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PubMed1995

The nature of gene evolution on the mammalian Y chromosome: lessons from Sry.

With the exception of a small region, heteromorphic sex chromosomes of mammals do not undergo recombination in male meiosis. As a result, the majority of the Y chromosome is clonally transmitted through paternal lineages. Numerous phenomena, including the Hill-Robertson effect, Muller's ratchet, genetic hitch-hiking, and male-driven molecular evolution, are associated with the special transmission properties of the Y chromosome, and can potentially explain the tempo and pattern of gene evolution on the mammalian Y. We explore these phenomena in light of comparative data from the Y-linked sex-determining locus, Sry. Sry exhibits rapid amino acid divergence between species and little to no variation within species. We find no evidence for directional selection acting on this locus. The pattern of evolution between species is consistent with the Hill-Robertson effect and Muller's ratchet. Lack of variation in Sry within species may reflect genetic hitch-hiking, however, we cannot exclude the confounding effects of small effective population size of Y chromosomes. We find no support for male-driven molecular evolution for Sry in Old World mice and rats. However, a more appropriate test of this hypothesis would be to compare the evolution of Sry to the X-linked Sox3 gene in these same species. Clearly, more comparative studies of Sry and other Y-linked loci are needed to characterize the effects of Y chromosome transmission on the evolution of Y-linked sequences.

Animals↗

PubMed2004

cis-Regulatory and protein evolution in orthologous and duplicate genes.

The relationship between protein and regulatory sequence evolution is a central question in molecular evolution. It is currently not known to what extent changes in gene expression are coupled with the evolution of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes). Here, we develop a method to measure the extent of functionally relevant cis-regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the genomes of Caenorhabditis elegans and C. briggsae, we found that protein and regulatory evolution is weakly coupled in orthologs but not paralogs, suggesting that selective pressure on gene expression and protein evolution is quite similar and persists for a significant amount of time following speciation but not gene duplication. Additionally, duplicates of both species exhibit a dramatic acceleration of both regulatory and protein evolution compared to orthologs, suggesting increased directional selection and/or relaxed selection on both gene expression patterns and protein function in duplicate genes.

Animals↗

PubMed2005

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates.

We investigated the evolution of the families of LINE-1 (L1) retrotransposons that have amplified in the human lineage since the origin of primates. We identified two phases in the evolution of L1. From approximately 70 million years ago (Mya) until approximately 40 Mya, three distinct L1 lineages were simultaneously active in the genome of ancestral primates. In contrast, during the last 40 million years (Myr), i.e., during the evolution of anthropoid primates, a single lineage of families has evolved and amplified. We found that novel (i.e., unrelated) regulatory regions (5'UTR) have been frequently recruited during the evolution of L1, whereas the two open-reading frames (ORF1 and ORF2) have remained relatively conserved. We found that L1 families coexisted and formed independently evolving L1 lineages only when they had different 5'UTRs. We propose that L1 families with different 5'UTR can coexist because they don't rely on the same host-encoded factors for their transcription and therefore do not compete with each other. The most prolific L1 families (families L1PA8 to L1PA3) amplified between 40 and 12 Mya. This period of high activity corresponds to an episode of adaptive evolution in a segment of ORF1. The correlation between the high activity of L1 families and adaptive evolution could result from the coevolution of L1 and a host-encoded repressor of L1 activity.

5' Untranslated Regions↗

PubMed2003

Dynamics of DNA in vitro evolution with Mnt-repressor: simulations and analysis.

The dynamics of DNA in vitro evolution with Mnt-repressor has been studied numerically and analytically. Based on experimental data and realistic energy landscape for DNA-Mnt-repressor interaction, we investigated the dynamics of DNA in vitro evolution using stochastic simulations. The binding energy of DNA to Mnt-repressor was considered to consist of two parts: the DNA sequence specific and nonspecific. The crossover observed in real experiments is numerically recovered. We demonstrate that the evolution trajectories are drastically dispersed and no typical evolution passage exists during the evolution. Particularly, Fisher's theorem of natural selection is verified. A theoretical analysis for the evolution is also included.

DNA↗

PubMed2002

A statistical test of unbiased evolution of body size in birds.

Of the approximately 9500 bird species, the vast majority is small-bodied. That is a general feature of evolutionary lineages, also observed for instance in mammals and plants. The avian interspecific body size distribution is right-skewed even on a logarithmic scale. That has previously been interpreted as evidence that body size evolution has been biased. However, a procedure to test for unbiased evolution from the shape of body size distributions was lacking. In the present paper unbiased body size evolution is defined precisely, and a statistical test is developed based on Monte Carlo simulation of unbiased evolution. Application of the test to birds suggests that it is highly unlikely that avian body size evolution has been unbiased as defined. Several possible explanations for this result are discussed. A plausible explanation is that the general model of unbiased evolution assumes that population size and generation time do not affect the evolutionary variability of body size; that is, that micro- and macroevolution are decoupled, which theory suggests is not likely to be the case.

Animals↗

PubMed2002

Evolution of morphological and behavioral ontogenies in females of a highly dimorphic clade of blennioid fishes.

Comparison of ontogenetic trajectories with those inferred for ancestors provides a powerful but underused tool for the study of the evolution of different types of phenotypic characters. This approach was used to study morphological and behavioral evolution of the highly dimorphic chaenopsid genus Coralliozetus (Teleostei: Blennioidei). All sexually dimorphic synapomorphies of Coralliozetus involved evolution in females only; one character evolved via terminal addition (peramorphosis), whereas six evolved via terminal deletion (paedomorphosis). Evolution of the ontogeny of two behavioral characters (microhabitat use and feeding rate), as inferred by focal animal observations of eight species of tube blennies, was also confined to females and conformed to terminal deletion. Both sexes of outgroups and males of all species of Coralliozetus exhibit an ontogenetic shift from the open as juveniles to shelters as adults. However, females of all species of Coralliozetus retain the juvenile behavior of residing in the open. Blennies residing in the open take significantly more feeding bites than conspecifics residing in shelters, consequently, female Coralliozetus retain the high feeding rate of juveniles. Several of the paedomorphic morphological features of Coralliozetus females are plausibly associated with their paedomorphosis in microhabitat use. These include their reduced conspicuousness and reduced robustness compared to conspecific males. In groups such as chaenopsids, which undergo significant ontogenetic changes in microhabitat, paedomorphosis provides a mechanism for rapid coevolution of behavior and morphology. This study, the first to document the evolution of sexual dimorphism via both behavioral and morphological paedomorphosis, demonstrates the unique insights to be gained from a multidimensional analysis of phenotypic evolution.

Animals↗

PubMed1989

Interactive analysis of phylogeny and character evolution using the computer program MacClade.

Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.

Animals↗

PubMed2006

Understanding linguistic evolution by visualizing the emergence of topographic mappings.

We show how cultural selection for learnability during the process of linguistic evolution can be visualized using a simple iterated learning model. Computational models of linguistic evolution typically focus on the nature of, and conditions for, stable states. We take a novel approach and focus on understanding the process of linguistic evolution itself. What kind of evolutionary system is this process? Using visualization techniques, we explore the nature of replicators in linguistic evolution, and argue that replicators correspond to local regions of regularity in the mapping between meaning and signals. Based on this argument, we draw parallels between phenomena observed in the model and linguistic phenomena observed across languages. We then go on to identify issues of replication and selection as key points of divergence in the parallels between the processes of linguistic evolution and biological evolution.

Artificial Intelligence↗

PubMed2006

The gain and loss of genes during 600 million years of vertebrate evolution.

BACKGROUND: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. RESULTS: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication (whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. CONCLUSION: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication (probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.

Animals↗

PubMed2004

Evolution of dominance in metabolic pathways.

Dominance is a form of phenotypic robustness to mutations. Understanding how such robustness can evolve provides a window into how the relation between genotype and phenotype can evolve. As such, the issue of dominance evolution is a question about the evolution of inheritance systems. Attempts at explaining the evolution of dominance have run into two problems. One is that selection for dominance is sensitive to the frequency of heterozygotes. Accordingly, dominance cannot evolve unless special conditions lead to the presence of a high frequency of mutant alleles in the population. Second, on the basis of theoretical results in metabolic control analysis, it has been proposed that metabolic systems possess inherent constraints. These hypothetical constraints imply the default manifestation of dominance of the wild type with respect to the effects of mutations at most loci. Hence, some biologists have maintained that an evolutionary explanation is not relevant to dominance. In this article, we put into question the hypothetical assumption of default metabolic constraints. We show that this assumption is based on an exclusion of important nonlinear interactions that can occur between enzymes in a pathway. With an a priori exclusion of such interactions, the possibility of epistasis and hence dominance modification is eliminated. We present a theoretical model that integrates enzyme kinetics and population genetics to address dominance evolution in metabolic pathways. In the case of mutations that decrease enzyme concentrations, and given the mechanistic constraints of Michaelis-Menten-type catalysis, it is shown that dominance of the wild type can be extensively modified in a two-enzyme pathway. Moreover, we discuss analytical results indicating that the conclusions from the two-enzyme case can be generalized to any number of enzymes. Dominance modification is achieved chiefly through changes in enzyme concentrations or kinetic parameters such as k(cat), both of which can alter saturation levels. Low saturation translates into higher levels of dominance with respect to mutations that decrease enzyme concentrations. Furthermore, it is shown that in the two-enzyme example, dominance evolves as a by-product of selection in a manner that is insensitive to the frequency of heterozygotes. Using variation in k(cat) as an example of modifier mutations, it is shown that the latter can have direct fitness effects in addition to dominance modification effects. Dominance evolution can occur in a frequency-insensitive manner as a result of selection for such dual-effects alleles. This type of selection may prove to be a common pattern for the evolution of phenotypic robustness to mutations.

Enzymes↗

PubMed2004

Acoustic evolution in crickets: need for phylogenetic study and a reappraisal of signal effectiveness.

Cricket stridulums and calls are highly stereotyped, except those with greatly modified tegmina and/or venation, or "unusual" frequency, duration and/or intensity. This acoustic diversity remained unsuspected until recently, and current models of acoustic evolution in crickets erroneously consider this clade homogeneous for acoustic features. The few phylogenetic studies analyzing acoustic evolution in crickets demonstrated that acoustic behavior could be particularly labile in some clades. The ensuing pattern for cricket evolution is consequently extremely complex. We argue that: (1) phylogeny should always be considered when analyzing acoustic evolution, whatever characters are considered (signals, stridulums or behaviors). Consequently, future studies should be devoted to entire clades, and not consider isolated taxa; character and character state definitions should allow significant reconstructions of character evolutionary transformations; and homologies should be carefully defined for all characters, including behavior. (2) The factors responsible for song effectiveness should be reconsidered and hypotheses on their potential influence on signal evolution tested jointly by phylogenies (for example, to assess correlated transformations of acoustic and ecological features), and population studies (for example, to correlate call range and population structure, or test the predation risk associated with a signal structure). Better understanding these points should help clarifying acoustic evolution in crickets.

Acoustics↗

PubMed1997

Cloning and characterisation of the gene encoding red deer (Cervus elaphus) growth hormone: implications for the molecular evolution of growth hormone in artiodactyls.

In mammals the structure of pituitary GH is generally strongly conserved, indicating a slow basal rate of molecular evolution. However, on two occasions, during the evolution of primates and of artiodactyls, the rate of evolution has increased dramatically (25- to 50-fold) so that the sequences of human and ruminant GHs differ markedly from those of other mammalian GHs. In order to define further the burst of GH evolution that occurred in artiodactyls we have cloned and characterised the GH gene of red deer (Cervus elaphus) using genomic DNA and a polymerase chain reaction technique. The deduced sequence for the mature GH from red deer is identical to that of bovine GH, indicating that the burst of rapid evolution of GH that occurred in Artiodactyla must have been completed before the divergence of Cervidae and Bovidae and suggesting that the rate of evolution during this burst must have been greater than previously estimated. In other aspects (signal sequence, 5' and 3' sequences, introns and synonymous substitutions in the coding sequence) the red deer GH gene differs considerably from the GH genes of other ruminants. Differences between the signal peptide sequences of red deer and bovid GHs probably explain why N-terminal heterogeneity is seen in bovine, ovine and caprine GHs but not GH from red deer, pig or most other mammals.

Amino Acid Sequence↗

PubMed2001

Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change.

Pituitary growth hormone (GH), like several other protein hormones, shows an unusual episodic pattern of molecular evolution in which sustained bursts of rapid change are imposed on long periods of very slow evolution (near-stasis). A marked period of rapid change occurred in the evolution of GH in primates or a primate ancestor, and gave rise to the species specificity that is characteristic of human GH. We have defined more precisely the position of this burst by cloning and sequencing the GH genes for a prosimian, the slow loris (Nycticebus pygmaeus) and a New World monkey, marmoset (Callithrix jacchus). Slow loris GH is very similar in sequence to pig GH, demonstrating that the period of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. The putative marmoset GH is similar in sequence to human GH, demonstrating that the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence for mature GH, and is not marked in other components of the gene sequence including signal peptide, 5' upstream region and introns. A number of factors support the idea that this episode of rapid change was due to positive adaptive selection. Thus (1) there is no apparent loss of function of GH in man compared with non-primates, (2) after the episode of rapid change the rate of evolution fell towards the slow basal level that is seen for most mammalian GHs, (3) the accelerated rate of substitution for the exons of the GH gene significantly exceeds that for introns, and (4) the amino acids contributing to the hydrophobic core of GH are strongly conserved when higher primate and other GH sequences are compared, and for coding sequences other than that coding for hydrophobic core residues the rate of substitution for non-synonymous sites (K(A)) is significantly greater than that for synonymous sites (K(S)). In slow loris, as in most non-primate mammals, there is no evidence for duplication of the GH gene, but in marmoset, as in rhesus monkey and man, the putative GH gene is one of a cluster of closely related genes.

Animals↗

PubMedDate not supplied

[Ecosystem evolution: main stages and potential mechanisms].

Major differences between the Western and "Russian" (Zavarzin, 1995) paradigms in ecology and evolutionary biology are described. The "Russian" paradigm suggests that there exist two, rather than one, quite independent lineages--species evolution and ecosystem evolution. This is based on the idea that life may exist just as a nutrient cycle. The main terms and concepts of the "Russian" paradigm are defined more exactly. An attempt is made to develop this paradigm so that it would be possible to describe not only phenomenology, but also mechanisms of ecosystem evolution. To simplify evolutionary phenomena logically, it is suggested to use the concept of conditionally complete causal explanation (Lekevicius, 1984; 1985), i.e. deduce evolutionary mechanisms from major principles of functioning. This methodology is adapted to model the main stages of the evolution of nutrient cycles (3.8-2.0 bln. y.a.) and the appearance and evolution of biophagy (1.7-0 bln. y.a.). Based on a multitude of examples, it is shown that these are functional constraints that are the forces directing evolution; those constraints emerge during the interaction of organisms and while the latter interact with the abiotic environment. Since the structure of an ecosystem is non-rigid, each species is able to accumulate features useful to both an ecosystem and itself. Those are individuals that die and reproduce, whereas all structures, from macromolecules to ecosystems, evolve.

Animals↗

PubMed2001

The human genome and the human control of natural evolution.

Recent advances in research on the Human Genome are provoking many critical problems in the global policy regarding the future status of human beings as well as in that of the whole life system on the earth, and consequently, these advances provoke the serious bioethical and philosophical questions. Firstly, how can we comprehend that we are going to have the complete technology to manipulate the system of the human genome and other non-human genomes? Though no science and technology can be complete, we will, I believe, take possession of an almost complete gene technology in the early stage of the next Century. Gene technology will soon fall into the hands of human beings instead of rendering in the province of God. Secondly, which gene technologies will we actually realize and utilize in the early stages of the 21st Century? Most probably, we will adopt these technologies to health care to treat some apparent bodily diseases, for instance, cancer, hemophilia, ADA deficiency, and so forth, and sooner or later we will adopt gene therapy to germ lines, which, in the long run, suggests the possibility of a future "artificial evolution" instead of the "natural evolution" of the past. Thirdly, how is the new concept of "artificial evolution" justified ethically? I believe this kind of manmade evolution is the only way for human beings to survive into the future global environment. There cannot be any serious ethical objection against the idea of artificial evolution. Fourthly, what is the background philosophy for the concept of "artificial evolution"? I will discuss the nature of modern European humanism with individual dignity and fundamental human rights which has led the philosophy of modern culture and modern society, and I will conclude by suggesting that we should abolish an essential part of modern humanism and newly devise some alternative philosophy to fit the new Millennium.

Biological Evolution↗

PubMed2005

[The influence of Janicki cercomer theory on the development of platyhelminthes systematics and evolution investigations].

The aim of this article was to present the development of ideas about the provenience of parasitic helminths and the phylogenetical relationships within this taxon, since the publication of the "cercomer theory" just to nowadays. The following essentials of the Janicki theory are outlined: main differences between free-living Turbellaria and parasitic platyhelminths (ciliated epithelium in Turbellaria versus unciliated surface in the others); universality of the cercomer presence in Monogenea, Digenea and Cestoda; evolutionary changes in the morphology and function of the cercomer; homology of the caudal appendices of all parasitic helminths; the subsequent evolution of parasitic platyhelminthes from the ancestor to Monogena, Digenea and Cestoda; proposition to establish a new common taxon--Cercomerophora--for these three groups. In this background the evolution of evolutionary ideas is reviewed, divided into two periods: up to the eighties of the XX century, and up to date. The first period can be characterised by the criticism of some points of the "cercomer theory" and formulation of some new hypotheses; these are those of Fuhrmann, Bychovsky, Llewellyn, Price and Malmberg, which: questioned the homology of the cercarial tail with the caudal appendices of Monogenea and Cestoda; rejected Digenea from the common group; established the common taxon--Cercomeromorpha--comprising only Monogenea and Cestoda; opposed the idea of radial evolution of three main groups of Platyhelmithes (Turbellaria, Digenea and Cercomeromorpha) to the idea of subsequent evolution presented by Janicki. The differences between these last hypotheses are also underlined, arising mainly from the different ideas on the importance of particular features as the evolutionary indicators of affinities between and within the taxons. As to the hypotheses dealing with the evolution of particular groups of parasitic platyhelminths formulated at the same period, the publications of Freeman and Jarecka (Cestoda), Heynemann, Ginetsinskaja, Pearson, Cable, Rhode and Gibson (Trematoda), Bychovsky, Lambert and Malmberg (Monogenea) are referred, with special emphasises on the differences in the ideas presented by their authors. In the second period two points are underlined: a dynamic development of new techniques and methods (including molecular investigations) allowing to gather more and more different data on the parasites, and, as a consequence of this phenomenon, a new approach to the evolutionary problems--the birth of numeric and phylogenetic systematics. In this period "the cercomer theory", as well as supporting the group Cercomeromorphae generally are not accepted (exception: Brooks et al.). In contrast, the new taxon--Neodermata has been created by Ehlers. The importance of this publication for further evolutionary study is stressed. In this background some publications are quoted, especially those, presenting the results of searching for monophyletic groups and joining them in hieratic kladograms (Brooks and al., Rohde at al., Littlewood at al., and the others). It is stated, that in spite of some differences in the kladograms builded by various authors (resulting mainly from the set of features being analysed) the monophyly of big taxons of Neodermata (Trematoda, Monogenea, Cestoda) is fairly well documented. In conclusion several points connected with the "cercomer theory" are emphasized. It is now obvious, that the base of this theory--homology of caudal appendices of Janicki's Cercomerophora has to be rejected, as well as his concept of subsequent evolution of Platyhelminthes. But the base of his joining of Monogena, Trematoda (in his theory--Digenea) and Cestoda in one group (lack of cilia on the body surface), opposite to the Turbellaria (ciliary ephitelium) is maintained by the creation of Neodermata, undoubtedly documented better and in a different way. Also his idea (after many years of rejecting) on close affinity of Digenea and Cestoda seems to have returned due to the study of Lockyer at al., who write: "Among the Neodermata, the Cercomeromorphae (Cestoda + Monogenea) was not supported, whereas Cestoda + Trematoda was supported".

Animals↗

PubMed1988

Evolution of cancer genes as a mutation-driven process.

Cancer is primarily a somatic genetic disease resulting from the accumulation of several precancerous mutations in a cell lineage. The evolution of highly oncogenic retroviruses has been used as a model for the evolution of a cancer cell. The properties of intermediates between one set of replication-competent retrovirus and protooncogene progenitors and the homologous highly oncogenic retrovirus were analyzed to differentiate between selection-driven and mutation-driven models of this evolution. In this case and in some other cases where sufficient data are available, it appears that the intermediates in the evolution of highly oncogenic retroviruses are not transforming, indicating that they were not formed in a purely selection-driven process. Furthermore, analysis of retrovirus mutation rates indicates that there is a high rate of mutation in retrovirus replication such that the evolution of highly oncogenic retroviruses could be mutation-driven. Other evidence is mentioned suggesting that oncogenesis in general is at least partially mutation-driven, although mutational mechanisms are involved that are different from those involved in the evolution of highly oncogenic retroviruses.

Biological Evolution↗

PubMedDate not supplied

[Biopolymers and evolution].

Biopolymers are usually studied being extracted from the whole system of a cell or of an organism. Some important features are lost during such a procedure. It is necessary to take into account the behavior of proteins and nucleic acids in metabolic networks and to investigate their evolution. The substitutions of amino-acids metabolic networks residues are biologically possible in the polypeptides and proteins if they do not influence their spatial structure and function. The correlations of the primary structure with these properties are degenerate. The protein can be treated as "an edited statistical copolymer" (Ptitsyn). In the process of "edition" an important role is played by the ions of transient metals. Nucleic acids possess similar properties. It can be shown that the deleterious mutations of proteins can be compensated by the changes of their amount, spatial and temporal characteristics of the synthesis. Not only the structure of the protein is important but also the exact answers of the questions: how much, when and where? The contemporary theory of evolution unites phylogeny and onthogeny. The directionality of evolution is determined both by natural selection and by the already existing structure of an organism. Hence many characters are not adaptive. This is valid also for the molecular level of the structure. Thus three independent groups of facts and suggestions are presented, which confirm the neutral theory of evolution (Kimura) and elucidate its physical meaning. The molecular evolution does not coincide with the biological evolution.

Amino Acid Sequence↗