• Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees

      Williams, PH; Byvaltsev, AM; Cederberg, B; Berezin, MV; Odegaard, F; Rasmussen, C; Richardson, LL; Huang, J; Sheffield, CS; Williams, ST; et al. (2015-12-10)
    • Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups

      Webster, BL; Emery, AM; Webster, JP; Gouvras, A; Garba, A; Diaw, O; Seye, MM; Tchuente, LAT; Simoonga, C; Mwanga, J; et al. (PLOS, 2012-10-25)
      Background Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected. Methodology/Principal Findings To elucidate the genetic diversity of Schistosoma haematobium, a DNA ‘barcoding’ study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands. Conclusions/Significance The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic ‘bottleneck’ followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis.
    • The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788

      Mead, D; Fingland, K; Cripps, R; PORTELA MIGUEZ, ROBERTO; Smith, M; Corton, C; Oliver, K; Skelton, J; Betteridge, E; Doulcan, J; et al. (F1000 Research Ltd, 2020-02-13)
      We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
    • The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758

      Mead, D; Fingland, K; Cripps, R; PORTELA MIGUEZ, ROBERTO; Smith, M; Corton, C; Oliver, K; Skelton, J; Betteridge, E; Dolucan, J; et al. (F1000 Research Ltd, 2020-02-03)
      We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
    • The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758

      Mead, D; Hailer, F; Chadwick, E; PORTELA MIGUEZ, ROBERTO; Smith, M; Corton, C; Oliver, K; Skelton, J; Betteridge, E; Doulcan, JD; et al. (F1000 Research Ltd, 2020-02-19)
      We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.
    • Genome-wide SNP data reveal an overestimation of species diversity in a group of hawkmoths.

      Hundsdoerfer, AK; Lee, KM; Kitching, IJ; Mutanen, M (Oxford University Press, 2019-05-29)
      The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of “when do nondiscrete entities become distinct,mutually exclusive evolutionary units”? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct.However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.
    • The Genomic Footprints of the Fall and Recovery of the Crested Ibis

      Feng, Shaohong; Fang, Qi; Barnett, Ross; Li, Cai; Han, Sojung; Kuhlwilm, Martin; Zhou, Long; Pan, Hailin; Deng, Yuan; Chen, Guangji; et al. (Elsevier BV, 2019-01-10)
      Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
    • Geographic range extension of Speke's Hinge-back Tortoise Kinixys spekii Gray, 1863

      Ihlow, F; Farooq, H; Qvozdik, V; Hofmeyr, M; Conradie, W; Harvey, J; Campbell, P; Verburgt, L; Fritz, U (Amphibian and Reptile Conservation, 2019-11-06)
      Kinixys spekii has a wide distribution range across sub-Saharan Africa, having been reported from Angola, Botswana, Burundi, the Democratic Republic of the Congo, eSwatini, Kenya, Malawi, Mozambique, Namibia, South Africa, Tanzania, Zambia, and Zimbabwe. Kinixys spekii inhabits savannah and dry bushveld habitats and was previously considered an inland species. However, recent records suggest a more extensive geographical distribution. Here, we provide genetically verifed records for Angola, South Africa, and Mozambique, and discuss reliable sightings for Rwanda. These new records extend the range signifcantly to the east and west, and provide evidence for the occurrence of this species along the coast of the Indian Ocean in South Africa and Mozambique.
    • Giant Sequoia: an extraordinary case study involving Carbopol® gel

      McKibbin, C; Allington-Jones, L; Verveniotou, E (Archetype Publishing LtdLondon, 2017-10-18)
      In 2016 a project was undertaken to stabilise and aestheticise the transverse section of giant sequoia on display at the Natural History Museum (NHM) in London, UK. This iconic specimen, which now dominates the top floor of the central hall, was 1300 years old when felled and has been part of the exhibitions for 122 years. Measuring over 4.5 metres in diameter, it posed many challenges during remedial conservation. The largest involved removal of the discoloured waxy substance and opacified shellac-based varnish that had been applied in the early 1980s. Solvent tests revealed that the coating was soluble in Industrial Methylated Spirits (IMS) and that the gel worked most effectively at a 1 hour application time. At longer durations the varnish itself gelled and the waxy component was re-deposited. The waxy substance was effectively removed by wiping with alternate white spirit and IMS swabs.
    • Glacial and gully erosion on Mars: A terrestrial perspective

      Conway, SJ; Butcher, FE; de Haas, T; Deijns, AA; M. Grindrod, P; Davis, JM (Elsevier, 2018-05-24)
      The mid- to high latitudes of Mars host assemblages of landforms consistent with a receding glacial landscape on Earth. These landforms are postulated to have formed >5 Ma under a different climate regime when Mars' orbital obliquity was on average 10° higher than today. Here, we investigate the spatiotemporal relationship between gullies and glacial landforms, both common in the mid-latitudes. Gullies are kilometre-scale landforms with a source alcove, transportation channel, and depositional apron. The glacial landforms comprise (1) extant viscous flow features (VFF) that extend from the base of crater walls into the interior of crater floors and are widely interpreted as debris-covered glaciers containing extant ice, and (2) landforms such as arcuate ridges at the base of crater walls that have been interpreted as relicts of more recent, less extensive glacial advances focussed on crater walls. We measure headwall retreat associated with glacial landforms and date their host-craters to constrain minimum headwall retreat rates. We record headwall retreat rates up to ~102 m My−1 for the youngest suite of glacial landforms, equivalent to erosion rates of wet-based glaciers on Earth and to headwall retreat rates associated with martian bedrock gully systems. We find extensive evidence for a single erosional episode dating 5–10 Ma, which postdates emplacement of the majority of VFF but seems to predate formation of the gullies. We propose that the wet-based glacial episode was associated with glaciation focussed on the crater walls rather than melting of the glacial ice deposits on the crater floors (VFF). This is consistent with our observations of crater wall morphologies, including the presence of arcuate ridges consistent with terrestrial glaciotectonic features that require liquid water to form, textural alteration of the eroded bedrock surface consistent with ice-segregation and frost-shattering, and the presence of downslope pasted-on terrain, tentatively interpreted here as glacial till deposits sourced from glacial erosion of the crater wall. The pasted-on terrain is usually interpreted as a thicker, latitude-dependant mantle located on sloping terrain formed from airfall of ice nucleated on dust, but we suggest that it has been reworked by glaciation and is predominantly glacial in origin. Although our results cannot substantiate that gullies are produced by meltwater, the discovery of this wet glacial event does provide evidence for widespread meltwater generation in Mars' recent history.
    • Glastonbury Lake Village Revisited: A Multi-proxy Palaeoenvironmental Investigation of an Iron Age Wetland Settlement

      Hill, T; Hill, G; Brunning, R; Banerjea, R; Fyfe, R; Hogg, A; Jones, J; Perez, M; Smith, D (Taylor & Francis, 2019-01-14)
      Glastonbury Lake Village is one of the most iconic late prehistoric wetland settlements in Europe. A new excavation in the core of Glastonbury Lake Village, for the first time since 1907, provided the opportunity for sampling of deposits associated with occupation of the site and for reconstructing the environmental conditions before the settlement was constructed. The results of a detailed multiproxy study are presented, including palaeoecological proxies (Coleoptera, plant macrofossils, diatoms, pollen, non-pollen palynomorphs), geoarchaeological methods (soil micromorphology), supported by new radiocarbon determinations. The results highlight how the difficult process of creating a settlement in a wetland was achieved, both within structures and in the spaces around them. Evidence for grain storage within the macrofossil assemblages, and the presence of animals on the settlement reflected in coleopteran assemblages and non-pollen palynomorphs has refined our understanding of the interaction between the settlement and the neighbouring dryland.
    • A global assessment of Zn isotope fractionation in secondary Zn minerals from sulfide and non-sulfide ore deposits and model for fractionation control

      Mondillo, N; Wilkinson, JJ; Boni, M; Weiss, DJ; Mathur, R (Elsevier, 2018-11-15)
      We investigated extent and direction of Zn isotope fractionation in secondary zinc minerals formed during low temperature hydrothermal and/or supergene oxidation of primary sulfide deposits. Zinc isotope data have been obtained from non-sulfide zinc mineral separates (willemite - Zn2SiO4, smithsonite - ZnCO3, hemimorphite - Zn4(Si2O7)(OH)2·H2O, hydrozincite - Zn5(CO3)2(OH)6, and sauconite - Na0.3Zn3(Si,Al)4O10(OH)2·4H2O) collected from several Zn deposits in Ireland, Belgium, Poland, Namibia, Peru, Yemen and Zambia. The data are compared with Zn isotope compositions measured on Zn sulfides collected in the same areas and/or derived from the existing literature, to establish the controls of direction and likely extent of any fractionations. We find that willemite has the greatest compositional variability, with measured δ66ZnJCM-Lyon values ranging from −0.42 to 1.39‰, spanning the entire range of terrestrial variation in Zn isotopes recorded to date. Overall, significant fractionations in positive and negative directions are recorded relative to the precursor phase (primary sphalerite or an earlier secondary phase), with primary sphalerite falling in a relatively narrow range of isotopic values (approximately −0.1 to +0.4‰). Most of the data observed on willemite, hemimorphite and hydrozincite can be explained with a model of isotopic fractionation, in which partial dissolution of primary sphalerite is followed by precipitation of an initial secondary phase that preferentially incorporates heavy Zn isotopes. Smithsonite, instead, preferentially incorporates light Zn isotopes. This reflects the variation in the Zn-x bond strengths of these secondary phases with respect to the original sulfides. We also observed that isotope compositions do not depend only on the difference between the fractionation factors of the involved phases but also on the amount of the secondary mineral precipitated after dissolution of primary sulfide, and that the greatest fractionations occur when only small amounts of secondary mineral are precipitated. Progressive precipitation from migrating fluids that form phases enriched in heavy zinc isotopes would lead to a gradual decrease in the δ66Zn values of such phases, and the fluids involved, in time and space. Strong negative isotopic shifts are almost only observed for late crystallizing phases, such as those in vugs. These are interpreted to reflect precipitation from residual, isotopically-light fluids that are the inevitable highly-fractionated product of the above-described process. Where a more complete replacement of primary sulfide has occurred, such as in the high-grade core of non-sulfide zinc orebodies, there is limited net isotopic fractionation because dissolved primary zinc is nearly quantitatively reprecipitated locally. In addition, in only one case (Yanque, Peru) we observed that the fringes of non-sulfide zinc deposit were characterized by isotopically fractionated compositions, with highly negative values implying extensive precipitation (earlier, or elsewhere) of isotopically heavy secondary phases. The higher-grade ore zones, where complete breakdown of primary sulfides and quantitative reprecipitation of zinc have occurred, show instead less fractionated compositions.
    • A global catalog of primary reptile type specimens

      Campbell, P; Uetz, P; CHERIKH, SAMI; Shea, G; Ineich, I; Doronin, I; ROSADO, J; WYNN, A; TIGHE, KA; MCDIARMID, R; et al. (Magnolia Press, 2019-11-12)
      We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located, were never designated, or we did not find any information about them. 51 species are based on iconotypes. To map all types to physical GLOBAL TYPE CATALOG OF REPTILES Zootaxa 4695 (5) © 2019 Magnolia Press · 439collections we have consolidated all synonymous and ambiguous collection acronyms into an unambiguous list of 364 collections holding these primary types. The 10 largest collections possess more than 50% of all (primary) reptile types, the 36 largest collections possess more than 10,000 types and the largest 73 collections possess over 90% of all types. Of the 364 collections, 107 hold type specimens of only 1 species or subspecies. Dozens of types are still in private collections. In order to increase their utility, we recommend that the description of type specimens be supplemented with data from high-resolution images and CT-scans, and clear links to tissue samples and DNA sequence data (when available). We request members of the herpetological community provide us with any missing type information to complete the list.
    • A global checklist of the Bombycoidea (Insecta: Lepidoptera)

      Kitching, I; Rougerie, R; Zwick, A; Hamilton, CA; St Laurent, RA; Naumann, S; Ballesteros Mejia, L; Kawahara, AY (2018-02-12)