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At least 973 records · Page 54Linked to original sources
PubMed1989

Evaluation of evolutionary divergence in the genus Naegleria by analysis of ribosomal DNA plasmid restriction patterns.

Ribosomal DNA (rDNA) plasmid restriction maps of 10 strains and rDNA hybridisation patterns of 61 additional strains have been used to assess inter- and intra-specific diversity and phylogenetic relationships in the genus Naegleria. The results obtained by this method largely confirm those of previous studies based on a variety of other criteria. They indicate that very little variation exists within the pathogenic species Naegleria fowleri despite its worldwide distribution and that it is closely related to the nonpathogenic Naegleria lovaniensis. Naegleria gruberi is most likely a polyphyletic grouping and care should be taken when using one strain as a reference point for this species. In addition, the two subspecies of the pathogenic Naegleria australiensis arose separately from within the range of variability encompassed by N. gruberi, as did the species Adelphamoeba galeacystis which should probably be assigned to the genus Naegleria. The species Naegleria jadini and Naegleria andersoni are not closely related to any other in the genus based on their rDNA patterns.

Animals↗
PubMed1989

The evolutionary origins of organelles.

Analysis of organellar genomes strongly supports the idea that chloroplasts and mitochondria originated in evolution as eubacteria-like endosymbionts, whose closest contemporaries are cyanobacteria and purple photosynthetic bacteria, respectively. However, there is still much debate about whether a single endosymbiotic event or multiple ones gave rise to each organelle in different eukaryotes, and considerable uncertainty about what has happened to the genomes of chloroplasts and mitochondria since their appearance in the eukaryotic cell.

Biological Evolution↗
PubMed2006

Civilization as a biosystem examined by the comparative analysis of biosystems.

Darwinian evolutionary theory has played a central role in the life sciences. However, this principle is rarely applied to exceptional life-like systems such as human societies and the life-like chemical systems associated with the origin of life. For a description of the nature of these exceptional life-like biosystems, the development of alternative approaches is necessary. The existence of analogies among biosystems at different hierarchical levels has frequently been discussed. The present paper, however, focuses on the analogies of the structures and functions of different biosystems, based on the following perspectives. The roles of an individual biosystem and its building blocks in relation to the environment are evaluated from the standpoint of the hierarchies of organisms, whereby the principle of which hierarchy is regarded as an "individual" biosystem is proposed. In addition, the definition and characteristics of civilization are discussed on the basis of this principle. The analogies between cell-type systems, civilizations, ecosystems, and other biosystems are qualitatively evaluated. It is reasonable to regard all biosystems as possessing clear or ambiguous boundaries. Biosystems at higher levels than prokaryotes comprise both living and non-living building blocks, while prokaryotes comprise only non-living building blocks. The similarities concerning the interactions among the building blocks in relation to their environment are also discussed. Furthermore, the analogy between different biosystems concerning metabolism, self-reproduction, mutation, the relationship between genotype and phenotype (information and function), individuality, and stability are evaluated. The proposed analytical approach not only provides an insight into the characteristics of civilizations as biosystems, but also the characteristics of biosystems at different hierarchical levels.

Biological Evolution↗
PubMed2004

Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements.

Canine tricuspid valve malformation (CTVM) maps to canine chromosome 9 (CFA9), in a region syntenic with gene-dense human chromosome 17q. To define synteny blocks, we analyzed 148 markers on CFA9 using radiation hybrid mapping and established a four-way comparative map for human, mouse, rat, and dog. We identified a large number of rearrangements, allowing us to reconstruct the evolutionary history of individual synteny blocks and large chromosomal segments. A most parsimonious rearrangement scenario for all four species reveals that human chromosome 17q differs from CFA9 and the syntenic rodent chromosomes through two macroreversals of 9.2 and 23 Mb. Compared to a recovered ancestral gene order, CFA9 has undergone 11 reversals of <3 Mb and 2 reversals of >3 Mb. Interspecies reuse of breakpoints for micro- and macrorearrangements was observed. Gene order and content of the ctvm interval are best extrapolated from murine data, showing that multispecies genome rearrangement scenarios contribute to identifying gene content in canine mapping studies.

Animals↗
PubMed1998

tRNA nucleotide 47: an evolutionary enigma.

A previous analysis of tRNA sequences suggested a correlation between the absence of a nucleotide at position 47 (nt 47) in the extra loop and the presence of a U13:G22 base pair in the D-stem. We have evaluated the significance of this correlation by determining the in vivo activity of tRNAs containing either a C13:G22 or a U13:G22 pair in tRNA molecules with or without nt 47. Although this correlation might reflect some malfunction of tRNAs lacking nt 47, but containing the C13:G22, assays of the in vivo suppressor activity showed that this tRNA is actually more active than the tRNA with the features found in the database, i.e., a U13:G22 base pair and no nt 47. Moreover, analogous constructs with a GGC anticodon permitted the growth of an Escherichia coli strain deleted for tRNA(Ala)GGC genes equally well. On the other hand, long-term growth experiments with competing E. coli strains harboring the tRNA lacking nt 47, either with the C13:G22 or the U13:G22 base pair demonstrated that the U13:G22 tRNA overtook the C13:G22 strain even when the starting proportion of strains favored the C13:G22 strain. Thus, the preference for the U13:G22 tRNA lacking nt 47 in the sequence database is most likely due to factors that come into play during extended growth or latency rather than to the ability of the tRNA to engage in protein synthesis.

Amidohydrolases↗
PubMed2004

Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale.

Statistical analysis of the distribution of transposable elements (TEs) and tRNA genes in the genome of yeast Saccharomyces cerevisiae indicated that, although tRNA genes and other genes transcribed by RNA polymerase III are targets for TE insertion, the distribution of TEs was significantly more clumped than that of tRNAs. Genomic blocks putatively duplicated as the result of an ancient polyploidization event contained fewer TEs than expected by their length, and nearly two thirds of duplicated blocks lacked TEs altogether. In addition, the edges of duplicated blocks tended to be located in TE-poor genomic regions. These results can be explained by the hypotheses: (1) that transposition events have occurred well after block duplication; (2) that TEs have frequently played a role in genomic rearrangement events in yeast. According to this model, duplicated blocks identifiable as such in the present-day yeast genome are found largely in regions with low TE density because in such regions the duplicated structure has not been obscured by TE-mediated rearrangements.

DNA Transposable Elements↗
PubMedDate not supplied

Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms.

The genetic relationships of human populations have been studied by comparing gene frequency data for protein and blood-group loci of different populations. DNA analysis now promises to be more informative since not only do the DNA coding sequences have more variation than their corresponding proteins but, in addition, noncoding DNA sequences display more extensive polymorphism. We have now studied the frequency of a group of closely linked nuclear DNA polymorphisms (haplotypes) in the beta-globin gene cluster of normal (beta A) chromosomes of individuals from eight diverse populations. We have found that all non-African populations share a limited number of common haplotypes whereas Africans have predominantly a different haplotype not found in other populations. Genetic distance analysis based on these nuclear DNA polymorphisms indicates a major division of human populations into an African and a Eurasian group.

Alleles↗
PubMed1999

DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.

A detailed analysis of the polbeta superfamily of nucleotidyltransferases was performed using computer methods for iterative database search, multiple alignment, motif analysis and structural modeling. Three previously uncharacterized families of predicted nucleotidyltransferases are described. One of these new families includes small proteins found in all archaea and some bacteria that appear to consist of the minimal nucleotidyltransferase domain and may resemble the ancestral state of this superfamily. Another new family that is specifically related to eukaryotic polyA polymerases is typified by yeast Trf4p and Trf5p proteins that are involved in chromatin remodeling. The TRF family is represented by multiple members in all eukaryotes and may be involved in yet unknown nucleotide polymerization reactions required for maintenance of chromatin structure. Another new family of bacterial and archaeal nucleotidyltransferases is predicted to function in signal transduction since, in addition to the nucleotidyltransferase domain, these proteins contain ligand-binding domains. It is further shown that the catalytic domain of gamma proteobacterial adenylyl cyclases is homologous to the polbeta superfamily nucleotidyltransferases which emphasizes the general trend for the origin of signal-transducing enzymes from those involved in replication, repair and RNA processing. Classification of the polbeta superfamily into distinct families and examination of their phyletic distribution suggests that the evolution of this type of nucleotidyltransferases may have included bursts of rapid divergence linked to the emergence of new functions as well as a number of horizontal gene transfer events.

Adenylyl Cyclases↗
PubMed2004

Forelimb proportions and the evolutionary radiation of Neornithes.

Analysis of a comprehensive dataset demonstrates that the brachial index (BI = humerus length/ulna length) of modern birds (Neornithes) varies significantly between clades at all taxonomic levels, yet is strongly correlated with recent phylogenetic hypotheses. Variance in BI at the infraclass level is low, but increases rapidly during the proposed major radiation of neornithines in the Palaeocene and Eocene. Although a BI of greater than 1 is primitive for Neornithes, more basal groups of Mesozoic birds (Confuciusornithidae and some members of the diverse Enantiornithidae) had BIs comparable with those of 'higher' modern clades. It is possible that occupation of ecological niches by these Mesozoic clades precluded the divergence of some groups of neornithines until after the Cretaceous-Tertiary boundary. We suggest that with further analysis and data collection the relationships between flight behaviour, ecology and BI can be determined. Hence, BI may provide a useful tool for characterizing the ecology of fossil birds.

Analysis of Variance↗
PubMed2004

Whole-genome analysis of Alu repeat elements reveals complex evolutionary history.

Alu repeats are the most abundant family of repeats in the human genome, with over 1 million copies comprising 10% of the genome. They have been implicated in human genetic disease and in the enrichment of gene-rich segmental duplications in the human genome, and they form a rich fossil record of primate and human history. Alu repeat elements are believed to have arisen from the replication of a small number of source elements, whose evolution over time gives rise to the 31 Alu subfamilies currently reported in Repbase Update. We apply a novel method to identify and statistically validate 213 Alu subfamilies. We build an evolutionary tree of these subfamilies and conclude that the history of Alu evolution is more complex than previous studies had indicated.

Alu Elements↗
PubMed1982

Nucleotide sequence analysis of the long terminal repeat of integrated simian sarcoma virus: evolutionary relationship with other mammalian retroviral long terminal repeats.

Nucleotide sequence analysis of the long terminal repeat (LTR) of the integrated simian sarcoma virus showed that the simian sarcoma virus LTR comprised 504 nucleotides with an inverted repeat of seven bases at its 5' and 3' termini. At the site of simian sarcoma virus integration, cellular flanking sequences adjacent to the proviral LTR contained a direct repeat of four bases. A 13-base sequence after the 5' LTR was found to be complementary to prolyl tRNA, suggesting that tRNAPro may serve as the primer for reverse transcription of simian sarcoma virus RNA. The U5 and R regions, derived respectively from the 5' end and terminally redundant sequences of the viral RNA, were found to have similar organization and sequence homology close to that of Moloney murine sarcoma virus or Moloney murine leukemia virus. These results indicate that regions within LTRs with known functionally important sequences have been most well conserved during retrovirus evolution.

Biological Evolution↗
PubMed2006

Evolutionary divergence of exon flanks: a dissection of mutability and selection.

The intronic sequences flanking exon-intron junctions (i.e., exon flanks) are important for splice site recognition and pre-mRNA splicing. Recent studies show a higher degree of sequence conservation at flanks of alternative exons, compared to flanks of constitutive exons. In this article we performed a detailed analysis on the evolutionary divergence of exon flanks between human and chimpanzee, aiming to dissect the impact of mutability and selection on their evolution. Inside exon flanks, sites that might reside in ancestral CpG dinucleotides evolved significantly faster than sites outside of ancestral CpG dinucleotides. This result reflects a systematic variation of mutation rates (mutability) at exon flanks, depending on the local CpG contexts. Remarkably, we observed a significant reduction of the nucleotide substitution rate in flanks of alternatively spliced exons, independent of the site-by-site variation in mutability due to different CpG contexts. Our data provide concrete evidence for increased purifying selection at exon flanks associated with regulation of alternative splicing.

Alternative Splicing↗
PubMed1992

Chemistry of the interstellar medium--an evolutionary dead end?

An analysis of the experimental data available and of the present theoretical concepts shows that even the initial physicochemical chemical precellular stages of biological evolution are impossible in the interstellar medium, while biomonomers possibly formed on asteroids and comets might have participated after transportation to the Earth in the final stages of the origin of the first precellular biological structures and then in the first living cells.

Aluminum Silicates↗
PubMed1976

The evolutionary role of gravity.

Analysis of the part played by gravity in development in the organic world shows that this factor has had an impact on evolution. All terrestrial organisms, including man, have adapted themselves to gravity by developing a number of important features of their composition and functions. Variations of gravitational field in any direction bring about numerous changes in organisms, ranging from metabolism to changes in more conservative systems which also include hereditary structures. Gravitational forces determine the form and the size of organisms, the development of skeletal supporting organs, and energetics. The study of the role of gravity in the variability of the organic world will be of great importance for long-term systems of life support and for work on space orbital stations or at bases on the moon and planets where gravitational forces may differ greatly those from on the earth.

Adaptation, Biological↗
PubMed1989

Molecular analysis of linear plasmid-encoded major surface proteins, OspA and OspB, of the Lyme disease spirochaete Borrelia burgdorferi.

The ospA and ospB genes encode the major outer membrane proteins of the Lyme disease spirochaete Borrelia burgdorferi. The deduced translation products from the ospA and ospB genes were: (OspA) 273 amino acids long with a molecular weight of 29,334, and (OspB) 296 amino acids long with a molecular weight of 31,739. The two Osp proteins showed a great degree of sequence similarity indicating a recent evolutionary event. Molecular analysis and sequence comparison of OspA and OspB with other proteins revealed a sequence similarity to the signal peptides of prokaryotic lipoproteins. These are the first sequences from Borrelia and provide interesting data on the evolutionary relationship between spirochaetes and other species as well as providing potential for spirochaete diagnostics and vaccines.

Amino Acid Sequence↗
PubMed2005

Marsupials and monotremes sort genome treasures from junk.

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.

Animals↗