Duplications of complement and non-complement genes of the H-2S region: evolutionary aspects of the C4 isotypes and molecular analysis of their expression variants.
Explore the source record for details and available documents.
Animals↗
SEARCH · Search PubMed
Results for “Evolutionary analysis”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Empirical analysis of locality, heritability and heuristic bias in evolutionary algorithms: a case study for the multidimensional knapsack problem.
Our main aim is to provide guidelines and practical help for the design of appropriate representations and operators for evolutionary algorithms (EAs). For this purpose, we propose techniques to obtain a better understanding of various effects in the interplay of the representation and the operators. We study six different representations and associated variation operators in the context of a steady-state evolutionary algorithm for the multidimensional knapsack problem. Four of them are indirect decoder-based techniques, and two are direct encodings combined with different initialization, repair, and local improvement strategies. The complex decoders and the local improvement and repair strategies make it practically impossible to completely analyze such EAs in a fully theoretical way. After comparing the general performance of the chosen EA variants for the multidimensional knapsack problem on two benchmark suites, we present a hands-on approach for empirically analyzing important aspects of initialization, mutation, and crossover in an isolated fashion. Static, inexpensive measurements based on randomly created solutions are performed in order to quantify and visualize specific properties with respect to heuristic bias, locality, and heritability. These tests shed light onto the complex behavior of such EAs and point out reasons for good or bad performance. In addition, the proposed measures are also examined during actual EA runs, which gives further insight into dynamic aspects of evolutionary search and verifies the validity of the isolated static measurements. All measurements are described in a general way, allowing for an easy adaption to other representations and problems.
Algorithms↗
Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.
BACKGROUND: Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes. RESULTS: We analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions. CONCLUSION: Syntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships.
Agrobacterium tumefaciens↗
New insights into the evolutionary growth of tumors revealed by Southern gel analysis of tumors genetically tagged with plasmid or proviral DNA insertions.
Explore the source record for details and available documents.
Animals↗
The evolutionary history of Drosophila buzzatii. XXXVI. Molecular structural analysis of Osvaldo retrotransposon insertions in colonizing populations unveils drift effects in founder events.
Previous work on transposable element distribution in colonizing populations of Drosophila buzzatii revealed a high frequency of occupancy in several chromosomal sites. Two explanatory hypotheses were advanced: the founder hypothesis, by which founder genetic drift was responsible, and the unstable hypothesis that assigns this unusual distribution to bursts of transposition toward some chromosomal sites. Here, we study the molecular structure of three euchromatic Osvaldo clones isolated from sites occupied at high (A4 and B9) and low frequency (B4) in colonizing populations, to test these hypotheses. Large insertions, duplications, and indels in the Osvaldo coding region and LTR were detected in the A4 clone and a truncated Osvaldo with many substitutions was found in the B9 clone. These altered sequences indicate that the two copies of this retroelement are precolonization insertions. Interestingly, the LTR of the A4 clone and the reverse transcriptase region of B9 show identical sequences in all colonizing populations indicating, most probably, that they are identical by descent. Moreover, Osvaldo is inserted at the same nucleotide site in all colonizing populations. On the other hand an almost identical LTR sequence, except by 1 base deletion, was found in the B4 clone compared to the canonical active Osvaldo element. These results suggest that Osvaldo copies in highly occupied sites are, most probably, identical by descent and strongly favor the founder hypothesis. On the other hand, low-insertion-frequency sites could represent recent transposition events. This work emphasizes the importance of molecular population studies to disentangle the effects of genetic drift and transposition in colonization.
Animals↗
[Theoretical analysis of the correspondence between the stages of evolutionary divergence and the functioning of multigene families of the immune system].
By means of phylogenetic comparison of main immunoglobulin-like multigene families (MF) and of different C-domain sequences representing them, the order of divergences of these MF in the process of evolution of the system was analysed. The order proved to be in good agreement with the ordered fashion of MF's involvement into recombinational rearrangements during the immune cell development. Indeed, according to topology of the tree for 34 C-domains, all MHC antigens are separated from the rest of Ig-like sequences, at first. Secondly, beta-chain of T-receptor is branched off the main stem of divergences, then there is a serium of divergences of CH-domains for different Ig-classes, and at last, kappa- and lambda-chains are separated. It is mu-chain of IgM which first of all branched off within an each group of isofunctional CH-sequences in the tree (CH1, CH2, CH3, CH4). The same order of events could be seen in ontogeny of the immune system. The results suggest that the appearance of a new MF of Ig-like type (or a new cluster of genetic segments within the MF) in the course of evolution could mean the addition of a new step in the regulatory system of immunologic gene expression already involved. In other words, this is unique example of recapitulation at the molecular-genetical level.
Amino Acid Sequence↗
Multifactorial analysis as a tool for the study of evolutionary and organizational aspects of mammalian structure and function. ANL-7635.
Explore the source record for details and available documents.
Animals↗
[Study on evolutionary genetics of Drosophila auraria species complex--cladistic analysis and phenetic analysis].
In the present paper, seventeen geographic strains of D. auraria species complex and five geographic strains of other four species, which belong to the montium species subgroup were biochemically examined for the construction of phylogenetic tree based on phenetic and cladistic analysis. Eighteen isoenzymes were analyzed by isoelectric focusing polyacrylamide gel electrophoresis in the above twenty two geographic strains. The phenogram of the D. auraria species complex is supported by UPGMA program of phenetic analysis. It was found that: 1. D. auraria, D. triauraria and D. quadraria grouped as an type are more closely related to one another, and D. biauraria, D. subauraria are more closely related to each other, while the former three species are distantly related to the latter two species. 2. The genetic identity between two geographic strains of same species is higher than the genetic identity between different species, except the geographic strain T-KM of D. triauraria. 3. The geographic strain T-KM, one of the D. triauraria from the southeast isolated islands Kametoku [symbol: see text] of Japan is far more distantly related to the other geographic strains of it. We suggest that the new species or subspecies are diverged from D. triauraria will be due to the geographic speciation mechanisms. 4. The genetic differentiation among eight geographic strains of D. triauraria are much larger than those among three geographic strains of D. auraria, which may be related to their different inhabitation environment as well as their flying ability. On the other hand, a cladistic analysis of the D. auraria species complex are made in the present paper.(ABSTRACT TRUNCATED AT 250 WORDS)
Animals↗
[An analysis of the trends in the development of evolutionary physiology based on the materials from conferences dedicated to L. A. Orbeli].
Explore the source record for details and available documents.
Animals↗
The puh structural gene coding for the H subunit of the Rhodospirillum rubrum photoreaction center.
The Rhodospirillum rubrum structural gene puh, coding for the photoreaction center H polypeptide, and three other putative genes that surround puh were cloned and sequenced. The deduced 257 amino acid H polypeptide has a molecular weight of 27,909, in close agreement with polyacrylamide gel electrophoresis determination. Hydropathy plots predict a single hydrophobic alpha helix. The H polypeptide of Rhodospirillum rubrum shares only 23% of its residues with all three of the H polypeptides from Rhodopseudomonas viridis, Rhodobacter capsulatus, and Rhodobacter sphaeroides. Despite this apparent low degree of similarity, statistical analysis leaves no doubt about their close relatedness. Interspecies evolutionary distance, assessed by this analysis, confirms the closeness of the two Rhodobacter species, Rhodospirillum rubrum and Rhodopseudomonas viridis being approximately equidistant from them. Three regions of the H polypeptide are highly conserved in all four species. They correspond to known contact points of H with the complex of the other two (L and M) subunits on the cytoplasmic side of the membrane. A glutamic acid residue (H polypeptide residue 177), conserved in the other bacteria and suggested to be involved in the binding of secondary quinone QB, is replaced by serine in Rhodospirillum rubrum. The open reading frames G115, I2372, and I3087 are predicted to, respectively, encode polypeptides of 480, 224, and 155 residues coiled in 10, 2, and 1 transmembrane helices. Open reading frame G115 shares 56% identical residues with F1696, a sequence arranged in the genome of Rhodobacter capsulatus. The gene product of ORF I3087 is predicted to share highly similar sequences with nitrogenase reductase (encoded by nifH) of 11 different bacterial species and is suggested to have a regulatory function.
Amino Acid Sequence↗
Field homology as a way to reconcile genetic and developmental variability with adult homology.
The theoretical and developmental fundament of field homology is here examined, particularly as applied by the authors to comparative neurobiology. Preliminary considerations explore conceptual differences between sameness (homology) and similarity. The source of sameness (the biological evolutionary relationship properly sought in homology analysis) is thought to lie in morphostatic evolutionary and morphogenetic processes, which constrain organismal variation at the level of its fundamental structural organization (Bauplan). This occurs via regulation of the branching mode of the morphogenetic sequence or epigenetic landscape. Of fundamental importance in this context is the role of developmental (morphogenetic) fields. The latter concept is analyzed in its general properties and is postulated to underpin the stability of the developing Bauplan down to the ultimate conserved details. Developmental fields subdivide during ontogenesis into ever smaller fields in a complex hierarchy, defining at each stage the developmental entities which are subjected to regulatory, morphostatic effects via the genome and indirect phenotypic selection. These fields thus represent the natural characters for considerations of embryonic homology, and underlie adult homology, rather than arbitrarily selected embryonic parts. Field subdivision proceeds into the constitution of individually specified cell populations. Field regulatory properties, however, do not extend to all differentiation phenomena observed in embryos. This means there is a limit to the applicability of field homology analysis, leaving space for biological variation and convergence outside of proper homology relationships. Genetic and developmental variability are compensated by the regulatory functions of the developmental fields insofar as they relate to correct Bauplan construction. These ideas suggest the convenience of a more systematic use of field homology methods, which start with appropriately identified developmental fields to expand knowledge on adult homology (sameness) and eventually also on accessory structural and functional similarities or differences.
Aging↗
Molecular evolution of hepatitis B virus over 25 years.
Determining the longitudinal molecular evolution of hepatitis B virus (HBV) is difficult due to HBV's genomic complexity and the need to study paired samples collected over long periods of time. In this study, serial samples were collected from eight hepatitis B virus e antigen-negative asymptomatic carriers of HBV genotype B in 1979 and 2004, thus providing a 25-year period to document the long-term molecular evolution of HBV. The rate, nature, and distribution of mutations that emerged over 25 years were determined by phylogenetic and linear regression analysis of full-length HBV genome sequences. Nucleotide hypervariability was observed within the polymerase and pre-S/S overlap region and within the core gene. The calculated mean number of nucleotide substitutions/site/year (7.9 x 10(-5)) was slightly higher than published estimates (1.5 x 10(-5) to 5 x 10(-5)). Nucleotide changes in the quasispecies population did not significantly alter the molecular evolutionary rate, based on linear regression analysis of evolutionary distances among serial clone pre-S region sequences. Therefore, the directly amplified or dominant sequence was sufficient to estimate the putative molecular evolutionary rate for these long-term serial samples. On average, the ratio of synonymous (dS) to nonsynonymous (dN) substitutions was highest for the polymerase-coding region and lowest for the core-coding region. The low dS/dN ratios observed within the core suggest that selection occurs within this gene region, possibly as an immune evasion strategy. The results of this study suggest that HBV sequence divergence may occur more rapidly than previously estimated, in a host immune phase-dependent manner.
Aged↗
Disparate evolution of prion protein domains and the distinct origin of Doppel- and prion-related loci revealed by fish-to-mammal comparisons.
Prions result from the misfolding and selective accumulation of the host-encoded prion protein (PrP) in the brain. Despite intensive research on mammalian models, basic questions about the biological role of PrP and the evolutionary origin of prion disease remain unanswered. Following our previous identification of novel fish PrP homologues, here we generated new fish PrP sequences and performed genomic analysis to demonstrate the existence of two homologous PrP loci in bony fish, which display extensive molecular variation and are highly expressed in adult and developing fish brains. The fish PrP genomic regions contain PrP-related loci directly downstream of each PrP locus, suggesting an independent origin of prion-related proteins in fish and mammals. Our structural prediction analysis uncovers a conserved molecular "bauplan" for all vertebrate PrPs. The C- and N-terminal protein domains have evolved independently from one another, the former having retained its basic globular structure despite high sequence divergence and the latter having undergone differential expansion-degeneration cycles in its repetitive domains. Our evolutionary analysis redefines fundamental concepts on the functional significance of PrP domains and opens up new possibilities for the experimental analysis of prion misfolding and neurodegeneration in a non-mammalian model like the zebrafish.
Amino Acid Sequence↗
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes.
Prokaryotic genomes seem to be optimized toward compactness and have therefore been thought to lack long redundant DNA sequences. However, we identified a large number of long strict repeats in eight prokaryotic complete genomes and found that their density is negatively correlated with genome size. A detailed analysis of the long repeats present in the genome of Bacillus subtilis revealed a very strict constraint on the spatial distribution of repeats in this genome. We interpret this as the hallmark of selection processes leading to the addition of new genetic information. Such addition is independent of insertion sequences and relies on the nonspecific DNA uptake by the competent cell and its subsequent integration in the chromosome in a circular form through a Campbell-like mechanism. Similar patterns are found in other competent genomes of Gram-negative bacteria and Archaea, suggesting a similar evolutionary mechanism. The correlation of the spatial distribution of repeats and the absence of insertion sequences in a genome may indicate, in the framework of our model, that mechanisms aiming at their avoidance/elimination have been developed.
Antigenic Variation↗
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks.
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
Animals↗
Molecular Evolution and Expression Analysis of the ADH Gene Family in Apple Bud Mutants.
Alcohol dehydrogenase (ADH) catalyzes the reduction of aldehydes to alcohols, key precursor substrates for volatile ester biosynthesis, which determines the characteristic aroma of apple fruit. However, a comprehensive genome-wide investigation of the ADH gene family in apple has been lacking. In this study, we systematically identified ADH genes in the apple genome using integrated bioinformatics approaches, including phylogenetic analysis, synteny evaluation, promoter cis-element prediction, codon usage bias assessment, and protein interaction network modeling. Expression patterns were examined through transcriptomic data and validated by RT-qPCR analysis across different organs and among 'Red Delicious' and its four bud mutant lines. We identified 44 ADH genes, with 12 forming a prominent cluster on chromosome 1. RT-qPCR analysis revealed that MdADH20 was dramatically upregulated in the 'Red Chief' mutant (relative expression of 59.38), suggesting its pivotal role. Phylogenetic analysis revealed a close evolutionary relationship with wild strawberry. The encoded proteins were generally stable and predominantly localized to the cytoplasm. Promoter analysis showed enrichment of growth/development-related and ARE elements, while codon usage analysis identified AGA, GCU, GUU, and CUU as preferred codons. Protein interaction prediction suggested MdADH19 and MdADH20 as hub proteins. Expression profiling and RT-qPCR further identified MdADH20 as a core candidate gene, characterized by its stable and high expression, particularly in the 'Red Delicious' mutant. Its central position in the predicted protein-protein interaction network suggests a potential regulatory role in the aroma biosynthesis pathway of apple fruit. This study provides the first systematic genome-wide characterization of the apple ADH gene family, establishing a theoretical groundwork for deciphering aroma biosynthesis mechanisms and offering potential target genes for flavor improvement through bud mutation breeding strategies.
ADH gene family↗
Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome B genes.
The Gobioidei is a large suborder in the order Perciformes and consists of more than 2000 species belonging to about 270 genera. The vast number of species and their morphological specialization adapted to diverse habits and habitats makes the classification of the gobioid fishes very difficult.A comprehensive estimation of the evolutionary scenario of all gobioid fishes using only morphological information is difficult for two major reasons: first, in addition to wide ecological diversification, there is a trend towards specialization and degeneration of morphological characters among these species; second, an appropriate outgroup of gobioid fishes has not been recognized. Based upon nucleotide sequence comparisons of gobioid mitochondrial cytochrome b genes, we established the phylogenetic relationships of their differentiation into many groups of morphological and ecological diversity. The phylogenetic trees obtained show that most species examined have diverged from each other almost simultaneously or during an extremely short period of time.
Animals↗
Adaptive Evolution of the PFK Gene Family in Chinese Longsnout Catfish, Leiocassis longirostris.
The Chinese longsnout catfish is a typical carnivorous fish with a relatively weak ability to utilize glucose. However, the genomic basis for its glucose metabolic adaptation remains unclear. In this study, we used comparative genomics methods to systematically analyze the evolutionary characteristics of glucose metabolism-related genes in the Chinese longsnout catfish, focusing on gene family evolution, patterns of expansion and contraction, and selective pressures. The results indicate that glucose metabolism-related genes have undergone significant reshaping during evolution. Genes involved in glucose digestion, absorption, and insulin signaling pathways demonstrate a tendency toward contraction, while those associated with protein and lipid metabolism exhibit expansion. This pattern is consistent with the species' long-term adaptation to a high-protein, high-fat diet. Comparative analysis further revealed that, compared to fish with different dietary habits, certain key genes involved in glycolysis in the Chinese longsnout catfish exhibit a reduction in copy number. Molecular evolutionary analysis showed that key genes involved in glycolysis and gluconeogenesis (including hexokinase 2 (hk2), phosphofructokinase, muscle/platelet (pfkm/p)) exhibit signs of accelerated evolution or positive selection. Notably, the PFK gene family exhibits complex evolutionary characteristics resulting from the combined effects of gene contraction, rapid evolution, and positive selection. In summary, this study reveals the genomic evolutionary basis for the glucose metabolic adaptation of the Chinese longsnout catfish and identifies the PFK gene family as a key candidate for elucidating its unique glucose metabolic characteristics.
Leiocassis longirostris↗