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PubMed1997

Hierarchical organization of biological systems and the structure of adaptation in evolution and tumorigenesis.

Biological systems are structurally organized according to patterns repeated at each hierarchical level. Complex units are composed of so-called interactors, systems that by cooperative interaction maintain the structure of the complex unit. Interactors are composed of large numbers of assemblies of complex units of a limited number of types of a lower hierarchical level. Thus, macromolecules, cells, organisms and ecological communities should be defined as complex units, and cellular organelles, organs and oligospecies populations as the interactors between those units. The similarity of organization at each level should make it possible to describe patterns of structure at one level and apply it to organization at another level. This was tested for the structural aspects of adaptation as viewed in a pathobiological context. Adaptation is then viewed as the result of stress seen at the level of the interactors or at the level of the lower complex units related to the type of stress. Subsequently, this structure of adaptation was applied to adaptation in biological evolution and tumorigenesis, which has led to the conclusion that stress is a driving force for both and that an increase in number of organisms or cells may precede heritable changes or mutations, respectively.

Adaptation, Physiological↗
PubMed2000

Gene conversion may aid adaptive peak shifts.

Gene conversion is often viewed as a homogenizing force that opposes adaptive evolution. The objective of this study is to suggest a potential role for gene conversion in adaptive evolution of proteins through aiding the transfer of a population from one adaptive peak to another. Our hypothesis starts with the observation that a tandem gene duplication may result in an extra gene copy that is released from selective constraints. In such cases, individually deleterious mutations may accumulate on the extra copy of the gene, and through gene conversion these mutations may subsequently be presented to the functioning gene for selection en masse. Thus, groups of mutations that jointly confer a selective advantage may regularly be made available for selection. We present a mathematical model of this process and identify the range of rates of gene conversion, gene duplication and mutation under which it may operate. The results indicate that the process may be biologically feasible if the rate of appearance of the potentially beneficial mutations is not too small in relation to the rates of null mutation and of gene conversion. This process appears to be a possible mechanism for effecting adaptive peak shifts in large populations. We show that all the evolutionary steps in the proposed model may have occurred in the evolution of primate gamma -globin genes. We suggest that hide-and-release mechanisms for genetic variation may constitute a more general principal of evolvability.

Adaptation, Physiological↗
PubMed1998

Rapid speciation, morphological evolution, and adaptation to extreme environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences.

Data derived from the morphology of the seven species of South African sand lizards, Meroles (Reptilia, Lacertidae), and their outgroups produce a robust estimate of phylogeny when a maximum parsimony approach is applied. The estimate is fully resolved with little character conflict and internal branches are relatively long. This analysis indicates that Meroles is a true clade that includes the aberrant lacertid long separated as Aporosaura anchietae. The tree is pectinate, its successive external branches representing species with increasing adaptation to desert conditions, especially aeolian sand habitats. This pattern, and the robustness of the tree, support a model of invasion of severe habitats in which successive rounds of speciation, displacement, and adaptation result in spread into extreme ecological situations. To test the robust morphological phylogeny and, indirectly, the model as well, DNA from mitochondrial 12S and 16S ribosomal genes was sequenced and analyzed by both maximum parsimony and maximum likelihood approaches. Trees produced were largely congruent with that derived from morphology, although different from ones resulting from protein electrophoresis. However, in contrast to the internal branches of the morphological tree, those of the DNA maximum likelihood tree are quite short. The DNA data provide some corroboration for the relationships within Meroles based on morphology and consequently for the model as well. The disparity in internal branch lengths between the maximum parsimony morphological and maximum likelihood DNA trees may well indicate that the multiple adaptations to desert conditions arising on the main lineage of Meroles evolved quite rapidly. In this study DNA thus not only corroborates the phylogeny but also provides evidence about another aspect of evolutionary history.

Adaptation, Physiological↗
PubMed2000

Population differentiation in an annual legume: local adaptation.

Studies of many plants species have demonstrated adaptive genetic differentiation to local environmental conditions. Typically these studies are conducted to evaluate adaptation to contrasting environments. As a consequence, although local adaptation has been frequently demonstrated, we have little information as to the spatial scale of adaptive evolution. We evaluated adaptive differentiation between populations of the annual legume Chamaecrista fasciculata using a replicated common-garden design. Study sites were established in three field locations that are home to native populations of C. fasciculata. Each location was planted for two years with seed from the population native to the study site (home population) and populations located six distances (0.1-2000 km) from each site (transplanted populations). Seeds were planted into the study sites with minimum disturbance to determine the scale of local adaptation, as measured by a home-site fitness advantage, for five fitness components: germination, survival, vegetative biomass, fruit production, and the number of fruit produced per seed planted (an estimate of cumulative fitness). For all characters there was little evidence for local adaptation, except at the furthest spatial scales. Patterns of adaptive differentiation were fairly consistent in two of the three sites, but varied between years. Little genetic variation was expressed at the third site. These results, combined with previous estimates of limited gene flow, suggest that metapopulation processes and temporal environmental variation act together to reduce local adaptation, except over long distances.

Adaptation, Physiological↗
PubMed2025

Harnessing fern stress adaptations: From evolution and ecophysiology to molecular biology.

Ferns are the second most diverse vascular plant lineage after angiosperms and have been a key ecological component of Earth's biodiversity for more than 380 million years. Importantly, ferns are sister to seed plants, providing a critical outgroup for understanding the evolution of seed plant features. Ferns are remarkably resilient to abiotic and biotic stresses due to a long evolutionary history with adaptations to diverse habitats, stresses, and herbivores. As a result, ferns produce a multitude of secondary metabolites with unique bioactivities; these chemicals are potentially linked to the adaptation of ferns to herbivory, various abiotic and biotic stresses, and changing environments. Assembled reference genomes and the identification of key metabolic compounds of multiple ferns have already made significant contributions to human health and well-being. Here, we review the recent scientific advances in fern research, including evolution, stress resistance, metabolites and medicinal utilization, and comparative multi-omics applications. We propose that integrated investigations involving ecological, physiological, and molecular techniques will facilitate the future research translation of fern resources in diverse areas including soil remediation, biopesticides, and medicine. Advances in our understanding of fern molecular biology will provide new insights into the evolution of land plants and promote the utilization of ferns for heightened environmental restoration, crop protection and human health.

Ferns↗
PubMed2024

Adaptive or non-adaptive? Cranial evolution in a radiation of miniaturized day geckos.

Lygodactylus geckos represent a well-documented radiation of miniaturized lizards with diverse life-history traits that are widely distributed in Africa, Madagascar, and South America. The group has diversified into numerous species with high levels of morphological similarity. The evolutionary processes underlying such diversification remain enigmatic, because species live in different ecological biomes, ecoregions and microhabitats, while suggesting strikingly high levels of homoplasy. To underscore this evolutionary pattern, here we explore the shape variation of skull elements (i.e., cranium, jaw and inner ear) using 3D geometric morphometrics and phylogenetic comparative methods on computed tomography scans (CT-scan) of a sample encompassing almost all recognized taxa within Lygodactylus. The results of this work show that skull and inner ear shape variation is low (i.e., there is high overlapping on the morphospace) across geographic regions, macrohabitats and lifestyles, implying extensive homoplasy. Furthermore, we also found a strong influence of allometry shaping cranial variation both at intra and interspecific levels, suggesting a major constraint underlying skull architecture, probably as a consequence of its miniaturization. The remaining variation that is not allometric is independent of phylogeny and ecological adaptation and can probably be interpreted as the result of intrinsic developmental plasticity. This, in turn, supports the interpretation that speciation in this group is largely concordant with a non-adaptive hypothesis, which results mainly from vicariant processes.

Animals↗
PubMed2000

Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution.

Many pathogen recognition genes, such as plant R-genes, undergo rapid adaptive evolution, providing evidence that these genes play a critical role in plant-pathogen coevolution. Surprisingly, whether rapid adaptive evolution also occurs in genes encoding other kinds of plant defense proteins is unknown. Unlike recognition proteins, plant chitinases attack pathogens directly, conferring disease resistance by degrading chitin, a component of fungal cell walls. Here, we show that nonsynonymous substitution rates in plant class I chitinase often exceed synonymous rates in the plant genus Arabis (Cruciferae) and in other dicots, indicating a succession of adaptively driven amino acid replacements. We identify individual residues that are likely subject to positive selection by using codon substitution models and determine the location of these residues on the three-dimensional structure of class I chitinase. In contrast to primate lysozymes and plant class III chitinases, structural and functional relatives of class I chitinase, the adaptive replacements of class I chitinase occur disproportionately in the active site cleft. This highly unusual pattern of replacements suggests that fungi directly defend against chitinolytic activity through enzymatic inhibition or other forms of chemical resistance and identifies target residues for manipulating chitinolytic activity. These data also provide empirical evidence that plant defense proteins not involved in pathogen recognition also evolve in a manner consistent with rapid coevolutionary interactions.

Amino Acid Sequence↗
PubMed1998

Evolution of adaptive neural networks: the role of voltage-dependent K+ channels.

The vestibular pathway of the mollusk Hermissenda crassicornis mediates a reflexive, unconditioned response to disorientation, clinging, that has been conserved during evolution even to the emergence of our own species. This response becomes associated with a visual stimulus (mediated by a precisely ordered visual-vestibular synaptic network) according to principles of Pavlovian conditioning that are also followed in human learning. It is not entirely surprising therefore that molecular and biophysical cascades responsible for this associative learning appear to function in both mollusks and mammals. In brief, combinational elevation of (Ca2+)i, diacylglycerol, and arachidonic acid activates protein kinase C to phosphorylate the Ca2+ and guanosine triphosphate-binding protein, cp20 (now called calexcitin (Nelson T, et al. Proc Natl Acad Sci USA 1996;93:13808-13)), which potently inactivates postsynaptic voltage-dependent K+ currents and thereby increases synaptic weight. Longer term changes included rearrangement of synaptic terminals and modified protein synthesis. This cascade has also been implicated in other associative-learning paradigms (e.g., spatial maze, olfactory discrimination) and as a pathophysiologic target in early Alzheimer's disease. Recent molecular biologic experiments also demonstrate the dependence of associative memory (but not long-term potentiation) on voltage-dependent K+ currents. Theoretic learning models based on these findings focus on dendritic spine clusters and yield computer implementations with powerful pattern-recognition capabilities.

Adaptation, Physiological↗
PubMed1991

Adaptive protein evolution at the Adh locus in Drosophila.

Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1.1) in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively advantageous mutations.

Alcohol Dehydrogenase↗
PubMed1985

Limits of adaptation: the evolution of selective neutrality.

Many enzymes in intermediary metabolism manifest saturation kinetics in which flux is a concave function of enzyme activity and often of the Michaelis-Menten form. The result is that, when natural selection favors increased enzyme activity so as to maximize flux, a point of diminishing returns will be attained in which any increase in flux results in a disproportionately small increase in fitness. Enzyme activity ultimately will reach a level at which the favorable effect of an increase in activity is of the order 1/(4Ne) or smaller, where Ne is the effective population number. At this point, many mutations that result in small changes in activity will result in negligible changes in fitness and will be selectively nearly neutral. We propose that this process is a mechanism whereby conditions for the occurrence of nearly neutral mutations and gene substitutions can be brought about by the long-continued action of natural selection. Evidence for the hypothesis derives from metabolic theory, direct studies of flux, studies of null and other types of alleles in Drosophila melanogaster and chemostat studies in Escherichia coli. Limitations and complications of the theory include changes in environment or genetic background, enzymes with sharply defined optima of activity, overdominance, pleiotropy, multifunctional enzymes and branched metabolic pathways. We conclude that the theory is a useful synthesis that unites many seemingly unrelated observations. The principal theoretical conclusion is that the conditions for the occurrence of neutral evolution can be brought about as an indirect result of the action of natural selection.

Adaptation, Physiological↗
PubMed1975

Temperature as a selective factor in protein evolution: the adaptational strategy of "compromise".

Most of the important functional and structural properties of enzymes are affected by temperature. In order to maintain critical enzymic properties such as regulatory sensitivity, catalytic potential and structural stability, significant changes have been made in enzymes during evolution in different thermal regimes. Regulatory function, as typified by substrate binding ability, has been especially conservative. For a given enzyme, substrate binding ability is maintained at a relatively stable level over the entire temperature range experienced by the organism (enzyme), in spite of wide variation in substrate affinity at temperatures outside the biological range. Similarities in substrate affinity among homologues and analogues of enzymes from bacteria, invertebrates, fishes and mammals, at respective physiological temperatures for the enzymes, demonstrate the crucial importance of regulatory abilities in enzymes. Two facts, (a) that enzymes function at sub-maximal rates, and (b) that low temperature compensation is not effected by wholesale reductions in apparent Km values, argue that regulation outweighs sheer catalytic potential in enzymic function. The efficiency of an enzyme to catalyze a reaction at a rapid rate appears highest in low cell-temperature forms. The finding that catalytic efficiency is inversely correlated with enzymic heat stability suggests that enzymes with relatively great abilities to undergo conformational changes during catalysis are capable of supplying the most energy for activation events, this energy arising in part from the exergonic formation of weak bonds during the activation step in catalysis. Energy changes due to conformational changes may also be used to reduce the net enthalpy change which occurs during ligand binding, a mechanism we refer to as "coupled-compensating enthalpy changes." Comparisons of amino acid compositions of enzyme homologues and analogues from differently thermally adapted species do not reveal major differences, for example, in the overall hydrophobicity of enzymes. We propose that observed differences in enzyme thermal stability derive more from quantitative differences, i.e., differences in total numbers of secondary interactions, than from quilitative differences, i.e., differences in the relative importance of different classes of weak bonds.

Adaptation, Physiological↗
PubMed1992

Evolutionary genetics of ruminant lysozymes.

Comparative studies of mammalian lysozymes and their genes have contributed to knowledge of how new functions arise during evolution. The recruitment of lysozymes for functioning in the stomach fluid of ruminants has occurred in response to selection pressures that are partly known and on a time-scale that is known. A semiquantitative analysis of adaptive evolution is thus made possible by the ruminant lysozyme system. Large-scale production of lysozyme by the stomach lining entailed gene duplication as well as a change in gene expression. Remoulding of the lysozyme for working and lasting in the stomach fluid involved accelerated amino acid replacements, which may have been facilitated by intergenic recombination. The possibility that multigene families can accelerate adaptive evolution, by virtue of their capacity for bringing together functionally coupled substitutions, receives emphasis in this review.

Adaptation, Physiological↗
PubMed2000

Evolution of adaptive immunity.

Antigen receptors and major histocompatibility molecules, key elements required for adaptive immunity, are first seen in jawed fish. So, how did they evolve and have they changed?

Animals↗
PubMed1999

Preserved close linkage between the genes encoding troponin I and troponin T, reflecting an evolution of adapter proteins coupling the Ca(2+) signaling of contractility.

Ca(2+)-regulated motility is essential to numerous cellular functions, including muscle contraction. Systems with troponin C, myosin light chain, or calmodulin as the Ca(2+) receptor have evolved in striated muscle and other types of cells to transduce the cytoplasm Ca(2+) signals into allosteric conformational changes of contractile proteins. While these Ca(2+) receptors are homologous proteins, their coupling to the responding elements is quite different in various cell types. The Ca(2+) regulatory system in vertebrate striated muscle represents a highly specialized such signal transduction pathway consisting of the troponin complex and tropomyosin associated with the actin filament. To understand the molecular mechanism in the Ca(2+) regulation of muscle contraction and cell motility, we have revealed a preserved ancestral close linkage between the genes encoding two of the troponin subunits, troponin I and troponin T, in the genome of mouse. The data suggest that the troponin I and troponin T genes may have originated from a single locus and evolved in parallel to encode a striated muscle-specific adapter to couple the Ca(2+) receptor, troponin C, to the actin-myosin contractile machinery. This hypothesis views the three troponin subunits as two structure-function domains: the Ca(2+) receptor and the signal transducing adapter. This model may help to further our understanding of the Ca(2+) regulation of muscle contraction and the structure-function relationship of other potential adapter proteins which are converged to constitute the Ca(2+) signal transduction pathways governing nonmuscle cell motility.

Aging↗
PubMed1997

The probability of fixation in populations of changing size.

The rate of adaptive evolution of a population ultimately depends on the rate of incorporation of beneficial mutations. Even beneficial mutations may, however, be lost from a population since mutant individuals may, by chance, fail to reproduce. In this paper, we calculate the probability of fixation of beneficial mutations that occur in populations of changing size. We examine a number of demographic models, including a population whose size changes once, a population experiencing exponential growth or decline, one that is experiencing logistic growth or decline, and a population that fluctuates in size. The results are based on a branching process model but are shown to be approximate solutions to the diffusion equation describing changes in the probability of fixation over time. Using the diffusion equation, the probability of fixation of deleterious alleles can also be determined for populations that are changing in size. The results developed in this paper can be used to estimate the fixation flux, defined as the rate at which beneficial alleles fix within a population. The fixation flux measures the rate of adaptive evolution of a population and, as we shall see, depends strongly on changes that occur in population size.

Alleles↗