation outcomes by natural history museum-led citizen science: Examining evidence and next steps

      Ballard, HL; Robinson, LD; Young, AN; Pauly, GB; Higgins, LM; Johnson, RF; Tweddle, JC (2017-04)