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At least 235 records · Page 13Linked to original sources
PubMed2003

Gene duplication and other evolutionary strategies: from the RNA world to the future.

Beginning with a hypothetical RNA world, it is apparent that many evolutionary transitions led to the complexity of extant species. The duplication of genetic material is rooted in the RNA world. One of two major routes of gene amplification, retroposition, originated from mechanisms that facilitated the transition to DNA as hereditary material. Even in modern genomes the process of retroposition leads to genetic novelties including the duplication of protein and RNA coding genes, as well as regulatory elements and their juxtapositon. We examine whether and to what extent known evolutionary principles can be applied to an RNA-based world. We conclude that the major basic Neo-Darwinian principles that include amplification, variation and selection already governed evolution in the RNA and RNP worlds. In this hypothetical RNA world there were few restrictions on the exchange of genetic material and principles that acted as borders at later stages, such as Weismann's Barrier, the Central Dogma of Molecular Biology, or the Darwinian Threshold were absent or rudimentary. RNA was more than a gene: it had a dual role harboring, genotypic and phenotypic capabilities, often in the same molecule. Nuons, any discrete nucleic acid sequences, were selected on an individual basis as well as in groups. The performance and success of an individual nuon was markedly dependent on the type of other nuons in a given cell. In the RNA world the transition may already have begun towards the linkage of nuons to yield a composite linear RNA genome, an arrangement necessitating the origin of RNA processing. A concatenated genome may have curbed unlimited exchange of genetic material; concomitantly, selfish nuons were more difficult to purge. A linked genome may also have constituted the beginning of the phenotype/genotype separation. This division of tasks was expanded when templated protein biosynthesis led to the RNP world, and more so when DNA took over as genetic material. The aforementioned barriers and thresholds increased and the significance and extent of horizontal gene transfer fluctuated over major evolutionary transitions. At the dawn of the most recent transformation, a fast evolutionary transition that we will be witnessing in our life times, a form of Lamarckism is raising its head.

Animals↗
PubMed2003

Evolutionary psychology and developmental dynamics: comment on Lickliter and Honeycutt (2003).

Evolutionary psychology provides a cogent metatheory for psychological science. It has furnished compelling theories of major domains of human functioning, including mating, parenting, kinship, morality, cooperation, conflict, aggression, and aesthetics. It has produced hundreds of empirical discoveries missed entirely by prior psychologists. Developmental dynamics, properly conceived, can add to the theoretical foundation of evolutionary psychology. But it has not provided alternative theories capable of explaining the many detailed empirical discoveries made by evolutionary' psychologists. Nor has it generated a comparable bounty of new empirical discoveries. By critical scientific standards--theoretical cogency, predictive accuracy, interdisciplinary consistency, and empirical harvest--modern evolutionary psychology fares well compared with alternatives.

Biological Evolution↗
PubMed2003

Evolutionary capacitance as a general feature of complex gene networks.

An evolutionary capacitor buffers genotypic variation under normal conditions, thereby promoting the accumulation of hidden polymorphism. But it occasionally fails, thereby revealing this variation phenotypically. The principal example of an evolutionary capacitor is Hsp90, a molecular chaperone that targets an important set of signal transduction proteins. Experiments in Drosophila and Arabidopsis have demonstrated three key properties of Hsp90: (1) it suppresses phenotypic variation under normal conditions and releases this variation when functionally compromised; (2) its function is overwhelmed by environmental stress; and (3) it exerts pleiotropic effects on key developmental processes. But whether these properties necessarily make Hsp90 a significant and unique facilitator of adaptation is unclear. Here we use numerical simulations of complex gene networks, as well as genome-scale expression data from yeast single-gene deletion strains, to present a mechanism that extends the scope of evolutionary capacitance beyond the action of Hsp90 alone. We illustrate that most, and perhaps all, genes reveal phenotypic variation when functionally compromised, and that the availability of loss-of-function mutations accelerates adaptation to a new optimum phenotype. However, this effect does not require the mutations to be conditional on the environment. Thus, there might exist a large class of evolutionary capacitors whose effects on phenotypic variation complement the systemic, environment-induced effects of Hsp90.

Adaptation, Physiological↗
PubMed2004

Genetic changes associated with floral adaptation restrict future evolutionary potential.

A commonly accepted evolutionary principle is that adaptive change constrains the potential directions of future evolutionary change. One manifestation of this is Dollo's law, which states that character elimination is irreversible. Although the common occurrence of irreversibility has been documented by phylogenetic analyses of phenotypic transitions, little is known about the underlying causes of this phenomenon. One explanation for evolutionary irreversibility relies on the fact that many characteristics result from interactions between multiple gene products. Such characteristics may often be eliminated by inactivation of just one gene in the network. If they serve no other functions, other genes of the network are then free to accumulate mutations or evolve new functions. Evolutionary change after character loss results in the accumulation of redundant loss-of-function mutations. Such pathway degeneration makes it very unlikely that the characteristic will re-evolve, because multiple simultaneous mutations would be required. Here we describe what appear to be the initial stages of such degeneration in the anthyocyanin pigment pathway associated with an adaptive change from blue to red flowers in the morning glory Ipomoea quamoclit.

Adaptation, Physiological↗
PubMed2005

Molecular and quantitative genetic divergence among populations of house mice with known evolutionary histories.

Evolutionary biologists have long been interested in the processes influencing population differentiation, but separating the effects of neutral and adaptive evolution has been an obstacle for studies of population subdivision. A recently developed method allows tests of whether disruptive (ie, spatially variable) or stabilizing (ie, spatially uniform) selection is influencing phenotypic differentiation among subpopulations. This method, referred to as the F(ST) vs Q(ST) comparison, separates the total additive genetic variance into within- and among-population components and evaluates this level of differentiation against a neutral hypothesis. Thus, levels of neutral molecular (F(ST)) and quantitative genetic (Q(ST)) divergence are compared to evaluate the effects of selection and genetic drift on phenotypic differentiation. Although the utility of such comparisons appears great, its accuracy has not yet been evaluated in populations with known evolutionary histories. In this study, F(ST) vs Q(ST) comparisons were evaluated using laboratory populations of house mice with known evolutionary histories. In this model system, the F(ST) vs Q(ST) comparisons between the selection groups should reveal quantitative trait differentiation consistent with disruptive selection, while the F(ST) vs Q(ST) comparisons among lines within the selection groups should suggest quantitative trait differentiation in agreement with drift. We find that F(ST) vs Q(ST) comparisons generally produce the correct evolutionary inference at each level in the population hierarchy. Additionally, we demonstrate that when strong selection is applied between populations Q(ST) increases relative to Q(ST) among populations diverging by drift. Finally, we show that the statistical properties of Q(ST), a variance component ratio, need further investigation.

Animals↗
PubMed2006

The active evolutionary lives of echinoderm larvae.

Echinoderms represent a researchable subset of a dynamic larval evolutionary cosmos. Evolution of echinoderm larvae has taken place over widely varying time scales from the origins of larvae of living classes in the early Palaeozoic, approximately 500 million years ago, to recent, rapid and large-scale changes that have occurred within living genera within a span of less than a million years to a few million years. It is these recent evolutionary events that offer a window into processes of larval evolution operating at a micro-evolutionary level of evolution of discrete developmental mechanisms. We review the evolution of the diverse larval forms of living echinoderms to outline the origins of echinoderm larval forms, their diversity among living echinoderms, molecular clocks and rates of larval evolution, and finally current studies on the roles of developmental regulatory mechanisms in the rapid and radical evolutionary changes observed between closely related congeneric species.

Animals↗
PubMed2005

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

Biological Evolution↗
PubMed1989

Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.

All extant organisms are though to be classified into three primary kingdoms, eubacteria, eukaryotes, and archaebacteria. The molecular evolutionary studies on the origin and evolution of archaebacteria to date have been carried out by inferring a molecular phylogenetic tree of the primary kingdoms based on comparison of a single molecule from a variety of extant species. From such comparison, it was not possible to derive the exact evolutionary relationship among the primary kingdoms, because the root of the tree could not be determined uniquely. To overcome this difficulty, we compared a pair of duplicated genes, elongation factors Tu and G, and the alpha and beta subunits of ATPase, which are thought to have diverged by gene duplication before divergence of the primary kingdoms. Using each protein pair, we inferred a composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely. The inferred composite trees reveal that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases. By bootstrap resamplings, this relationship is reproduced with probabilities of 0.96, 0.79, 1.0, and 1.0 for elongation factors Tu and G and for ATPase subunits alpha and beta, respectively. There are also several lines of evidence for the close sequence similarity between archaebacteria and eukaryotes. Thus we propose that this tree topology represents the general evolutionary relationship among the three primary kingdoms.

Adenosine Triphosphatases↗
PubMed1999

Evolutionary consequences of niche construction and their implications for ecology.

Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

Alleles↗
PubMed2003

The power of evo-devo to explore evolutionary constraints: experiments with butterfly eyespots.

Examples of adaptive radiation by Darwinian evolution will always enthral, and the theory of natural selection binds the whole of biology. But is selection all-powerful? Evolutionary developmental biology is beginning to provide the background to understanding how the internal organisation of organisms can influence the tempo and direction of evolutionary change. Do the mechanisms that generate the phenotype channel, bias or limit morphological evolution? The formation of eyespots on the wings of the butterfly Bicyclus anynana is a process which is becoming comparatively well understood from the genetical, developmental and ecological perspectives. We have begun to combine this knowledge with artificial selection experiments to examine the rates at which morphological changes of a particular eyespot pattern in different directions can be achieved. Our initial selection experiment performed over twenty-five generations has shown that in contrast to predictions based on shared genetical and developmental properties, two butterfly eyespots on the same wing surface can be freely uncoupled from each other with respect to their pattern of relative sizes. This flexibility in development and in response to selection may occur because our base population is part of a lineage with a long legacy of natural selection building up genetic variation that enables independent behaviour for eyespot size, and thus it no longer reflects a tightly modular organisation of eyespots as may well have existed close to their evolutionary origin in basal Lepidoptera. Comparisons can be made between such descriptions of the potential for short-term changes in morphology in B. anynana and observed patterns of divergence among all extant species in this species-rich genus. Being able to map phenotypes onto genotypes via developmental processes provides a powerful basis for exploring genetical and developmental constraints. This will eventually lead to examples of evolutionary constraints that represent more than 'just-so' stories, and thus to a more balanced view of Darwinian evolution.

Journal Article↗
PubMed2004

Evolutionary medicine.

Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

Adaptation, Biological↗
PubMedDate not supplied

Toward an evolutionary forensic psychology.

Most theories of crime have not explored intensively biological and especially evolutionary explanations for criminal behavior. Ellis presents a valuable new perspective that proposes that attention to physiological mechanisms shaped by evolutionary forces can provide insights into the causes of crime and sex differences in the patterns of crime. We discuss other theories and research relevant to Ellis' theory. We also propose that an evolutionary psychological perspective of crime will help to invigorate research and lead to a better understanding of criminality. An integrated evolutionary forensic psychology will help to explain sources of conflict between individuals, situations in which conflict leads to victimization, and victim defenses and coping mechanisms.

Age Factors↗
PubMed2003

Erasmus Darwin, Herbert Spencer, and the origins of the evolutionary worldview in British provincial scientific culture, 1770-1850.

The significance of Herbert Spencer's evolutionary philosophy has been generally recognized for over a century, as the familiarity of his phrase "survival of the fittest" indicates, yet accounts of the origins of his system still tend to follow too closely his own description, written many decades later. This essay argues that Spencer's own interpretation of his intellectual development gives an inadequate impression of the debt he owed to provincial scientific culture and its institutions. Most important, it shows that his evolutionism was originally stimulated by his association with the Derby philosophical community, for it was through this group--of which his father, who also appears to have espoused a deistic evolutionary theory, was a member--that he was first exposed to progressive Englightenment social and educational philosophies and to the evolutionary worldview of Erasmus Darwin, the first president of the Derby Philosophical Society. Darwin's scheme was the first to incorporate biological evolution, associationist psychology, evolutionary geology, and cosmological developmentalism. Spencer's own implicit denials of the link with Darwin are shown to be implausible in the face of Darwin's continuing influence on the Derby savants, the product of insecurity in his later years when he feared for his reputation as Lamarckism became increasingly untenable.

Biological Evolution↗
PubMed2004

Shared and unique features of evolutionary diversification.

A fundamental question in evolutionary biology asks whether organisms experiencing similar selective pressures will evolve similar solutions or whether historical contingencies dominate the evolutionary process and yield disparate evolutionary outcomes. It is perhaps most likely that both shared selective forces as well as unique histories play key roles in the course of evolution. Consequently, when multiple species face a common environmental gradient, their patterns of divergence might exhibit both shared and unique elements. Here we describe a general framework for investigating and evaluating the relative importance of these contrasting features of diversification. We examined morphological diversification in three species of livebearing fishes across a predation gradient. All species (Gambusia affinis from the United States of America, Brachyrhaphis rhabdophora from Costa Rica, and Poecilia reticulata from Trinidad) exhibited more elongate bodies, a larger caudal peduncle, and a relatively lower position of the eye in predator populations. This shared response suggests that common selective pressures generated parallel outcomes within three different species. However, each species also exhibited unique features of divergence, which might reflect phylogenetic tendencies, chance events, or localized environmental differences. In this system, we found that shared aspects of divergence were of larger magnitude than unique elements, suggesting common natural selective forces have played a greater role than unique histories in producing the observed patterns of morphological diversification. Assessing the nature and relative importance of shared and unique responses should aid in elucidating the relative generality or peculiarity in evolutionary divergence.

Animals↗
PubMed2006

Biological stoichiometry: a chemical bridge between ecosystem ecology and evolutionary biology.

The mission of the American Society of Naturalists is "to advance and diffuse knowledge of organic evolution and other broad biological principles so as to enhance the conceptual unification of the biological sciences." In this article, I argue that the area of biology least integrated with knowledge of organic evolution is the field of ecosystem ecology, as evidenced by a semiquantitative literature survey of use of terms in the scientific literature. I present an overview of recent theoretical developments and empirical findings in the emerging field of biological stoichiometry (the study of the balance of energy and multiple chemical elements in living systems). These developments hold some promise as a means to conceptually integrate ecosystem ecology, with its emphasis on flows and pools of energy and chemical elements, with evolutionary biology, with its emphasis on genetic fitness and the biochemical products of the genome. For example, recent evidence indicates that organismal C : P and N : P ratios have a major impact on biologically mediated flows of energy and phosphorus; in turn, variations among taxa in these ratios are connected to evolved differences in organismal growth rate because of the connection between growth rate and the need for increased allocation to P-rich ribosomal RNA. In this way, evolutionary change in growth-related traits, by altering organismal P requirements, has direct biogeochemical implications, while ecosystem conditions can constrain evolutionary acceleration of growth rates by imposing a direct P limitation on production of the needed biochemical machinery of growth. Thus, stoichiometric theory provides a broad biological principle that can interconvert the currencies and concerns of ecosystem ecology and evolutionary biology, facilitating integration of diverse fields of study and contributing to conceptual unification of the biological sciences.

Biological Evolution↗
PubMed2026

MaizeGDB Phylostrata Tool: exploring evolutionary origins of maize proteins.

MOTIVATION: Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics. RESULTS: We developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of proteins in maize (Zea mays), a globally important crop and model organism. This tool features interactive visualizations and detailed gene pages incorporating subcellular localization, Gene Ontology (GO) terms, and links to resources for homologs, facilitating comparison of gene functions across evolutionary time. The tool also provides downloadable links for full-proteome phylostratigraphic results for 26 maize inbreds (B73 and the NAM founders). From these, we identified genome- and subgenome-wide trends, finding that more conserved proteins tended to be longer and more highly expressed. Finally, we provide code including updates to the "phylostratr" R package to make it more robust against taxonomic updates, as well as example scripts for phylostratigraphic analysis and web tool development for researchers and curators of other species. AVAILABILITY AND IMPLEMENTATION: The MaizeGDB Phylostrata Tool is freely available at https://phylostrata.maizegdb.org. Scripts used for the analysis and web tool are available at https://github.com/LTibbs/PhylostrataWebtool.

Journal Article↗
PubMed1993

TREECON: a software package for the construction and drawing of evolutionary trees.

A package of programs (run by a management program called TREECON) was developed for the construction and drawing of evolutionary trees. The program MATRIX calculates dissimilarity values and can perform boostrap analysis on nucleic acid sequences. TREE implements different evolutionary tree constructing methods based on distance matrices. Because some of these methods produce unrooted evolutionary trees, a program ROOT places a root on the tree. Finally, the program DRAW draws the evolutionary tree, changes its size or topology, and produces drawings suitable for publication. Whereas, MATRIX is suited only for nucleic acids, the modules TREE, ROOT and DRAW are applicable to any kind of dissimilarity matrix. The programs run on IBM-compatible microcomputers using the DOS operating system.

Algorithms↗
PubMed2003

RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events.

SUMMARY: RED-T is a Java application for phylogenetic analysis based on a unique method, RED, that utilizes the ratios of evolutionary distances E(d) to distinguish between alternative evolutionary histories. RED-T allows the user to examine if any given experimental gene shares the same evolutionary history as the designated control gene(s). Moreover, the tool detects any differences in evolutionary history and allows the user to examine comparisons of E(d) for a likely explanation. Lateral gene transfer, which may have a significant influence in organismal evolution is one mechanism that could explain the findings of these RED-T analyses. AVAILABILITY: The application is available online at http://www.arches.uga.edu/~whitman/RED.

Biological Evolution↗