Search results for "phylogeny"
showing 10 items of 1398 documents
Comparison of genomic sequences clustering using Normalized Compression Distance and Evolutionary Distance
2008
Genomic sequences are usually compared using evolutionary distance, a procedure that implies the alignment of the sequences. Alignment of long sequences is a long procedure and the obtained dissimilarity results is not a metric. Recently the normalized compression distance was introduced as a method to calculate the distance between two generic digital objects, and it seems a suitable way to compare genomic strings. In this paper the clustering and the mapping, obtained using a SOM, with the traditional evolutionary distance and the compression distance are compared in order to understand if the two distances sets are similar. The first results indicate that the two distances catch differen…
A factory-scale application of secondary adjunct cultures selected from lactin acid becteria during Puzzone di Moena cheese ripening
2008
The lactic acid populations of 2 seasonal Puzzone di Moena cheeses made from winter and summer raw cow's milk were characterized at different ripening times. Lactic acid bacteria (LAB) were isolated on selective media and subjected to genetic typing and identification. The species most frequently found during ripening were Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, and Pediococcus pentosaceus. The different strains recognized by random amplification of polymorphic DNA-PCR were characterized for their acidifying and proteolytic activities to select nonstarter LAB to be used as secondary adjunct cultures (SAC). For each of the 3 above species, a strain showing weak acidi…
Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.
1994
Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted…
Asexual multiplication of larval parasitic worms: a predictor of adult life-history traits in Taeniidae?
2001
The hypothesis that asexual multiplication inside the intermediate host and adult life-history traits within the final host are independent is tested among Cestoda. Using phylogenetic relationships among the Cestoda species, we can show that asexual multiplication appears to have been lost and recovered several times throughout Taeniidae evolution; this allows a comparison of the adult life-history traits of species with and without asexual multiplication at the larval stage. The adult trait considered is the size of the parasite, since numerous life-history traits, such as fecundity and longevity, are correlated with size. If adult traits are independent of whether the larval stage reprodu…
Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensiv…
2017
Abstract The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure. We are the…
Species-specific genes under selection characterize the co-evolution of slavemaker and host lifestyles.
2017
Background The transition to a parasitic lifestyle entails comprehensive changes to the selective regime. In parasites, genes encoding for traits that facilitate host detection, exploitation and transmission should be under selection. Slavemaking ants are social parasites that exploit the altruistic behaviour of their hosts by stealing heterospecific host brood during raids, which afterwards serve as slaves in slavemaker nests. Here we search for evidence of selection in the transcriptomes of three slavemaker species and three closely related hosts. We expected selection on genes underlying recognition and raiding or defense behaviour. Analyses of selective forces in species with a slavemak…
Expansion of the CRF19_cpx Variant in Spain
2015
Abstract Background HIV-1 CRF19_cpx, is a recombinant variant found almost exclusively in Cuba and recently associated to a faster AIDS onset. Infection with this variant leads to higher viral loads and levels of RANTES and CXCR4 co-receptor use. Objectives The goal of this study was to assess the presence of CRF19_cpx in the Spanish province of Valencia, given its high pathogenicity. Study design 1294 HIV-1 protease-reverse transcriptase (PR/RT) sequences were obtained in Valencia (Spain), between 2005 and 2014. After subtyping, the detected CRF19_cpx sequences were aligned with 201 CRF19_cpx and 66 subtype D sequences retrieved from LANL, and subjected to maximum-likelihood phylogenetic a…
Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs
2012
The metazoan taxon Syndermata (Monogononta, Bdelloidea, Seisonidea, Acanthocephala) comprises species with vastly different lifestyles. The focus of this study is on the phylogeny within the syndermatan subtaxon Acanthocephala (thorny-headed worms, obligate endoparasites). In order to investigate the controversially discussed phylogenetic relationships of acanthocephalan subtaxa we have sequenced the mitochondrial (mt) genomes of Echinorhynchus truttae (Palaeacanthocephala), Paratenuisentis ambiguus (Eoacanthocephala), Macracanthorhynchus hirudinaceus (Archiacanthocephala), and Philodina citrina (Bdelloidea). In doing so, we present the largest molecular phylogenetic dataset so far for this…
Taxonomic complexity in the halophyte Limonium vulgare and related taxa (Plumbaginaceae): insights from analysis of morphological, reproductive and k…
2014
Part of a special issue on halophytes and saline adaptations Background and Aims Limonium is awell-known example of a group of plants that is taxonomically complex due to certain biological characteristics that hamper species’ delineation. The closely related polyploid species Limonium vulgare Mill., L. humile Mill. and L. narbonense Mill. are defined species and can be used for studying patterns of morphological and reproductive variation. The first two taxa are usually found in Atlantic Europe and the third in the Mediterranean region, but a numberof intermediate morphological formsmay be present alongside typical examples of these species. This study attempts to elucidate morphological, …
Molecular phylogeny of the Notostraca
2012
Abstract We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the gener…