Search results for "phylogenetic"
showing 10 items of 1179 documents
Basal growth hormone concentrations in blood and the risk for prostate cancer: A case-control study
2005
OBJECTIVE To assess the relationship between basal serum growth hormone (GH) levels and prostate cancer risk. METHODS We conducted a population-based case-control study; cases included 68 men, aged 45–85 years, diagnosed with incident, primary, histologically confirmed, and clinically apparent (stage B and higher) prostate cancer. Controls included 240 men, frequency matched on age and residential area. Age, race, BMI, waist circumference, history of enlarged prostate, education, and current smoking status, were all considered as possible confounders. RESULTS We found a statistically significant trend of decreasing prostate cancer risk across increasing GH quintiles, in both crude (OR: 0.31…
Basal Cerebral Computed Tomography as Diagnostic Tool to Improve Patient Selection in Asymptomatic Carotid Artery Stenosis
2012
One-hundred patients were included to evaluate the role of cerebral computed tomography (CT) to improve patient selection in asymptomatic internal carotid stenosis. Symptomatic patients were assigned to group A, asymptomatic patients to group B. A cerebral CT pattern A was observed in groups A and B in 60% and 20%, respectively ( P < .0001). Between A and B groups, type 6 plaques were found, respectively, in 26.7% and 7.5% of patients ( P = .01); a type 5 in 51.7% and 45% ( P = .32) of patients; and a type 4 in 21.7% and 47.5% of patients, respectively ( P = .006). Within B group, the association of CT pattern A and histological plaque level 4, 5, and 6 was, respectively, 25% ( P = .15)…
Aposematism facilitates the diversification of parental care strategies in poison frogs
2021
AbstractMany organisms have evolved adaptations to increase the odds of survival of their offspring. Parental care has evolved several times in animals including ectotherms. In amphibians, ~ 10% of species exhibit parental care. Among these, poison frogs (Dendrobatidae) are well-known for their extensive care, which includes egg guarding, larval transport, and specialized tadpole provisioning with trophic eggs. At least one third of dendrobatids displaying aposematism by exhibiting warning coloration that informs potential predators about the presence of defensive skin toxins. Aposematism has a central role in poison frog diversification, including diet specialization, and visual and acoust…
Formation of new genes explains lower intron density in mammalian Rhodopsin G protein-coupled receptors
2007
Mammalian G protein-coupled receptor (GPCR) genes are characterised by a large proportion of intronless genes or a lower density of introns when compared with GPCRs of invertebrates. It is unclear which mechanisms have influenced intron density in this protein family, which is one of the largest in the mammalian genomes. We used a combination of Hidden Markov Models (HMM) and BLAST searches to establish the comprehensive repertoire of Rhodopsin GPCRs from seven species and performed overall alignments and phylogenetic analysis using the maximum parsimony method for over 1400 receptors in 12 subgroups. We identified 14 different Ancestral Receptor Groups (ARGs) that have members in both vert…
Molecular phylogeny of Malagasy poison frogs, genus Mantella (Anura: Mantellidae): homoplastic evolution of colour pattern in aposematic amphibians
2002
Abstract We studied the evolution of colour pattern in Malagasy poison frogs, genus Mantella , a group of diurnal and toxic frogs endemic to Madagascar. Based on a phylogeny reconstructed using 1130 bp of the mitochondrial 16S rRNA gene, the genus can be divided into five species groups. Within some of these groups, interspecific genetic divergences were very low (1.2–2.8% sequence divergence) while colour patterns were markedly different. In contrast, Mantella madagascariensis and M . baroni , two species which show extremely similar dorsal coloration patterns, were not included in the same clade. This conclusion was supported by high bootstrap values and by significant rejection of altern…
On the phylogeny and zoogeography of the leptarctines (Carnivora, Mammalia)
1982
A restudy of the skull and mandible ofLeptarctus neimenguensis Zhai from the Middle Miocene of China and the preparation of its auditory region led to the recognition of new features. The most important among them is the presence of a small suprameatal fossa partly hidden in the bony mastoid process corresponding to the structure described inPlesiogale andParagale (Schmidt-Kittler 1981) and representing the most primitive type of the mustelid middle ear.
GWideCodeML: A python package for testing evolutionary hypotheses at the genome-wide level
2020
One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codeml with the option of parallelization. To maximize the number of analy…
Phylogeography and demographic inference in Nacella (Patinigera) concinna (Strebel, 1908) in the western Antarctic Peninsula
2011
10 pages; International audience; Endemic to Antarctic ecosystems, the limpet Nacella (Patinigera) concinna (Strebel, 1908) is an abundant and dominant marine benthic invertebrate of the intertidal and shallow subtidal zone. In order to examine the phylogeographic pattern and historical demography of the species along the western Antarctic Peninsula, we amplified 663 bp of the mitochondrial DNA cytochrome oxidase subunit I of 161 N. concinna specimens from five localities, as well as two specimens from South Georgia and Sub-Antarctic Marion Island. As two different morphotypes, one characterized by an elevated shell in the intertidal and the other by a flat one in the subtidal, have been re…
Testing Taxonomic and Biogeographical Relationships in a Narrow Mediterranean Endemic Complex (Hippocrepis balearica) using RAPD Markers
2002
Analyses of RAPD profiles from 17 populations of the Hippocrepis balearica complex revealed a highly structured geographic pattern, not only among continental–insular areas but also within the eastern Balearic islands. In marked contrast to previous morphometric results, a clear separation between continental and insular samples was found, and intermediates between H. balearica and H. valentina samples were not detected. Molecular data indicated that western and eastern Balearic populations of the complex (H. grosii and H. balearica) were more closely related to each other than to continental populations (H. valentina). Multivariate analyses of the RAPD data clearly indicated that the simil…
DNA barcoding for species assignment: the case of Mediterranean marine fishes
2014
Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes…