Search results for "common ancestor"
showing 10 items of 22 documents
Paleohistological estimation of bone growth rate in extinct archosaurs
2012
The clade Archosauria contains two very different sister groups in terms of diversity (number of species) and disparity (phenotypic variation): Crurotarsi (taxa more closely related to crocodiles than to birds) and Ornithodira (pterosaurs and dinosaurs including birds). The extant species of Crurotarsi may constitute a biased sample of past biodiversity regarding growth patterns and metabolic rates. Bone histological characters can be conserved over hundreds of millions of years in the fossil record and potentially contain information about individual age at death, age at sexual maturity, bone growth rates, and basal metabolic rates of extinct vertebrates. Using a sample of extant amniotes,…
Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within Lachninae aphids.
2016
SummaryVirtually all aphids maintain an obligate mutualistic symbiosis with bacteria from theBuchneragenus, which produce essential nutrients for their aphid hosts. Most aphids from the Lachninae subfamily have been consistently found to house additional endosymbionts, mainlySerratia symbiotica. This apparent dependence on secondary endosymbionts was proposed to have been triggered by the loss of the riboflavin biosynthetic capability byBuchnerain the Lachninae last common ancestor. However, an integral large-scale analysis of secondary endosymbionts in the Lachninae is still missing, hampering the interpretation of the evolutionary and genomic analyses of these endosymbionts. Here, we anal…
The substitution rate of HIV-1 subtypes: a genomic approach
2017
Abstract HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant diff…
Global emergence of the widespread Pseudomonas aeruginosa ST235 clone
2018
Abstract Objectives Despite the non-clonal epidemic population structure of Pseudomonas aeruginosa , several multi-locus sequence types are distributed worldwide and are frequently associated with epidemics where multidrug resistance confounds treatment. ST235 is the most prevalent of these widespread clones. In this study we aimed to understand the origin of ST235 and the molecular basis for its success. Methods The genomes of 79 P. aeruginosa ST235 isolates collected worldwide over a 27-year period were examined. A phylogenetic network was built, using a Bayesian approach to find the Most Recent Common Ancestor, and we identified antibiotic resistance determinants and ST235-specific genes…
Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins.
2016
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. Results Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number …
Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts
2019
Abstract In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pe…
La evolución en los tribunales: aplicaciones forenses de las filogenias moleculares
2013
En las dos últimas décadas se ha generalizado el uso de pruebas genéticas en los tribunales, permitiendo la identificación de criminales a partir de restos biológicos, la determinación de paternidades o la identificación de cadáveres. Menos conocidas son las periciales basadas en el uso de filogenias moleculares. En ellas se estudia la ancestralidad común de organismos, normalmente virus o bacterias, para establecer su asociación a una fuente de infección. Desde el caso del dentista de Florida, que infectó con el VIH a varios de sus pacientes, hasta el más próximo del anestesista Juan Maeso, que transmitió el VHC a cerca de 300 pacientes, la teoría evolutiva tiene un papel esencial en estas…
Chromosomes and the origins of apes and australopithecins
1996
Comparison of molecular data suggests that the higher apes (Gorilla, Pan) and humankind (Homo) are closely related and that they diverged from the common ancestor through two speciation events situated very closely together in time. Examination of the chromosomal formulas of the living species reveals a paradox in the distribution of mutated chromosomes which can only be resolved by a model of trichotomic diversification. This new model of divergence from the common ancestor is characterized by the transition from (1) a monotypic phase to (2) a polytypic phase of three sub-species — pre-gorilla, pre-chimpanzee and preaustralopithecine. The quadruped ancestors ofAustralopithecus appear to ha…
On the longest common factor problem
2008
The Longest Common Factor (LCF) of a set of strings is a well studied problem having a wide range of applications in Bioinformatics: from microarrays to DNA sequences analysis. This problem has been solved by Hui (2000) who uses a famous constant-time solution to the Lowest Common Ancestor (LCA) problem in trees coupled with use of suffix trees. A data structure for the LCA problem, although linear in space and construction time, introduces a multiplicative constant in both space and time that reduces the range of applications in many biological applications. In this article we present a new method for solving the LCF problem using the suffix tree structure with an auxiliary array that take…
Six3 demarcates the anterior-most developing brain region in bilaterian animals
2010
Abstract Background The heads of annelids (earthworms, polychaetes, and others) and arthropods (insects, myriapods, spiders, and others) and the arthropod-related onychophorans (velvet worms) show similar brain architecture and for this reason have long been considered homologous. However, this view is challenged by the 'new phylogeny' placing arthropods and annelids into distinct superphyla, Ecdysozoa and Lophotrochozoa, together with many other phyla lacking elaborate heads or brains. To compare the organisation of annelid and arthropod heads and brains at the molecular level, we investigated head regionalisation genes in various groups. Regionalisation genes subdivide developing animals …