Browsing by Subject "MULTIPLE SEQUENCE ALIGNMENT"

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  • Lavikainen, Antti; Iwaki, Takashi; Haukisalmi, Voitto; Konyaev, Sergey V.; Casiraghi, Maurizio; Dokuchaev, Nikolai E.; Galimberti, Andrea; Halajian, Ali; Henttonen, Heikki; Ichikawa-Seki, Madoka; Itagaki, Tadashi; Krivopalov, Anton V.; Meri, Seppo; Morand, Serge; Nareaho, Anu; Olsson, Gert E.; Ribas, Alexis; Terefe, Yitagele; Nakao, Minoru (2016)
    The common cat tapeworm Hydatigera taeniaeformis is a complex of three morphologically cryptic entities, which can be differentiated genetically. To clarify the biogeography and the host spectrum of the cryptic lineages, 150 specimens of H. taeniaeformis in various definitive and intermediate hosts from Eurasia, Africa and Australia were identified with DNA barcoding using partial mitochondrial cytochrome c oxidase subunit 1 gene sequences and compared with previously published data. Additional phylogenetic analyses of selected isolates were performed using nuclear DNA and mitochondrial genome sequences. Based on molecular data and morphological analysis, Hydatigera kamiyai n. sp. Iwaki is proposed for a cryptic lineage, which is predominantly northern Eurasian and uses mainly arvicoline rodents (voles) and mice of the genus Apodemus as intermediate hosts. Hydatigera taeniaeformis sensu stricto (s.s.) is restricted to murine rodents (rats and mice) as intermediate hosts. It probably originates from Asia but has spread worldwide. Despite remarkable genetic divergence between H. taeniaeformis s.s. and H. kamiyai, interspecific morphological differences are evident only in dimensions of rostellar hooks. The third cryptic lineage is closely related to H. kamiyai, but its taxonomic status remains unresolved due to limited morphological, molecular, biogeographical and ecological data. This Hydatigera sp. is confined to the Mediterranean and its intermediate hosts are unknown. Further studies are needed to classify Hydatigera sp. either as a distinct species or a variant of H. kamiyai. According to previously published limited data, all three entities occur in the Americas, probably due to human-mediated introductions. (C) 2016 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.
  • Vujic, Ante; Likov, Laura; Radenkovic, Snezana; Tubic, Natasa Kocis; Djan, Mihajla; Sebic, Anja; Perez-Banon, Celeste; Barkalov, Anatolij; Hayat, Rustem; Rojo, Santos; Andric, Andrijana; Stahls, Gunilla (2020)
    The phytophagous hoverfly genus Merodon Meigen, 1803 (Diptera, Syrphidae), which comprises more than 160 species distributed in Palaearctic and Afrotropical regions, can be differentiated into multiple groups of species that harbor high levels of hidden diversity. In this work, the serrulatus species group of Merodon is revised, providing an illustrated key to species, a detailed discussion on the taxonomic characters and a morphological diagnosis, including also the first data about the preimaginal morphology of this species group. The study includes characteristics of the 13 species of the M. serrulatus group, along with the available distributional data. Moreover, descriptions are provided for seven new species, namely M. defectus Vujic, Likov & Radenkovic sp. nov., M. disjunctus Vujic, Likov & Radenkovic sp. nov., M. medium Vujic, Likov & Radenkovic sp. nov., M. nigrocapillatus Vujic, Likov & Radenkovk sp. nov., M. nigropunctum Vujic, Likov & Radenkovic sp. nov., M. opacus Vujic, Likov & Radenkovk sp. nov., and M. trianguloculus Vujic, Likov & Radenkovk sp. nov. In addition, the taxa M. serrulatus (Wiedemann in Meigen, 1822), M. bequaerti Hurkmans, 1993, M. birsutus Sack, 1913, M. kawamurae Matsumura, 1916, M. sacki (Paramonov, 1936) and M. sophron Hurkmans, 1993 are redefined and redescribed. Following a detailed study of the type material sourced from different entomological collections, the status of all available taxa related to M. serrulatus is revised and a new synonymy is proposed: M. tener Sack, 1913 syn. nov. (junior synonym of M. serrulatus). The identity of M. trizonus (Szilady, 1940) could not be assessed as the type specimens are lost. Thus, the name M. trizonus is considered as nomen dubium. The monophyly and composition of this species group are assessed through Maximum Parsimony and Maximum Likelihood analyses of the mitochondrial COI and nuclear 28S rRNA gene sequences.
  • MacAlasdair, Neil; Pesonen, Maiju; Brynildsrud, Ola; Eldholm, Vegard; Kristiansen, Paul A.; Corander, Jukka; Caugant, Dominique A.; Bentley, Stephen D. (2021)
    Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here, we fill this knowledge gap by a detailed analysis of 2839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009-2012. Our findings indicate that the meningococcal genome is highly dynamic, with highly recombinant loci and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate how population structure can correlate with genome flexibility, as some lineages in Burkina Faso are orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programs and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.
  • Kistenich, Sonja; Rikkinen, Jouko K.; Thüs, Holger; Vairappan, Charles S.; Wolseley, Patricia A.; Timdal, Einar (2018)
    Krogia borneensis Kistenich & Timdal, K. isidiata Kistenich & Timdal and K. macrophylla Kistenich & Timdal are described as new species, the first from Borneo and the two latter from New Caledonia. The new species are supported by morphology, secondary chemistry and DNA sequence data. Krogia borneensis and K. isidiata contain sekikaic and homosekikaic acid, both compounds reported here for the first time from the genus. Krogia macrophylla contains an unknown compound apparently related to boninic acid as the major compound. DNA sequences (mtSSU and nrITS) are provided for the first time for Krogia and a phylogeny of the genus based on 15 accessions of five of the six accepted species is presented. Krogia antillarum is reported as new to Brazil, Guatemala and Mexico.