• Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics

      Timmermans, MJTN; Barton, C; Haran, J; Ahrens, D; Culverwell, CL; Ollikainen, A; Dodsworth, S; Foster, PG; Bocak, L; Vogler, AP (Oxford University Press, 2016-01-01)
      Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2 , nad4 , nad5 , and nad6 genes. Credible tree topologies were obtained with the nhPhyML (“nonhomogeneous”) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.
    • Fauna Europaea: Hymenoptera – Apocrita (excl. Ichneumonoidea)

      Mitroiu, M-D; Noyes, J; Cetkovic, A; Nonveiller, G; Radchenko, A; Polaszek, Andrew; Ronquist, F; Forshage, M; Pagliano, G; Gusenleitner, J; et al. (2015-03-20)
      Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, ‘Hymenoptera - Apocrita (excluding Ichneumonoidea)’ comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.
    • Field sampling is biased against small‑ranged species of high conservation value: a case study on the sphingid moths of East Africa

      Beck, J; Takano, H; Ballesteros-Mejia, L; Kitching, I; McCain, CM (Springer Verlag, 2018-08-23)
      The range size of species co-occurring in local assemblages is a pivotal variable in assessments of a site’s conservation value. Assemblages featuring many small-ranged species are given more priority than assemblages consisting mainly of wide-ranging species. However, the assembly of relevant information can be challenging and local range size distributions of tropical invertebrates are rarely available for conservation planning. We present such data for sphingid moths in East Africa, a highly diverse region of high conservation value. We compare geographic range size distributions based on field samples with predictions from modelled range map data. Using this system as a case study, we provide evidence for a systematic sampling bias when inferring average local range sizes from field data. Unseen species (i.e., species present but missed in local sampling) are often those with small ranges (hence, of high conservation value). Using an elevational gradient, we illustrate how this bias can lead to false, counterintuitive assessments of environmental effects on local range size distributions. Furthermore, with particular reference to sphingid moths in the study region, we show that current protected areas appear unrelated to the spatial distribution of species richness or average geographic range sizes at a local scale. We discuss the need to treat field sampled data with caution and in concert with other data sources such as probabilistic models.
    • First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO 2

      Field, KJ; Rimington, WR; Bidartondo, MI; Allinson, KE; Beerling, DJ; Cameron, DD; Duckett, JG; Leake, JR; Pressel, S (2015-01)
    • The first global deep-sea stable isotope assessment reveals the unique trophic ecology of Vampire Squid Vampyroteuthis infernalis (Cephalopoda)

      Golikov, A; Ceia, F; Sabirov, R; Ablett, J; Gleadall, I; Gudmundsson, G; Hoving, H; Heather, J; Pálsson, J; Reid, AL; et al. (Nature Publishing Group, 2019-12-13)
      Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δ15N and TL. Our results, presenting the first global comparison for a deep-sea invertebrate, demonstrate that V. infernalis has an ontogenetic decrease in δ15N and TL, coupled with niche broadening. Juveniles are mobile zooplanktivores, while larger Vampyroteuthis are slow-swimming opportunistic consumers and ingest particulate organic matter. Vampyroteuthis infernalis occupies the same TL (3.0–4.3) over its global range and has a unique niche in deep-sea ecosystems. These traits have enabled the success and abundance of this relict species inhabiting the largest ecological realm on the planet.
    • The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

      Vanhove, Maarten PM; Briscoe, Andrew G; Jorissen, Michiel WP; Littlewood, T; Huyse, Tine (Springer Science and Business Media LLC, 2018-07-04)
      BACKGROUND:Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. RESULTS:Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. CONCLUSIONS:The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.
    • First record of Acaenitinae (Hymenoptera, Ichneumonidae) from South America with description of a new species and a key to the world species of Arotes Gravenhorst

      Castillo, C; Saaksjarvi, L; Bennett, A; Broad, G (Pensoft, 2011-10-14)
      A new species of Acaenitinae, Arotes ucumari Castillo & Sääksjärvi, sp. n., is described and illustrated representing the first record of the subfamily from South America. The new species was collected from a premontane tropical rain forest in the Peruvian Andes at 1500 m. A key to the world species of Arotes Gravenhorst, 1829 is provided. The subspecies Arotes albicinctus moiwanus (Matsumura, 1912) is raised to species rank, Arotes moiwanus stat. n.
    • A first record of Clanis hyperion Cadiou & Kitching, 1990 (Lepidoptera: Sphingidae) in Bhutan, and a preliminary checklist of the hawkmoths of Mendrelgang, Bhutan

      Singh, IJ; Kitching, I (2014-01-26)
      An inventory of hawkmoths (Sphingidae) of Mendrelgang division of Tsirang District, Bhutan was undertaken between December 2011 and September 2012. A total of 27 species was recorded belonging to three subfamilies. The most notable was Clanis hyperion Cadiou and Kitching 1990. The present record extends the known distribution of C. hyperion to the eastern Himalaya, and significantly it is the first record of the species from northwest of the Brahmaputra River.
    • First report of ' Candidatus Liberibacter solanacearum' in the United Kingdom in the psyllid Trioza anthrisci

      Sjölund, MJ; Clark, M; Carnegie, M; Greenslade, AFC; Ouvrard, DNM; Highet, F; Sigvald, R; Bell, JR; Arnsdorf, YM; Cairns, R; et al. (2017-12-31)
    • 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)