• Form and metabolic scaling in colonial animals

      Hartikainen, H; Humphries, S; Okamura, B (2014-03-01)
    • A foundation monograph of Convolvulus L. (Convolvulaceae)

      Wood, JRI; Williams, BRM; Mitchell, TC; Carine, MA; Harris, DJ; Scotland, RW (2015-06-18)
    • Four new non-spiny Solanum (Solanaceae) species from South America

      Särkinen, T; Gonzáles, P; Knapp, S (2015-01-13)
    • From text to structured data: Converting a word-processed floristic checklist into Darwin Core Archive format

      Remsen, D; Knapp, S; Georgiev, Teodor; Stoev, Pavel; Penev, Lyubomir (Pensoft Publishers, 2012-01-30)
      The paper describes a pilot project to convert a conventional floristic checklist, written in a standard word processing program, into structured data in the Darwin Core Archive format. After peer-review and editorial acceptance, the final revised version of the checklist was converted into Darwin Core Archive by means of regular expressions and published thereafter in both human-readable form as traditional botanical publication and Darwin Core Archive data files. The data were published and indexed through the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT) and significant portions of the text of the paper were used to describe the metadata on IPT. After publication, the data will become available through the GBIF infrastructure and can be re-used on their own or collated with other data.
    • From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

      Lindh, MV; Maillot, BM; Shulse, CN; Gooday, AJ; Amon, Diva; Smith, CR; Church, MJ (Frontiers, 2017-09-08)
      Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.
    • Further karyosystematic studies of the Boreonectes griseostriatus (De Geer) group of sibling species (Coleoptera, Dytiscidae)–characterisation of B. emmerichi (Falkenström, 1936) and additional European data

      Angus, RB; Angus, EM; Jia, F; Chen, Z-N; Zhang, Y (2015-03-31)
      A lectotype is designated for the Tibetan species Deronectes emmerichi Falkenström, 1936 (Currently Boreonectes emmerichi (Falkenström)), and its habitus, as well as the median lobe and parameres of its aedeagus, are figured along with additional comparative material. Material of B. emmerichi from Sikkim (BMNH) represents the first record of a Boreonectes Angus, 2010 species from India. The karyotype of B. emmerichi is described as having 26 pairs of autosomes plus sex chromosomes which are X0 (♂), XX (♀). The karyotype is most like that of B. macedonicus (Géuorguiev, 1959), but with slight differences. Additional chromosomal information is given for B. griseostriatus griseostriatus (De Geer, 1774) in the French Alps, B. g. strandi (Brinck, 1943) on the Kola Peninsula, B. multilineatus (Falkenström, 1922) in the Pyrenees and B. ibericus (Dutton & Angus, 2007) in the Spanish Picos de Europa.
    • Further studies on Boreonectes Angus, 2010, with a molecular phylogeny of the Palaearctic species of the genus

      Angus, RB; Ribera, I; Jia, F (Pensoft, 2017-03-22)
      Karyotypes are given for Boreonectes emmerichi (Falkenström, 1936) from its type locality at Kangding, China, and for B. alpestris (Dutton & Angus, 2007) from the St Gotthard and San Bernardino passes in the Swiss Alps. A phylogeny based on sequence data from a combination of mitochondrial and nuclear genes recovered western Palaearctic species of Boreonectes as monophyletic with strong support. Boreonectes emmerichi was placed as sister to the north American forms of B. griseostriatus (De Geer, 1774), although with low support. The diversity of Palaearctic species of the B. griseostriatus species group is discussed.
    • 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.
    • 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.