Search results for "phylogenetics"

1993

We may state that the path of development of an organism can play an important role in its immediate realization and also in its possible transformation. This leads to the problem of the existence of a causative link between individual development (ontogeny) and evolutionary history (phylogeny). This problem which has been dealt with by numerous authors, has led to contradictory answers, depending on the direction of the supposed connection: from the evolutionary history to individual development or vice versa, that is, from individual development to the evolutionary history.

CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

2023

The increasing availability of high-quality genomic, annotation and phenotypic data for different species contrasts with the lack of general software for comparative genomics that integrates these data types in a statistically sound framework in order to produce biologically meaningful knowledge. In this work, we present CALANGO (Comparative AnaLysis with ANnotation-based Genomic cOmponentes), a first-principles comparative genomics tool to search for annotation terms, such as GO terms or Pfam domain IDs, associated with a quantitative variable used to rank species data, after correcting for phylogenetic relatedness. This information can be used to annotate genomes at any level, including p…

2015

The eggshell is an important physiological structure for the embryo. It enables gas exchange, physical protection and is a calcium reserve. Most squamates (lizards, snakes, worm lizards) lay parchment-shelled eggs, whereas only some gekkotan species, a subgroup of lizards, have strongly calcified eggshells. In viviparous (live-bearing) squamates the eggshell is reduced or completely missing (hereafter “shell-less”). Recent studies showed that life-history strategies of gekkotan species differ between species with parchment- and rigid-shelled eggshells. Here we test if the three different eggshell types found in the squamates are also associated with different life-history strategies. We fir…

Dietary Intake, Serum Hormones, Muscle Mass and Strength During Strength Training in 49 - 73-Year-Old Men

2007

Effects of dietary intake on serum hormones, muscle cross-sectional area (CSA) and strength during strength training were studied in two groups of men: 1) strength training + nutritional counseling (n = 22, 59.1 +/- 6.1 yrs), and 2) strength training (n = 23, 58.5 +/- 7.1 yrs). Both groups performed strength training twice a week for 21 weeks. Counseling increased carbohydrate (p < 0.01) and fiber intake (p < 0.001) and polyunsaturated/saturated fat-ratio (p < 0.05) and decreased fat intake (p < 0.01). Muscle strength and CSA increased by 16 - 20 % and by 5.4 - 5.9 % in both groups (p < 0.001). Changes in protein content of diet correlated with the changes in the acute postexercise concentr…

MIF from mussel: coding sequence, phylogeny, polymorphism, 3D model and regulation of expression.

2012

Abstract Three macrophage migration inhibitory factor (MIF)-related sequences were identified from a Mytilus galloprovincialis EST library. The consensus sequence included a 5′-UTR of 32 nucleotides, the complete ORF of 345 nucleotides, and a 3′-UTR of 349 nucleotides. As for other MIFs, M. galloprovincialis ORF does not include any signal or C-terminus extensions. The translated sequence of 115 amino acids possesses a molecular mass of 12,681.4, a pI of 6.27 and a stability index of 21.48. Its 3D structure resembles human MIF except for one shorter α-helix. Although evolutionary separated from ticks and vertebrates, Mg-MIF appeared to be closely related to Pinctada fucata and Haliotis, but…

Study of the Evolutionary Relationships among Limonium Species (Plumbaginaceae) Using Nuclear and Cytoplasmic Molecular Markers

2000

The genus Limonium, due to the patchiness of the natural habitats of its species as well as the high frequency of hybridization and polyploidy and the possibility of reproduction by apomixis, provides an example of all the principal mechanisms of rapid speciation of plants. As an initial study of evolution in this genus, we have analyzed intra- and interspecific variability in 17 species from section Limonium, the largest in the genus, based on RFLPs of cpDNA and nuclear rDNA ITS sequences. In the cpDNA analysis, 21 restriction enzymes were used, resulting in 779 fragments, 490 of which were variable and 339 parsimony informative. L. furfuraceum exhibited two relatively divergent cpDNA hapl…

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

2008

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The …

Selecting Microbial Strains from Pine Tree Resin: Biotechnological Applications from a Terpene World

2014

Resin is a chemical and physical defensive barrier secreted by many plants, especially coniferous trees, with insecticidal and antimicrobial properties. The degradation of terpenes, the main components accounting for the toxicity of resin, is highly relevant for a vast range of biotechnological processes, including bioremediation. In the present work, we used a resin-based selective medium in order to study the resin-tolerant microbial communities associated with the galls formed by the moth Retinia resinella; as well as resin from Pinus sylvestris forests, one of the largest ecosystems on Earth and a yet-unexplored source of terpene-degrading microorganisms. The taxonomic and functional di…

Vip3C, a novel class of vegetative insectidal proteins from Bacillus thuringiensis

2012

Three vip3 genes were identified in two Bacillus thuringiensis Spanish collections. Sequence analysis revealed a novel Vip3 protein class (Vip3C). Preliminary bioassays of larvae from 10 different lepidopteran species indicated that Vip3Ca3 caused more than 70% mortality in four species after 10 days at 4 οg/cm 2. © 2012, American Society for Microbiology.

A single primer pair gives a specific ortholog amplicon in a wide range of Cyanobacteria and plastid-bearing organisms: applicability in inventory of…

2010

The scarcity of universally applied molecular markers for algae has resulted in the development of multiple, independent and not easily comparable systems. The goal of this work is to increase the number of available molecular markers and to generate easily comparable systems. Thereby, we have designed a primer pair capable of amplifying a broad range of organisms: Cyanobacteria, Chlorophyta, Chlorarachniophyta, Cryptophyta, Euglenida, Glaucophyta, Rhodophyta, Stramenopiles and Streptophyta including plants. This primer pair can amplify a portion of the 23S rRNA gene with sufficient variability to identify reference material form collections across a broad range of taxa and perform phylogen…