Search results for "Tree"
showing 10 items of 1841 documents
GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critic…
2018
22 Pags.- 3 Tabls.- 7 Figs. Creative Commons License Attribution 4.0 International (CC BY 4.0).
Convergent Evolution in Intracellular Elements: Plasmids as Model Endosymbionts
2018
Endosymbionts are organisms that live inside the cells of other species. This lifestyle is ubiquitous across the tree of life and is featured by unicellular eukaryotes, prokaryotes, and by extrachromosomal genetic elements such as plasmids. Given that all of these elements dwell in the cytoplasm of their host cell, they should be subject to similar selection pressures. Here we show that strikingly similar features have evolved in both bacterial endosymbionts and plasmids. Since host and endosymbiont are often metabolically tightly intertwined, they are difficult to disentangle experimentally. We propose that using plasmids as tractable model systems can help to solve this problem, thus allo…
Symbiont Acquisition and Replacement as a Source of Ecological Innovation
2017
Nutritional symbionts play a major role in the ecology and evolution of insects. The recent accumulation of knowledge on the identity, function, genomics, and phylogenetic relationships of insect-bacteria symbioses provides the opportunity to assess the effects of symbiont acquisitions and replacements on the shift into novel ecological niches and subsequent lineage diversification. The megadiverse insect order Hemiptera presents a particularly large diversity of symbiotic associations that has frequently undergone shifts in symbiont localization and identity, which have contributed to the exploitation of nutritionally imbalanced diets such as plant saps or vertebrate blood. Here we review …
A New Phylogenetic Framework for the Animal-adaptedMycobacterium tuberculosisComplex
2018
Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely relate…
Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011-2016 reveals a replacement of lineages and complex recombination history.
2019
Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 …
A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model.
2018
International audience; In this article, a new Python package for nucleotide sequences clustering is proposed. This package, freely available on-line, implements a Laplacian eigenmap embedding and a Gaussian Mixture Model for DNA clustering. It takes nucleotide sequences as input, and produces the optimal number of clusters along with a relevant visualization. Despite the fact that we did not optimise the computational speed, our method still performs reasonably well in practice. Our focus was mainly on data analytics and accuracy and as a result, our approach outperforms the state of the art, even in the case of divergent sequences. Furthermore, an a priori knowledge on the number of clust…
Morphological and molecular characterization of Paragonimus caliensis Little, 1968 (Trematoda: Paragonimidae) from Medellin and Pichinde, Colombia
2018
Paragonimiasis is a subacute to chronic inflammatory granulomatous lung disease caused by the genus Paragonimus. In Latin America Paragonimus mexicanus Miyazaki & Ishii, 1968 is the only confirmed species to cause human infections. Paragonimus caliensis Little, 1968 is an uncommon species often regarded as a synonym of P. mexicanus. Recently, the study of two types of Paragonimus metacercariae from Costa Rica has provided new molecular and morphological evidence that P. caliensis is a separate species from P. mexicanus. In the present study, molecular, morphological and phylogenetic tools have been used to characterize two populations of Paragonimus located at west of Medellin, Antioquia an…
Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest
2016
ABSTRACT Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the co…
Distribution of Interstitial Telomeric Sequences in Primates and the Pygmy Tree Shrew (Scandentia).
2017
It has been hypothesized that interstitial telomeric sequences (ITSs), i.e., repeated telomeric DNA sequences found at intrachromosomal sites in many vertebrates, could be correlated to chromosomal rearrangements and plasticity. To test this hypothesis, we hybridized a telomeric PNA probe through FISH on representative species of 2 primate infraorders, Strepsirrhini (<i>Lemur catta, Otolemur garnettii, Nycticebus coucang</i>) and Catarrhini (<i>Erythrocebus patas, Cercopithecus petaurista, Chlorocebus aethiops, Colobus guereza</i>), as well as on 1 species of the order Scandentia, <i>Tupaia minor</i>, used as an outgroup for primates in phylogenetic recon…