Search results for "Phylogenetics"

Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): Implications for systematics, biogeography, flower and fruit evolution, and the…

2011

 Premise of the study : Atripliceae (Chenopodiaceae), including Atriplex (300 spp.) as the largest genus of the family, are an ecologically important group of steppes and semideserts worldwide. Relationships in Atripliceae are poorly understood due to obscure and potentially convergent morphological characters.  Methods : Using sequence variation of two chloroplast markers ( rbcL gene, atpB-rbcL spacer) and one nrDNA marker (ITS) analyzed with BEAST, we investigated the systematics and biogeography of Atripliceae. We surveyed fl ower morphology and fruit anatomy to study the evolution of fland fruits in the tribe.  Key results : Female fl owers with persistent foliar cover (the diagnosti…

Phylogeny of Early Cretaceous spatangoids (Echinodermata: Echinoidea) and taxonomic implications

2004

A phylogenetic analysis of 36 species provides a test for the taxonomy and the history of Early Cretaceous spatangoids. Most taxonomic units from genera to suborders are consistent with the proposed phylogenetic framework. We retain Hemiasterina, Micrasterina, Hemiasteridae, Schizasteridae, Hemiaster, Heteraster, Mecaster, and Periaster as original monophyletic groups. However, all of these clades originate without the classical apomorphies normally ascribed to them. We suggest a revision of their diagnoses and of the generic attributions of basal species. Some ill-defined, ‘primitive’, and paraphyletic taxa are recognised: Toxaster, Epiaster, Palhemiaster, and Toxasteridae. Even if they do…

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

2018

Abstract Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of …

Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer.

1996

A phylogenetic study of the isopenicillin-N-synthetase (IPNS) gene sequence from prokaryotic and lower eukaryotic producers of beta-lactam antibiotics by means of a maximum-likelihood approach has been carried out. After performing an extensive search, rather than invoking a global molecular clock, the results obtained are best explained by a model with three rates of evolution. Grouped in decreasing order, these correspond to A. nidulans and then to the rest of the eukaryotes and prokaryotes, respectively. The estimated branching date between prokaryotic and fungal IPNS sequences (852 +/- 106 MY) strongly supports the hypothesis that the IPNS gene was horizontally transferred from bacteria…

Tirant is a new member of the gypsy family of retrotransposons in Drosophila melanogaster.

2000

In this paper, we propose a consensus sequence for a putative complete Tirant retrotransposon. Several defective copies, as well as relevant sequences available in databases have been analyzed. The putative complete Tirant element is 8533 bp long, and presents all the structural features of a retroviruslike transposable element of the gypsy family. It contains three ORFs (open reading frames) that encode putative products resembling the retroviral Gag, Pol, and Env proteins. Southern blot analyses show that complete and defective Tirant elements are widespread in Drosophila melanogaster. The different hybridization patterns observed in several natural populations of this species suggest tha…

Suitability of chloroplast LSU rDNA and its diverse group I introns for species recognition and phylogenetic analyses of lichen-forming Trebouxia alg…

2009

To date, species identification of lichen photobionts has been performed principally on the basis of microscopic examinations and molecular data from nuclear-encoded genes. In plants, the chloroplast genome has been more readily exploited than the nuclear genome for systematic investigations. At the present time, very little information is available about the chloroplast genome of lichen-forming algae. For this reason, we have sequenced a portion of the gene encoding for the chloroplast large sub-unit rRNA (LSU rDNA) as a new molecular marker. Sequencing of the chloroplast LSU rDNAs revealed the existence of an unusual diversity of group I introns (a total of 31) within 15 analyzed Trebouxi…

The diversification of the northern temperate woody flora – A case study of the Elm family (Ulmaceae) based on phylogenomic and paleobotanical eviden…

2021

A method for determining the position and size of optimal sequence regions for phylogenetic analysis.

1995

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and posit…

Molecular Phylogenetic Analyses in Court Trials

2010

Molecular phylogenetics allows reconstructing of the genealogy and evolutionary history of organisms from information on their nucleotide or amino acid sequences. When sequences are derived from very fast evolving organisms, such as ribonucleic acid (RNA) viruses, changes accumulate in a few days or weeks, thus allowing the reconstruction of very recent evolutionary events in the history of these populations. One such event is the transmission of one of these viruses, for instance human immunodeficiency virus (HIV) or hepatitis C virus (HCV), from an infected person to another. This occasionally results in a legal demand seeking for compensation and/or punishment for the transmitter. Hence,…

Wickerhamomyces sylviae f.a., sp. nov., an ascomycetous yeast species isolated from migratory birds.

2013

In the present work, we investigated the phylogenetic position and phenotypic characteristics of eight yeast isolates collected from migratory birds on the island of Ustica, Italy. A phylogenetic analysis based on the D1/D2 region of the large-subunit rRNA gene showed that all isolates clustered as a single separate lineage within the Wickerhamomyces clade. They exhibited distinct morphological and physiological characteristics and were clearly separated from their closest relatives, Wickerhamomyces lynferdii, Wickerhamomyces anomalus and Wickerhamomyces subpelliculosus, in blastn searches. On the basis of the isolation source, physiological features and molecular strain typing carried out …