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At least 19 recordsLinked to original sources
PubMed1996

Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates.

To determine a possible relationship between organismal and molecular evolution, the divergence patterns of gene families were examined by taking special notice of functional difference, tissue distribution, and intracellular localization of the members. A phylogenetic analysis of 25 different gene families revealed interesting patterns of divergence of these families: Most gene duplications giving rise to different functions antedate the vertebrates-arthropods separation. On the other hand, in a group of members carrying virtually identical function to one another but differing in tissue distribution (tissue-specific isoform), most gene duplications have occurred independently in each of vertebrates and arthropods after the separation of the two animal groups. In family members encoding molecules localizing in cell compartments (compartmentalized isoforms), the gene duplications antedate the animals-fungi separation. In the cases of the Ca2+ pump and rab subfamilies, the compartmentalized isoforms were shown to have diverged during the early evolution of eukaryotes. A phylogenetic analysis of the tissue-specific isoforms from 26 different subfamilies revealed extensive gene duplications and rapid rates of amino acid substitutions in the early evolution of chordates before the separation of fishes and tetrapods. On the contrary, the genetic variations are relatively low in the later period. This pattern of evolution observed at the molecular level is correlated well with that of tissue evolution based on fossil evidence and morphological data, and thus evolution at the two levels may be related.

Animals↗
PubMed1980

The evolution of the protein synthesis system, II. From chemical evolution to biological evolution.

The sequence of events previously proposed for modern protein synthesis is reviewed. It begins with an abiological synthesis of a template, and evolves through two model autocatalytic systems to a primitive cell that has a rudimentary biological protein synthesis system. A possible scheme for the origin of tRNA's is described so as to fill the gap between the model and the modern system. Fragments of genes that existed in and around the primitive system are proposed to be precursors of tRNA's. Since these fragments must have been undesirable components for the system, the origin and evolution of tRNA's may be regarded as an excellent answer by the primitive system to adverse circumstances.

Animals↗
PubMed1996

On evolutive systems and the initial evolution of structure and function.

As an instrument for the study of the early stages of evolution, we introduce evolutive systems, defined as systems that have the capacity to evolve given appropriate conditions in their environment. They consist of building blocks (e.g. monomers) that are either stable or in steady supply, and of transient assemblies (e.g. polymers) that are entities of great variety, some of which are capable of function. Evolution leads to the accumulation of structure within the transient assemblies during repeated cycles of disintegration (partial or total) and reassembly, on account of the selective advantages associated with transient assembly functions. Transient assemblies must be either inherently unstable or subject to disintegration by agents in their environment. Evolutive systems must have access to a negentropy input in the form of energy in packets larger than typical thermal energies. Reproduction, although not a prerequisite, greatly affects the capacity of evolutive systems to evolve, and thus can be expected to appear in an evolutive system if at all possible. Similarly, functions that require the expenditure of negentropy (for example mobility, breathing, circulation, sensing, communicating, etc.) are not prerequisites for evolution, but can be expected to become established in evolutive systems during evolution through the selective advantages that they confer. A computer-based evolutive automaton is used to explore possible evolutionary scenarios. In the presence of spatial and temporal inhomogeneities, one can construct a multitude of evolutionary scenarios through which various functions, such as the operation of genetic code, can become established within the evolutive automaton. This variety of possible evolutionary scenarios is all the more remarkable because the automaton does not include many important physical processes that would be present in a real system and would greatly multiply the number of possible evolutionary mechanisms and scenarios. Some evolutionary mechanisms are based on survival related selection, while others are based on generation related selection. Previously explored scenarios for the initiation of life have been based mostly on generation related selection. In this paper, we give particular emphasis to survival related selection which is more general in that it does apply to structures and functions related to reproduction but, unlike generation related selection, it is not limited to them. Some of the most basic features of terrestrial living systems can be seen either as prerequisite features of an evolutive system (such as the mortality of living organisms, instability of biological polymers, imperfect reproduction caused by mutations, and the need for a negentropy input) or as features that one can reasonably expect to become established in an evolutive system (such as reproduction and the multitude of living functions that require expenditure of negentropy). This suggests the possibility that an independent definition of living systems may not be necessary if features of living systems substantially overlap with features that one may expect to find in evolutive systems.

Animals↗
PubMed2003

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.

BACKGROUND: Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. RESULTS: We addressed the problem of constructing parsimonious scenarios for individual sets of orthologous genes given a species tree. The orthologous sets were taken from the database of Clusters of Orthologous Groups of proteins (COGs). We show that the phyletic patterns (patterns of presence-absence in completely sequenced genomes) of almost 90% of the COGs are inconsistent with the hypothetical species tree. Algorithms were developed to reconcile the phyletic patterns with the species tree by postulating gene loss, COG emergence and HGT (the latter two classes of events were collectively treated as gene gains). We prove that each of these algorithms produces a parsimonious evolutionary scenario, which can be represented as mapping of loss and gain events on the species tree. The distribution of the evolutionary events among the tree nodes substantially depends on the underlying assumptions of the reconciliation algorithm, e.g. whether or not independent gene gains (gain after loss after gain) are permitted. Biological considerations suggest that, on average, gene loss might be a more likely event than gene gain. Therefore different gain penalties were used and the resulting series of reconstructed gene sets for the last universal common ancestor (LUCA) of the extant life forms were analysed. The number of genes in the reconstructed LUCA gene sets grows as the gain penalty increases. However, qualitative examination of the LUCA versions reconstructed with different gain penalties indicates that, even with a gain penalty of 1 (equal weights assigned to a gain and a loss), the set of 572 genes assigned to LUCA might be nearly sufficient to sustain a functioning organism. Under this gain penalty value, the numbers of horizontal gene transfer and gene loss events are nearly identical. This result holds true for two alternative topologies of the species tree and even under random shuffling of the tree. Therefore, the results seem to be compatible with approximately equal likelihoods of HGT and gene loss in the evolution of prokaryotes. CONCLUSIONS: The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree. Algorithms were developed for constructing parsimonious evolutionary scenarios, which include gene loss and gain events, for orthologous gene sets, given a species tree. This analysis shows, contrary to expectations, that the number of predicted HGT events that occurred during the evolution of prokaryotes might be approximately the same as the number of gene losses. The approach to the reconstruction of evolutionary scenarios employed here is conservative with regard to the detection of HGT because only patterns of gene presence-absence in sequenced genomes are taken into account. In reality, horizontal transfer might have contributed to the evolution of many other genes also, which makes it a dominant force in prokaryotic evolution.

Algorithms↗
PubMed1999

Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps.

A likely scenario of evolution of biosynthetic pathways is believed to have occurred by retro-evolution through recruitment of existing enzymes rather than generation of de novo classes. It had been proposed that such retro-evolution occurred in steps as a response to depletion of an essential metabolite and availability of another related substance in the environment. In this article, I argue that because of instability of many such extant intermediates, it is unlikely that retro-evolution had occurred in steps. I further propose that such evolution in many cases has taken place by jumps, i.e., by recruitment of a multifunctional enzyme capable of catalyzing several steps at a time, albeit inefficiently. I further speculate that in some cases one primordial multienzyme may have catalyzed the whole sequence of reaction of a biosynthetic pathway, i.e., the pathway may have evolved by a single leap. Gene duplications and further evolution to more efficient enzymes led to extant pathways. Such a mechanism predicts that some or all enzymes of a pathway must have descended from a common ancestor. Sequence and structural homologies among extant enzymes of a biosynthetic pathway have been examined.

Amino Acids↗
PubMed1984

Molecular evolution in Drosophila and the higher Diptera II. A time scale for fly evolution.

In this paper, we examine first the steadiness of the rate of evolutionary change in a larval hemolymph protein, LHP, in numerous Drosophila species. We estimated amino acid sequence divergence from immunological distances measured with the quantitative microcomplement fixation technique. Using tests not depending on knowledge of absolute times of divergence, we estimated the variance of the rate of evolutionary change to be at least 4 times as large as that for a process resembling radioactive decay. Thus, the rate of evolution of this protein is as uniform as that of vertebrate proteins. Our analysis indicates no acceleration of protein evolution in the lineages leading to Hawaiian drosophilines. Second, we give an explicit description of a procedure for calculating the absolute value of the mean rate of evolutionary change in this protein. This procedure is suggested for general use in calculating absolute rates of molecular evolution. The mean rate of evolution of LHP is about 1.2 immunological distance units per million years, which probably corresponds to a unit evolutionary period of 4 million years; LHP thus evolves at a rate comparable to that of mammalian hemoglobins. Finally, we utilize the calibrated rate of LHP evolution to derive a time scale of evolution in the Drosophilidae and higher Diptera.

Animals↗
PubMed2000

Episodic evolution of protein hormones: molecular evolution of pituitary prolactin.

Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin shows a similar pattern. During much of tetrapod evolution the sequence of prolactin has been strongly conserved, showing a slow basal rate of change (approx 0.27x10(9) substitutions/amino acid site/year). This rate has increased substantially ( approximately 12- to 38-fold) on at least four occasions during eutherian evolution, during the evolution of primates, artiodactyls, rodents, and elephants. That these increases are real and not a consequence of inadvertant comparison of paralogous genes is shown (for at least the first three groups) by the fact that they are confined to mature protein coding sequence and not apparent in sequences coding for signal peptides or when synonymous substitutions are examined. Sequences of teleost prolactins differ markedly from those of tetrapods and lungfish, but during the course of teleost evolution the rate of change of prolactin has been less variable than that of growth hormone. It is concluded that the evolutionary pattern seen for prolactin shows long periods of near-stasis interrupted by occasional bursts of rapid change, resembling the pattern seen for growth hormone in general but not in detail. The most likely basis for these bursts appears to be adaptive evolution though the biological changes involved are relatively small.

Animals↗
PubMed1985

On the evolution of dominance modifiers II: a non-equilibrium approach to the evolution of genetic systems.

The evolution of dominance is both the simplest and best investigated example of the evolution of genetic systems. Nevertheless, there exists striking empirical material, e.g. industrial melanism, for which no satisfactory explanation could so far be provided. In this paper we take an approach to this classical problem based on a global analysis together with computer simulations. It reveals that during the evolution of dominance one has to distinguish a "nonequilibrium phase" and a "Fisherian phase". The non-equilibrium phase appears to be characterized by the fact that in general the selection intensity at the primary locus does not affect the degree of modifier selection but only the time necessary for passing through this phase. A further essential conclusion is that modifier evolution only obtains a reasonable amount of efficiency if the population reaches the Fisherian phase already with a high modifier frequency. Using these results, predictions on the population genetic prerequisites for the evolution of dominance are derived. From these we conclude that even in populations in which dominance evolution has occurred it cannot be expected that back-crosses into relics of the ancestral population lead to a breakdown of dominance within a few generations. These predictions are in accordance with empirical data on Biston betularia and Odontopera bidentata.

Animals↗
PubMed1998

Asymmetrical DNA replication promotes evolution: disparity theory of evolution.

Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication. This contradiction existing between heredity and evolution cannot be resolved in an individual organism, but only in terms of a population, in that a delicate balance exists between wild type and variants in a population which is necessary for the survival of the species. Namely, there seems to be a key in the mechanism of DNA replication to solve some problems of evolution. DNA is replicated semiconservatively using the leading and discontinuous lagging strands. According to our 'disparity theory of evolution', the existence of a sufficient fidelity difference between the leading and lagging strands is advantageous in terms of evolution, because the diversity of genotypes is enlarged but genotypes that have occurred in the past are guaranteed. In theory, by artificially increasing the fidelity difference between the leading and lagging strand ('disparity mutator'), evolution is accelerated while avoiding the extinction of the population. Using a disparity mutator, we should be able to improve living things, including multicellular organisms, within constrained conditions. A double-stranded algorithm, which mimics the structure and replication manner of DNA, is promising for solving optimization problems.

Animals↗
PubMed1989

Hydrogen evolution of Enterobacter aerogenes depending on culture pH: mechanism of hydrogen evolution from NADH by means of membrane-bound hydrogenase.

The pH dependency of cell mass productivity, the hydrogen evolution rate and the yield of hydrogen from glucose was measured by controlling the pH of the culture automatically. The cell mass productivity of Enterobacter aerogenes increased in a linear fashion up to a pH value of approx. 7.0. In contrast, both the evolution rate and the yield of hydrogen showed convex relationships up to a pH value of 7.0, both having maximum values at a pH of approx. 5.8. The maximum evolution rate was approx. 11.3 mmol H2 per g dry cell per h at 38 degrees C. A hypothetical mechanism for hydrogen evolution was proposed by taking our results and other research work into consideration. The proposed mechanism of hydrogen evolution was that NADH was oxidized on the inside surface of the cell membrane and protons were reduced on the outside surface by means of membrane-bound hydrogenase. This mechanism explains in a thermodynamic context the relation between the activity of the hydrogen evolution and the pH of the culture.

Cell Membrane↗
PubMed1999

Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation.

The amino acid sequences of 25 archaeal retinal proteins from 13 different strains of extreme halophiles were analyzed to establish their molecular phylogenetic relationship. On the basis of amino acid sequence similarity, these proteins apparently formed a distinct family designated as the archaeal rhodopsin family (ARF), which was not related to other known proteins, including G protein-coupled receptors. The archaeal rhodopsin family was further divided into four clusters with different functions; H+ pump (bacteriorhodopsin), Cl- pump (halorhodopsin), and two kinds of sensor (sensory rhodopsin and phoborhodopsin). These four rhodopsin clusters seemed to have occurred by gene duplication(s) before the generic speciation of halophilic archaea, based on phylogenetic analysis. Therefore, the degrees of differences in amino acid sequences within each cluster simply reflected the divergent evolution of halophilic archaea. By comparing the branch lengths after speciation points of the reconstituted tree, we calculated the relative evolution rates of the four archaeal rhodopsins bacteriorhodopsin:halorhodopsin:sensory rhodopsin: phoborhodopsin to be 5:4:3:10. From these values, the degrees of functional and structural restriction of each protein can be inferred. The branching topology of four clusters grouped bacteriorhodopsin and halorhodopsin versus sensory rhodopsin and phoborhodopsin by likelihood mapping. Using bacteriorhodopsin (and halorhodopsin) as an outgroup, the gene duplication point of sensory rhodopsin/phoborhodopsin was determined. By calculating the branch lengths between the gene duplication point and each halophilic archaea speciation point, we could speculate upon the relative evolution rate of pre-sensory rhodopsin and pre-phoborhodopsin. The evolution rate of pre-sensory rhodopsin was fivefold faster than that of pre-phoborhodopsin, which suggests that the original function of the ancestral sensor was similar to that of phoborhodopsin, and that sensory rhodopsin evolved from pre-sensory rhodopsin by the accumulation of mutations. The changes in evolution rate by gene duplication and functional differentiation were demonstrated in the archaeal rhodopsin family using the gene duplication date and halobacterial speciation date as common time stamps.

Amino Acid Sequence↗
PubMed2002

A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents.

We present a new likelihood method for detecting constrained evolution at synonymous sites and other forms of nonneutral evolution in putative pseudogenes. The model is applicable whenever the DNA sequence is available from a protein-coding functional gene, a pseudogene derived from the protein-coding gene, and an orthologous functional copy of the gene. Two nested likelihood ratio tests are developed to test the hypotheses that (1) the putative pseudogene has equal rates of silent and replacement substitutions; and (2) the rate of synonymous substitution in the functional gene equals the rate of substitution in the pseudogene. The method is applied to a data set containing 74 human processed-pseudogene loci, 25 mouse processed-pseudogene loci, and 22 rat processed-pseudogene loci. Using the informatics resources of the Human Genome Project, we localized 67 of the human-pseudogene pairs in the genome and estimated the GC content of a large surrounding genomic region for each. We find that, for pseudogenes deposited in GC regions similar to those of their paralogs, the assumption of equal rates of silent and replacement site evolution in the pseudogene is upheld; in these cases, the rate of silent site evolution in the functional genes is approximately 70% the rate of evolution in the pseudogene. On the other hand, for pseudogenes located in genomic regions of much lower GC than their functional gene, we see a sharp increase in the rate of silent site substitutions, leading to a large rate of rejection for the pseudogene equality likelihood ratio test.

Animals↗
PubMed1994

Divergent evolution and evolution by the birth-and-death process in the immunoglobulin VH gene family.

Immunoglobulin diversity is generated primarily by the heavy- and light-chain variable-region gene families. To understand the pattern of long-term evolution of the heavy-chain variable-region (VH) gene family, which is composed of a large number of member genes, the evolutionary relationships of representative VH genes from diverse organisms of vertebrates were studied by constructing a phylogenetic tree. This tree indicates that the vertebrate VH genes can be classified into group A, B, C, D, and E genes. All VH genes from cartilaginous fishes such as sharks and skates from a monophyletic group and belong to group E, whereas group D consists of bony-fish VH genes. By contrast, group C includes not only some fish genes but also amphibian, reptile, bird, and mammalian genes. Group A and B genes were composed of the genes from mammals and amphibians. The phylogenetic analysis also suggests that mammalian VH genes are classified into three clusters--i.e., mammalian clans I, II, and III-and that these clans have coexisted in the genome for >400 Myr. To study the short-term evolution of VH genes, the phylogenetic analysis of human group A (clan I) and C (clan III) genes was also conducted. The results obtained show that VH pseudogenes have evolved much faster than functional genes and that they have branched off from various functional VH genes. There is little indication that the VH gene family has been subject to concerted evolution that homogenizes member genes. These observations indicate that the VH genes are subject to divergent evolution due to diversifying selection and evolution by the birth-and-death process caused by gene duplication and dysfunctioning mutation. Thus, the evolutionary pattern of this monofunctional multigene family is quite different from that of such gene families as the ribosomal RNA and histone gene families.

Amino Acid Sequence↗