Search results for "phylogenetic"
showing 10 items of 1179 documents
Megaphylogenetic Specimen-level Approaches to the <I>Carex</I> (Cyperaceae) Phylogeny Using ITS, ETS, and <I>matK</I> Sequenc…
2016
Abstract We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, histo…
A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).
2013
Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even …
The concept of genus within the family Phytoseiidae (Acari: Parasitiformes): historical review and phylogenetic analyses of the genus Neoseiulus Hugh…
2012
Systematic studies on the family Phytoseiidae were first conducted at the beginning of the 20th century but increased greatly after the Second World War. Various classifications have been proposed based on different characters such as: dorsal, ventral, and leg chaetotaxy; the shape of ventrianal and sternal shields; the shape of the insemination apparatus (spermatheca) and spermatodactylus; the number of teeth on the movable digit of chelicera; and dorsal and ventral adenotaxy. The genus concepts developed over the last five decades can be divided into two main categories or hypotheses. The first, supported mainly by Chant and McMurtry, focuses on dorsal and ventral chaetotaxy, and the gene…
Molecular phylogeny of the marine dinoflagellate genus Heterodinium (Dinophyceae)
2012
The dinoflagellate genus Heterodinium has unusual morphological characters such as a mid-ventral intercalary plate with a pore, a small plate in the left side of the dorsal epitheca, three antapical plates, and a well-developed anterior cingular list. We obtained the first SSU rDNA sequences from single cells of six species of Heterodinium from Mediterranean coastal and open waters. They included the type species H. scrippsii and H. rigdeniae and representatives of the other subgenera, Sphaerodinium (H. doma, H. milneri, H. globosum) and Platydinium (H. pavillardii). SSU rDNA phylogeny showed that Heterodinium spp. formed a well-supported monophyletic group (100% bootstrap support) composed…
Multilocus sequence typing confirms the close genetic inter-relatedness between three distinct flavescence doree phytoplasma strain clusters and grou…
2007
ABSTRACT Vineyards of southern France and northern Italy are affected by the flavescence dorée (FD) phytoplasma, a quarantine pathogen transmitted by the leafhopper of Nearctic origin Scaphoideus titanus . To better trace propagation of FD strains and identify possible passage between the vineyard and wild plant compartments, molecular typing of phytoplasma strains was applied. The sequences of the two genetic loci map and uvrB - degV , along with the sequence of the secY gene, were determined among a collection of FD and FD-related phytoplasmas infecting grapevine, alder, elm, blackberry, and Spanish broom in Europe. Sequence comparisons and phylogenetic analyses consistently indicated the…
New records of phytoseiid mites from Italy, with description of a new species and a redescription of other two (Parasitiformes, Phytoseiidae)
2020
The Italian phytoseiid fauna consists of 91 valid species. Eighteen of them were described as new species from materials collected in various Italian localities. In the present paper we report nine new records from the Italian fauna and describe the new species, Neoseiulus mediterraneus belonging to the subfamily Amblyseiinae. Complementary descriptions of two rare species, namely: Typhlodromus (Anthoseius) singularis and Typhlodromus (Typhlodromus) knisleyi, were also added.
Identity of the Calcarata species complex in Viola sect. Melanium (Violaceae)
2020
The Calcarata species complex in Viola sect. Melanium (Violaceae) is a group of species from Italy and neighbouring islands. The complex is of considerable evolutionary interest because several hypotheses about hybrid speciation within the group have been previously proposed. Because the Calcarata complex is not well characterized morphologically, we used 142 samples representing 92 (of c. 120) species of V. sect. Melanium plus three outgroup species. Nuclear ITS and ETS and plastid trnS–trnG intergenic spacer sequences were analysed to test the monophyly of the Calcarata complex and to infer relationships among the constituent species. Both nuclear and plastid sequences resulted in very li…
The gypsy database (GyDB) of mobile genetic elements: release 2.0
2011
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analys…
The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling.
2013
14 pages; International audience; In corals, biocalcification is a major function that may be drastically affected by ocean acidification (OA). Scleractinian corals grow by building up aragonitic exoskeletons that provide support and protection for soft tissues. Although this process has been extensively studied, the molecular basis of biocalcification is poorly understood. Notably lacking is a comprehensive catalog of the skeleton-occluded proteins-the skeletal organic matrix proteins (SOMPs) that are thought to regulate the mineral deposition. Using a combination of proteomics and transcriptomics, we report the first survey of such proteins in the staghorn coral Acropora millepora. The or…
Northern refugia and recent expansion in the North Sea: The case of the wrasse Symphodus melops (Linnaeus, 1758)
2011
Pleistocene climate changes have imposed extreme conditions to intertidal rocky marine communities, forcing many species to significant range shifts in their geographical distributions. Phylogeographic analyses based on both mitochondrial and nuclear genetic markers provide a useful approach to unravel phylogeographic patterns and processes of species after this time period, to gain general knowledge of how climatic changes affect shifts in species distributions. We analyzed these patterns on the corkwing wrasse (Symphodus melops, Labridae), a rocky shore species inhabiting North Sea waters and temperate northeastern Atlantic Ocean from Norway to Morocco including the Azores, using a fragme…