Search results for "common ancestor"

Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome

2009

The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%. In particular, the presence of a modal haplotype coming from the southern…

Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction

2007

We have reconstructed the gene content and order of the last common ancestor of the human pathogens Mycobacterium leprae and Mycobacterium tuberculosis. During the reductive evolution of M. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. We find evidence that a massive gene inactivation took place very recently in the M. leprae lineage, leading to the loss of hundreds of ancestral genes. A large proportion of their nucleotide content (∼89%) still remains in the genome, which allowed us to characterize and date them. The age of the pseudogenes was computed using a new methodology based on the rates and patterns of substitution in the…

Evolution of arginine deiminase (ADI) pathway genes

2002

We have analyzed the evolution of the three genes encoding structural enzymes of the arginine deiminase (ADI) pathway, arginine deiminase (ADI), ornithine transcarbamoylase (OTC), and carbamate kinase (CK) in a wide range of organisms, including Archaea, Bacteria, and Eukarya. This catabolic route was probably present in the last common ancestor to all the domains of life. The results obtained indicate that these genes have undergone a complex evolutionary history, including horizontal transfer events, duplications, and losses. Therefore, these genes are not adequate to infer organismal relationships at deep branching levels, but they provide an insight into how catabolic genes evolved and …

Ligand Diversity of Human and Chimpanzee CYP3A4: Activation of Human CYP3A4 by Lithocholic Acid Results from Positive SelectionS⃞

2009

For currently unknown reasons, the evolution of CYP3A4 underwent acceleration in the human lineage after the split from chimpanzee. We investigated the significance of this event by comparing Escherichia coli-expressed CYP3A4 from humans, chimpanzee, and their most recent common ancestor. The expression level of chimpanzee CYP3A4 was ∼50% of the human CYP3A4, whereas ancestral CYP3A4 did not express in E. coli. Steady-state kinetic analysis with 7-benzyloxyquinoline, 7-benzyloxy-4-(trifluoromethyl)coumarin (7-BFC), and testosterone showed no significant differences between human and chimpanzee CYP3A4. Upon addition of α-naphthoflavone (25 μM), human CYP3A4 showed a slightly decreased substr…

Analysis of DNA sequence variation within marine species using Beta-coalescents

2013

We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock's "reproduction sweepstakes". Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman's coalescent), allowing multiple mergers of genealogies. The choice of the underlying…

2021

Studies on the function of PRDM9 in model systems and its evolution during vertebrate divergence shed light on the basic molecular mechanisms of hybrid sterility and its evolutionary consequences. However, information regarding PRDM9-homolog, PRDM7, whose origin is placed in the primate evolutionary tree, as well as information about the fast-evolving DNA-binding zinc finger array of strepsirrhine PRDM9 are scarce. Thus, we aimed to narrow down the date of the duplication event leading to the emergence of PRDM7 during primate evolution by comparing the phylogenetic tree reconstructions of representative primate samples of PRDM orthologs and paralogs. To confirm our PRDM7 paralogization patt…

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

2015

Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aega…

Protein SRP54 iz morske spužve Geodia cydonium

2002

In the systematic search for phylogenetically conserved proteins in the simplest and most ancient extant metazoan phylum – Porifera, we have identified and analyzed a cDNA encoding the signal recognition particle 54 kD protein (SRP54) from the marine sponge Geodia cydonium (Demospongiae). The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex of a very ancient origin, comprising SRP RNA and several proteins (six in mammals). The nucleotide sequence of the sponge cDNA predicts a protein of 499 amino acid residues with a calculated Mr of 55175. G. cydonium SRP54 displays unusually high overall similarity (90 %) with human/mammalian SRP54 proteins, higher th…

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,…

The universal ancestor : an unfinished reconstruction

2015

El cenancestro se define como el ultimo ancestro comun de todos los seres vivos que existen actualmente. Su naturaleza se ha inferido a partir de la identificacion de los genes homologos entre los linajes de arqueas, bacterias y eucariontes. Estas inferencias indican que el cenancestro poseia un sistema de traduccion de proteinas relativamente moderno y era similar en complejidad a una celula actual. Sin embargo, las enzimas claves que se encargan tanto de la replicacion del material genetico como de la biosintesis de membranas celulares no son homologas entre los linajes celulares. Aqui revisamos brevemente la historia del concepto del ultimo ancestro comun y las distintas hipotesis que se…