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At least 19 recordsLinked to original sources
PubMed2001

Extremely reduced evolutionary rate of TATA-box binding protein in higher vertebrates and its evolutionary implications.

Previously we showed that the evolutionary rates of the Pax proteins are markedly reduced in higher vertebrates, as compared with those in the ancestral lineage of vertebrates, and we suggested that the reduced Pax protein evolution might be explained by increased functional constraints due to gene recruitment for other purposes or repeated expression in different developmental stages. To clarify the problem of whether the evolutionary rate variation found in the Pax proteins is an evolutionary feature generally recognized in most transcription factors, we have cloned and sequenced cDNAs encoding the TATA-box binding protein (TBP), a general transcription factor of eukaryotes, from Oryzias latipes, a Japanese medaka, Lampetra reissneri, a lamprey, and Ephydatia fluviatilis, a freshwater sponge. An evolutionary rate analysis of TBP has revealed that the evolutionary rate of TBP is extremely low in higher vertebrates, but not in the ancestral lineage of vertebrates, as found in the Pax proteins. In contrast, no marked reduction of the evolutionary rate in higher vertebrates is observed in the aldolase C, a house keeping enzyme. It is therefore likely that the increased functional constraint on TBP is responsible for the extremely low evolutionary rate in higher vertebrates. The temporal pattern of the evolutionary rate variation during vertebrate evolution was discussed.

Animals↗
PubMed1999

Evolutionary feedback: a new mechanism for stasis and punctuated evolutionary change based on integration of the organism.

This paper argues that organisms are integrated, holistic systems whose phenotypic traits and genes interact with each other and natural selection. More than this, organisms are feedback systems. I introduce the term integration of the organism to refer to this idea that organisms are such interacting systems. Integration of the organisms is a major reason why most mutations are deleterious, and why the larger a mutation's effect, the greater the probability that a mutation will be deleterious. Yet, it is also why macromutations can occasionally be adaptive. Such adaptive mutations of large effect, an example of which is neoteny, must be coordinated with the generic system and ontogeny of the organism. Integration of the organism and the ability of both the phenotype and genotype to influence and interact with natural selection means a species can undergo sequential evolution, a term I coin in this paper to refer to a change in a trait causing a change in selection on a second trait, which leads to a change in the second trait, which in turn causes a change in selection on a third trait, changing it, and so on. Sequential evolution can sometimes result in closed feedback loops, in which a trait farther down the sequence affects a trait earlier in the sequence of traits. I call this process evolutionary feedback. Both sequential evolution and evolutionary feedback can sometimes cause punctuated evolutionary change. Evolutionary feedback can also act as a mechanism for stasis. Hence, evolutionary feedback is a mechanism for punctuated equilibrium. I propose that species to a large extent influence, even drive, their own evolution. This, of course, is not to suggest they do so willfully or consciously. It is proposed that there are three mechanisms for punctuated evolutionary change; these are described. Examples of and evidence for sequential evolution and punctuated evolution by evolutionary feedback are presented.

Adaptation, Physiological↗
PubMed2006

Exploring evolutionary constraints is a task for an integrative evolutionary biology.

Judging by the volume of writings about evolutionary constraints, they are an important topic in evolutionary biology. However, their involvement in shaping patterns of evolutionary change from morphological stasis to adaptive radiation remains contentious. This is at least in part because of the paucity of robust analyses of potential examples of constraints, whether of a more absolute or a relative nature. Here, we argue that what is needed to explore the type of constraints and bias on evolutionary change that may emerge from the way in which phenotypic variation is generated is an integrative approach applied to systems that can be tackled at different levels of biological organization. This is illustrated using research on the evolution of patterns in butterfly wing eyespots that has applied a combination of evolutionary genetics and evo-devo to an emerging model species with the beginnings of a comparative approach to describe patterns of variability among the extant taxa of two species-rich genera.

Animals↗
PubMed2006

Coevolution of slow-fast populations: evolutionary sliding, evolutionary pseudo-equilibria and complex Red Queen dynamics.

We study the interplay of ecological and evolutionary dynamics in communities composed of populations with contrasting time-scales. In such communities, genetic variation of individual traits can cause population transitions between stationary and cyclic ecological regimes, hence abrupt variations in fitness. Such abrupt variations raise ridges in the adaptive landscape, where the populations are poised between equilibrium and cyclic coexistence and along which evolutionary trajectories can remain sliding for long times or halt at special points called evolutionary pseudo-equilibria. These novel phenomena should be generic to all systems in which ecological interactions cause fitness to vary discontinuously. They are demonstrated by the analysis of a predator-prey community, with one adaptive trait for each population. The eco-evolutionary dynamics of the system show a number of other distinctive features, including evolutionary extinction and two forms of Red Queen dynamics. One of them is characterized by intermittent bouts of cyclic oscillations of the two populations.

Adaptation, Physiological↗
PubMed2004

Markedly reduced evolutionary rates of transcription factors and cytoplasmic ribosomal RNAs and proteins in higher vertebrates and their evolutionary implications.

To reveal the relationship between organismal evolution and the molecular evolutionary rate, the temporal pattern of evolutionary rates were investigated for various genes during the course of deuterostome evolution. Deuterostome lineage leading to extant mammals was tentatively divided into two periods (the First and the Latter periods) by the time of divergence of bony fishes and mammals. For each of the First and the Latter period, evolutionary rates of 207 gene sets were calculated. In the Latter period, the evolutionary rate was significantly reduced in such informational genes as transcription factors and cytoplasmic ribosomal RNAs and proteins. In contrast, a variety of enzymes and mitochondrial ribosomal proteins evolve at nearly constant rate throughout the First and the Latter periods. The present result suggests that the increase of gene number by extensive gene duplications in the early evolution of vertebrates is responsible for the decrease of evolutionary rate.

Animals↗
PubMed2003

Evolutionary pace of chromosomal polymorphism in colonizing populations of Drosophila subobscura: an evolutionary time series.

Biologists have long debated the speed, uniformity, and predictability of evolutionary change. However, evaluating such patterns on a geographic scale requires time-series data on replicate sets of natural populations. Drosophila subobscura has proven an ideal model system for such studies. This fly is broadly distributed in the Old World, but was introduced into both North and South America just over two decades ago and then spread rapidly. Rapid, uniform, and predictable evolution would be demonstrated if the invading flies evolved latitudinal clines that progressively converged on those of the native populations. Evolutionary geneticists quickly capitalized on this opportunity to monitor evolutionary dynamics. Just a few years after the introduction, they surveyed chromosomal inversion frequencies in both North and South America. On both continents they detected incipient latitudinal clines in chromosome inversion frequencies that almost always had the same sign with latitude as in the Old World. Thus the initial evolution of chromosomal polymorphisms on a continental scale was remarkably rapid and consistent. Here we report newer samples of inversion frequencies for the colonizing populations: the time series now spans almost one decade for North America and almost two decades for South America. Almost all inversions in the New World continue to show the same sign of frequency with latitude as in the Old World. Nevertheless, inversion clines have not consistently increased in steepness over time; nor have they consistently continued to converge on the Old World baseline. However, five arrangements in South America show directional, continentwide shifts in frequency. Overall, the initial consistency of clinal evolutionary trajectories seen in the first surveys seems not to have been maintained.

Animals↗
PubMed2004

The integration of Darwinism and evolutionary morphology: Alexej Nikolajevich Sewertzoff (1866-1936) and the developmental basis of evolutionary change.

The growth of evolutionary morphology in the late 19th and early 20th centuries was inspired by the work of Carl Gegenbaur (1826-1903) and his protégé and friend Ernst Haeckel (1834-1919). However, neither of them succeeded in creating and applying a strictly Darwinian (selectionist) methodology. This task was left to the next generation of evolutionary morphologists. In this paper we present a relatively unknown researcher, Alexej Nikolajevich Sewertzoff (1866-1936) who made important contributions towards a synthesis of Darwinism and evolutionary morphology.

Anatomy, Comparative↗
PubMed1986

Methodological problems in evolutionary biology. VI. The force of evolutionary epistemology.

Evolutionary epistemology takes various forms. As a philosophical discipline, it may use analogies by borrowing concepts from evolutionary biology to establish new foundations. This is not a very successful enterprise because the analogies involved are so weak that they hardly have explanatory force. It may also veil itself with the garbs of biology. Proponents of this strategy have only produced irrelevant theories by transforming epistemology's concepts beyond recognition. Sensible theories about "knowledge and biology" should presuppose that various long-standing problems concerning relations between the mental and the physical are solved. Such problems are wrongly disregarded by evolutionary epistemologists.

Animals↗
PubMed1992

Evolutionary pattern of the H 3 haemagglutinin of equine influenza viruses: multiple evolutionary lineages and frozen replication.

The nucleotide and deduced amino acid sequences of the haemagglutinin genes coding for the HA 1 domain of H3N8 equine influenza viruses isolated over wide regions of the world were analyzed in detail to determine their evolutionary relationships. We have constructed a phylogenetic model tree by the neighbour-joining method using nucleotide sequences of 15 haemagglutinin genes, including those of five viruses determined in the present study. This gene tree revealed the existence of two major evolutionary pathways during a twenty five-year period between 1963 to 1988, and each pathway appeared to consist of two distinct lineages of haemagglutinin genes. Furthermore, our analysis of nucleotide sequences showed that two distinct lineages of equine H3N8 viruses were involved in an equine influenza outbreak during the period of December 1971-January 1972 in Japan. The number of nucleotide changes between strains was proportional to the length of time (in years) between their isolation except for three of the HA genes. However, there are three exceptional strains isolated in 1971, 1987, and 1988, respectively. The haemagglutinin gene in these strains showed a small number of nucleotide substitutions after they branched off around 1963, suggesting an example of frozen replication. Although the estimated rate (0.0094/site/year) of synonymous (silent) substitutions of the haemagglutinin gene of equine H3N8 viruses was nearly the same as that of human H 1 and H 3 haemagglutinin genes, the rate of nonsynonymous (amino-acid changing) substitutions of the former equine virus gene was estimated to be 0.00041/site/year--that is about 5 times lower than that estimated for the human H 3 haemagglutinin gene. The present study is the first demonstration that multiple evolutionary lineages of equine H3N8 influenza virus circulated since 1963.

Amino Acid Sequence↗
PubMed1976

Evolutionary processes and evolutionary noise at the molecular level. II. A selectionist model for random fixations in proteins.

On account, notably, of a competition between different component functions for individual sites in polypeptide chains, each protein molecule represents a functional compromise, with some functions optimized, but the overall state of the molecule "suboptimal". The proposal is made that the selection coefficient relating to a protein molecule under given conditions can in principle be broken down into partial selection coefficients relevant to the different functions that the molecule carries out. At general-function sites, each fixation improves some function, while others deteriorate, at first nonsignificantly, and the overall adaptive state of the molecule fluctuates around its maximum. A selective mechanism is described whereby kaleidoscopic changes in primary structure at variable sites are indefinitely promoted, independently of any environmental changes and with the molecule remaining close to a state of maximal overall adaptation. The paradoxical aspect of this proposal is analyzed. The implication of specific functions in substitutions at general-function sites is noted. Further, it is shown that a certain category of changes in the internal environment of the organism can be integrated into the constant-environmental model for selection. Genetic sufficiency is considered a notion more adequate than genetic optimality for describing biological fitness and for providing a basis for the present model. On this basis selection occurs without genetic load. Multipolymorphism is one of the consequences. Several lines of evidence, in particular observations on polymorphism in deep sea organisms, seem to support the model. It is pointed out that it provides a theoretical foundation for a molecular evolutionary clock. The theoretical constancy of the clock depends on the constancy of functional density. The question of the evolution of functional density is examined. Comparisons of observed substitution frequencies with values expected on a random basis are rejected as a measure of the contribution to evolution of nondetermination. They are considered to reflect a hierarchy in the resistance of the molecules to different amino acid residues as substituents. A limited component of "true" randomness, again accompanied by selection, is on the other hand provided by the model. Most amino acid substitutions are considered evolutionary noise, even though noise compatible with selection. It is proposed that evolutionary significant substitutions may be identified by monitoring changes in functional density and weighted functional density.

Alleles↗
PubMed1976

Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins.

The distinction between molecular sites that mainly carry out general functions and sites committed to specific functions is analyzed, notably in terms of different evolutionary variabilities. Functional density is defined as the proportion of sites involved in specific functions. Weighted functional density, by representing the relative variability at specific-function sites is to some extent a measure of the specificity of molecular interactions. The relationship between general- and specific-function sites on the one hand the covarions of Fitch on the other is discussed. The functional "degeneracy" of amino acids is described as increasing the interdependence of general functions. It is predicted that proteins tht do not possess general-function sites besides their specific-function sites tend to "freeze" their primary structure, according to an evolutionary process that is an autocatalytic function of the decrease in site variability. This limits the use of weighted functional density as an indicator of the overall degree of interaction specificity of a protein to values that are not close to unity.

Amino Acid Sequence↗
PubMed2001

Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons.

This study examined the evolutionary dynamics of Bov-B LINEs in vertebrates and the evolution of the RTE clade of non-LTR retrotransposons. The first full-length reptilian Bov-B LINE element is described; it is 3.2 kb in length, with a structural organization typical of the RTE clade of non-LTR retrotransposons. The long-term evolution of Bov-B LINEs was studied in 10 species of Squamata by analysis of a PCR-amplified 1.8-kb fragment encoding part of apurinic/apyrimidinic endonuclease, the intervening domain, and the palm/fingers subdomain of reverse transcriptase. A very high level of conservation in Squamata Bov-B long interspersed nuclear elements has been found, reaching 86% identity in the nearly 600 amino acids of ORF2. The same level of conservation exists between the ancestral snake lineage and Ruminantia. Such a high level is exceptional when compared with the level of conservation observed in nuclear and mitochondrial proteins and in other transposable elements. The RTE clade has been found to be much more widely distributed than previously thought, and novel representatives have been discovered in plants, brown algae, annelids, crustaceans, mollusks, echinoderms, and teleost fishes. Evolutionary relationships in the RTE clade were deduced at the amino acid level from three separate regions of ORF2. By using different independent methods, including the divergence-versus-age analysis, several examples of horizontal transfer in the RTE clade were recognized, with important implications for the existence of HT in non-LTR retrotransposons.

Amino Acid Sequence↗
PubMedDate not supplied

Environmental signaling and evolutionary change: can exposure of pregnant mammals to environmental estrogens lead to epigenetically induced evolutionary changes in embryos?

DNA methylation is one of the epigenetic and hereditary mechanisms regulating genetic expression in mammalian cells. In this review, we propose how certain natural agents, through their dietary consumption, could induce changes in physiological aspects in mammalian mothers, leading to alterations in DNA methylation patterns of the developing fetus and to the emergence of new phenotypes and evolutionary change. Nevertheless, we hypothesize that this process would require (i) certain key periods in the ontogeny of the organism where the environmental stimuli could produce effects, (ii) particular environmental agents as such stimuli, and (iii) that a genomic persistent change be consequently produced in a population. Depending on the persistence of the environmental stimuli and on whether the affected genes are imprinted genes, induced changes in DNA methylation patterns could become persistent. Moreover, some fragments could be more frequently methylated than others over several generations, leading to biased base change and evolutionary consequences.

Animals↗
PubMed2004

Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved.

In this study we systematically examined the differences between the proteomes of Metazoa and other eukaryotes. Metazoans (Homo sapiens, Ceanorhabditis elegans and Drosophila melanogaster) were compared with a plant (Arabidopsis thaliana), fungi (Saccharomyces cerevisiae and Schizosaccaromyces pombe) and Encephalitozoan cuniculi. We identified 159 gene families that were probably lost in the Metazoan branch and 1263 orthologous families that were specific to Metazoa and were likely to have originated in their last common ancestor (LCA). We analyzed the evolutionary rates of pan-eukaryotic protein families and identified those with higher rates in animals. The acceleration was shown to occur in: (i) the LCA of Metazoa or (ii) independently in the Metazoan phyla. A high proportion of the accelerated Metazoan protein families was found to participate in translation and ribosome biogenesis, particularly mitochondrial. By functional analysis we show that no metabolic pathway in animals evolved faster than in other organisms. We conclude that evolution in the LCA of Metazoa was extensive and proceeded largely by gene duplication and/or invention rather than by modification of extant proteins. Finally, we show that the rate of evolution of a gene family in animals has a clear, but not absolute, tendency to be conserved.

Animals↗
PubMed1997

Structural and evolutionary studies on sterol 14-demethylase P450 (CYP51), the most conserved P450 monooxygenase: II. Evolutionary analysis of protein and gene structures.

Phylogenetic analyses based on protein sequence data indicated that sterol 14-demethylase P450 (CYP51) and bacterial CYP51-like protein were joined into a distinctive evolutionary cluster, CYP51 cluster, within the CYP protein superfamily. The most probable branch topology of the CYP51 phylogenetic tree was (bacteria, (plants, (fungi, mammals))), which is comparable to the phylogeny of major kingdoms of living matter, suggesting that CYP51 has been conserved from the era of prokaryotic evolution. This may be strong evidence supporting the prokaryotic origin of P450. Structure of flanking regions and the number and insertion sites of introns are quite different between mammalian and fungal CYP51s. This fact indicates that different mechanisms are operative in evolution of protein sequences and gene structures. CYP51 is the first example violating the well-documented rule that the basic structure of a gene, including intron insertion sites, is well conserved in each P450 family. One CYP51 processed a pseudogene was found in rat genome. Nonsynonymous nucleotide divergence observed between the pseudogene and CYP51 cDNA was less than one-fifth of the synonymous divergence. This unusually low rate of nonsynonymous nucleotide changes in the pseudogene suggests that it may be derived from another CYP51, which might have been active for a significant duration in the past.

Amino Acid Sequence↗
PubMed2002

Diffuse pulmonary hemorrhage: evolutionary 'flaw' or consequence of evolutionary progress?

Diffuse alveolar hemorrhage (DAH), a serious and frequently life-threatening process, can occur in a wide variety of disorders, including mitral stenosis, systemic autoimmune diseases, conditions associated with anti-neutrophil cytoplasmic antibodies, anti-glomerular basement membrane antibody, inhaled toxins or infection, and drug allergies. These causes have no common denominator, but the end result, of capillary inflammation and hemorrhage, is the same. The capillaritis seen in DAH is present exclusively in the lung and is not part of a more generalized systemic vasculitis. In a recent article, I highlighted the central role of the neutrophils in this process, and suggested that in DAH the neutrophils present in the lung may sift the associated immune complexes and transfer them out of the vascular system into the alveoli. In this article, we document the inflammation seen during the remission period and during the acute lung bleeding of DAH in 2 patients. Because DAH is a common finding in a variety of pathological conditions, we then explore the possible evolutionary mechanisms behind DAH.

Adolescent↗
PubMed2006

Understanding the course and state of evolutionary optimizations using visualization: ten years of industry experience with evolutionary algorithms.

Evolutionary algorithms (EAs) are widely employed to solve a broad range of optimization problems. Even though they work in an algorithmically simple manner, it is not always easy to understand what is going on during a particular optimization run. It is especially desirable to gain further insight into the state and course of the algorithm if the optimization does not yield the expected results or if we are not sure whether the result achieved is really the best result possible. During an optimization run an EA produces a vast amount of data. The extraction of useful information is a nontrivial task. In this article, we review visualization methods used to extract this useful information. We also demonstrate the application of visualization techniques and explain how they help us to understand the course and state of the EA. This extra information gained by the use of visualization techniques is often the difference between a good result and a very good result. In complex real-world applications, merely achieving a good result often means that the approach has failed. On the other hand, a success means large gains in productivity or safety or a decrease in costs.

Algorithms↗