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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↗
PubMed1990

[Quantitative analysis of the teleost brain: evolution and adaptation. 1. A comparative interspecies study].

The intraspecific brain-body weight allometric coefficient, although high in Teleosts (0.49), is different enough from the interspecific one (0.65, almost 2/3) to use only adult specimens for quantitative studies. The low encephalization level of species of great size makes the use of a quadratic curve preferable, although not well adapted to small species. The mean variability of encephalization indices within the species is 8%. Differences of encephalization are noted either between sexes (Misgurnus fossilis) or between ecological milieus (Ictalurus melas). The variability increases progressively from species to genus, family and order; the allometric coefficient grows also, following the general trend for a larger encephalization when the body size is greater. The correlation between the encephalization index and the position within the classification is low; the great number of exceptions makes it necessary to look for other biological and ecological factors, such as the body form, the type of locomotion, the general activity level, the food habits, the way fishes avoid predation and social organization. The index value is due either to the modification of the body size (overweight due to the elongated form of the body, the ballast of poor diets: limivores, coral or sponge eaters, the passive protection against predators of thick scales, spines, etc), or to that of the brain size. In that case, a better encephalization is to be noted in species with a fusiform body, swimming with lateral beats of the caudal peduncle, in active species from mid-waters or pelagic, in predators actively hunting their prey, in species using active ways of protection against predation, in diurnal fishes and in those which have a social way of life needing a good knowledge either of their milieu (territorial behaviour) or of their congeners (social behaviour).

Animals↗
PubMed1997

Sequence divergence of measles virus haemagglutinin during natural evolution and adaptation to cell culture.

Phylogenetic analysis of the sequence of the H gene of 75 measles virus (MV) strains (32 published and 43 new sequences) was carried out. The lineage groups described from comparison of the nucleotide sequences encoding the C-terminal regions of the N protein of MV were the same as those derived from the H gene sequences in almost all cases. The databases document a number of distinct genotype switches that have occurred in Madrid (Spain). Well-documented is the complete replacement of lineage group C2, the common European genotype at that time, with that of group D3 around the autumn of 1993. No further isolations of group C2 took place in Madrid after this time. The rate of mutation of the H gene sequences of MV genotype D3 circulating in Madrid from 1993 to 1996 was very low (5 x 10(-4) per annum for a given nucleotide position). This is an order of magnitude lower than the rates of mutation observed in the HN genes of human influenza A viruses. The ratio of expressed over silent mutations indicated that the divergence was not driven by immune selection in this gene. Variations in amino acid 117 of the H protein (F or L) may be related to the ability of some strains to haemagglutinate only in the presence of salt. Adaptation of MV to different primate cell types was associated with very small numbers of mutations in the H gene. The changes could not be predicted when virus previously grown in human B cell lines was adapted to monkey Vero cells. In contrast, rodent brain-adapted viruses displayed a lot of amino acid sequence variation from normal MV strains. There was no convincing evidence for recombination between MV genotypes.

Animals↗
PubMed1998

Adaptive mutation: has the unicorn landed?

Reversion of an episomal Lac- allele during lactose selection has been studied as a model for adaptive mutation. Although recent results show that the mutations that arise during selection are not "adaptive" in the original sense, the mutagenic mechanism that produces these mutations may nonetheless be of evolutionary significance. In addition, a transient mutational state induced in a subpopulation of starving cells could provide a species with a mechanism for adaptive evolution.

Adaptation, Biological↗
PubMed1998

Barriers to horizontal gene transfer by natural transformation in soil bacteria.

Bacteria can utilize horizontally transferred DNA from other bacterial species to adapt and evolve to their changing environments. Natural transformation is a process that allows bacteria, which are able to express a regulated physiological state of competence, to take up and integrate free DNA from their surroundings. This uptake of DNA does not necessarily depend on DNA sequence, thus, indicating the potential of gene transfer from diverged donor organisms. Barriers active against such interspecies transfer are present at different phases of the transformation process. The functionality of these barriers will be discussed, and seen in relation to mechanisms that may enable bacterial cells to respond to environmental stress by adaptive evolution.

Adaptation, Biological↗
PubMed2026

Structural genome variation drives adaptation of the xylose-fermenting yeast Scheffersomyces stipitis to lignocellulosic hydrolysates.

Second-generation (2G) bioethanol from lignocellulosic feedstocks is a sustainable alternative to fossil fuels. However, its production is constrained by the poor performance of industrial microbes in hydrolysates that are generated during biomass pretreatment. Scheffersomyces stipitis is a native xylose fermenting yeast and a promising platform for 2G bioethanol production, and adaptive evolution under hydrolysate stress has yielded strains with enhanced performance. However, the chromosomal basis of this adaptation is unknown. Here, we demonstrate that chromosome scale structural variation, rather than point mutations, underlies the improved phenotype of the evolved strains. By integrating long- and short-read genome sequencing, we identify two major chromosomal rearrangements in the top performing isolate: a reciprocal translocation between chromosomes 1 and 2 that disrupts the NUDIX hydrolase gene YSA1, and the formation of a mitotically stable 175 kb minichromosome derived from chromosome 5. Functional analyses show that disruption of YSA1 enhances xylose utilisation and ethanol yield, while the minichromosome contributes to improved performance in hydrolysate conditions. These findings provide direct evidence that balanced rearrangements and minichromosome formation can be selected during prolonged stress and can generate adaptive phenotypes. Taken together, our study establishes genome reorganisation as a key driver of adaptation in S. stipitis.

Xylose↗
PubMed1997

Detection of convergent and parallel evolution at the amino acid sequence level.

Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sites that have experienced convergent or parallel changes on independent evolutionary lineages can then be identified by comparing the amino acids at the beginning and end of each lineage. At present, the efficiency of the methods of ancestral sequence inference in identifying convergent and parallel changes is unknown. More seriously, when we identify convergent or parallel changes, it is unclear whether these changes are attributable to random chance. For these reasons, claims of convergent and parallel evolution at the amino acid sequence level have been disputed. We have conducted computer simulations to assess the efficiencies, of the parsimony and Bayesian methods of ancestral sequence inference in identifying convergent and parallel-change sites. Our results showed that the Bayesian method performs better than the parsimony method in identifying parallel changes, and both methods are inefficient in identifying convergent changes. However, the Bayesian method is recommended for estimating the number of convergent-change sites because it gives a conservative estimate. We have developed statistical tests for examining whether the observed numbers of convergent and parallel changes are due to random chance. As an example, we reanalyzed the stomach lysozyme sequences of foregut fermenters and found that parallel evolution is statistically significant, whereas convergent evolution is not well supported.

Amino Acid Sequence↗
PubMed2026

Rapid and repeated evolution of increased competitive ability in a global invader.

Rapid adaptive evolution can increase the competitive ability of invasive species in their non-native ranges. However, whether this increase is a general response and what drives it remain uncertain because the evidence is largely based on studies with limited sampling, inadequate consideration of population co-ancestry, and oversimplified estimates of competitive ability. We conduct a large-scale glasshouse experiment testing the effects of competition and drought on 100 native and 165 non-native populations of Erigeron canadensis, all genotyped to account for co-ancestry. Plants from non-native populations are significantly more competitive against other species than the conspecifics from native populations under both mesic and dry conditions. Genetic clustering indicates that the rapid evolution of competitive ability occurs independently in two out of four clusters in the non-native range. This advantage is present only during interspecific interactions and is absent during intraspecific competition. Repeated evolution of increased competitive ability suggests that adaptation following introduction can reshape species interactions and promote invasion success, even under future drought conditions, highlighting the importance of rapid evolution in determining the ecological impacts of invasive plants.

Biological Evolution↗