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PubMed2006

Thermodynamics of neutral protein evolution.

Naturally evolving proteins gradually accumulate mutations while continuing to fold to stable structures. This process of neutral evolution is an important mode of genetic change and forms the basis for the molecular clock. We present a mathematical theory that predicts the number of accumulated mutations, the index of dispersion, and the distribution of stabilities in an evolving protein population from knowledge of the stability effects (delta deltaG values) for single mutations. Our theory quantitatively describes how neutral evolution leads to marginally stable proteins and provides formulas for calculating how fluctuations in stability can overdisperse the molecular clock. It also shows that the structural influences on the rate of sequence evolution observed in earlier simulations can be calculated using just the single-mutation delta deltaG values. We consider both the case when the product of the population size and mutation rate is small and the case when this product is large, and show that in the latter case the proteins evolve excess mutational robustness that is manifested by extra stability and an increase in the rate of sequence evolution. All our theoretical predictions are confirmed by simulations with lattice proteins. Our work provides a mathematical foundation for understanding how protein biophysics shapes the process of evolution.

Computer Simulation↗

PubMed2006

The evolution of gender specialization from dimorphic hermaphroditism: paths from heterodichogamy to gynodioecy and androdioecy.

Several different pathways for the evolution of dioecy from hermaphroditism have been invoked and analyzed. These have largely considered either the spread of male- or female-sterility mutations in a monomorphic hermaphroditic population (i.e., the evolution of gynodioecy or androdioecy, respectively) or the gradual divergence in sex allocation of two classes of individuals, one that becomes increasingly male and the other that becomes increasingly female in functional gender (the paradioecy pathway). Here we assess the conditions under which male- or female-sterility mutations may invade and spread in a heterodichogamous population, that is, a dimorphic population composed of protandrous and protogynous individuals. Our model is formally applied to heterodichogamous populations, but the ideas we explore may also apply to the evolution of separate sexes in distylous species, where plants are either long- or short-styled. The model predicts that, under many circumstances, conditions for the evolution of gynodioecy and androdioecy in a heterodichogamous population are the same as those for their evolution from monomorphic populations. However, if one or the other of the two morphs are already somewhat specialized in their functional gender, as might occur if the quality or quantity of seed set is time dependent, the conditions for the invasion of males or females are relaxed. In particular, androdioecy can evolve more easily under such circumstances in heterodichogamous populations than in monomorphic hermaphroditic populations.

Evolution, Molecular↗

PubMed2001

Source-sink dynamics between transgenic and non-transgenic habitats and their role in the evolution of resistance.

The interaction of population dynamics and movement among two habitat types (toxic transgenic fields and nontoxic refuge fields) on the evolution of insecticide resistance was examined in two different simulation models. The two models were developed to test the hypothesis that increasing habitat grain from fine-grained to coarse-grained, and the resultant increase in nonrandom mating, would increase the rate of local adaptation, here the evolution of resistance. The first model, a complex, stochastic spatially explicit model, altered habitat grain by varying adult dispersal rates between habitat patches. In contrast to the expectation that increasing patch isolation and increasing the coarseness of the habitats would increase the rate of resistance evolution, intermediate levels of dispersal actually delayed resistance by as much as fivefold over the range of dispersal levels observed. Source-sink dynamics related to ovipositional patterns and the related population dynamics appear to explain the results. A simple deterministic model was developed to abstract out the separate impacts of mating and ovipositional behaviors. This model showed qualitatively the same results, although under similar assumptions it predicted much longer delays in resistance evolution. In this model, nonrandom mating alone always increased the rate at which insects adapted to transgenic crops, but nonrandom mating in combination with nonrandom oviposition could significantly delay resistance evolution. Differences between the two models may be due to the population regulation incorporated in the spatially explicit model. The models clearly suggest that resistance management programs using untreated refuges should not over-emphasize random mating at the cost of making the habitat too fine-grained.

Animals↗

PubMed2006

Niche evolution and adaptive radiation: testing the order of trait divergence.

In the course of an adaptive radiation, the evolution of niche parameters is of particular interest for understanding modes of speciation and the consequences for coexistence of related species within communities. We pose a general question: In the course of an evolutionary radiation, do traits related to within-community niche differences (alpha niche) evolve before or after differentiation of macrohabitat affinity or climatic tolerances (beta niche)? Here we introduce a new test to address this question, based on a modification of the method of independent contrasts. The divergence order test (DOT) is based on the average age of the nodes on a tree, weighted by the absolute magnitude of the contrast at each node for a particular trait. The comparison of these weighted averages reveals whether large divergences for one trait have occurred earlier or later in the course of diversification, relative to a second trait; significance is determined by bootstrapping from maximum-likelihood ancestral state reconstructions. The method is applied to the evolution of Ceanothus, a woody plant group in California, in which co-occurring species exhibit significant differences in a key leaf trait (specific leaf area) associated with contrasting physiological and life history strategies. Co-occurring species differ more for this trait than expected under a null model of community assembly. This alpha niche difference evolved early in the divergence of two major subclades within Ceanothus, whereas climatic distributions (beta niche traits) diversified later within each of the subclades. However, rapid evolution of climate parameters makes inferences of early divergence events highly uncertain, and differentiation of the beta niche might have taken place throughout the evolution of the group, without leaving a clear phylogenetic signal. Similar patterns observed in several plant and animal groups suggest that early divergence of alpha niche traits might be a common feature of niche evolution in many adaptive radiations.

Adaptation, Biological↗

PubMed2001

Evolution of the periodicity and the self-similarity in DNA sequence: a Fourier transform analysis.

Fourier transform analysis was applied to elucidate the periodical and self-similar properties in the DNA sequences mainly of beta-globin genes in different species, and the evolutionary change in those properties was then investigated. Map patterns of a two-dimensional DNA walk showed that the stretches of exons are significantly shorter than those of introns, suggesting that the evolution of exons is driven by natural selection, whereas that of introns is generated by unknown internal rules. Using a monomer analysis, we obtained the power spectra of four different bases, A, G, C, and T, in DNA sequences. Periodicities in the short- (2 to 10 base pairs [bp]), medium- (10 to 50 bp) and long-range order (50 to 300 bp) of beta-globin gene sequences could be observed, and power spectral densities of these periodicities were increased with evolution. These results suggest the existence of the internal rules in the occurrence of the synonymous and nonsynonymous substitutions in the sequences, the destabilization of the interaction between DNA and histone protein, and the stabilization of the chromatin structure, respectively. Moreover, 1/f(alpha) analysis of the power spectra (log-log plot) in the far long-range region (160 to 16,000 bp) suggested the increase in the self-similarity (the fractal structure) of DNA sequences with evolution. A general trend of the increase in a 3 bp periodicity with evolution might be functionally related to the CAG trinucleotide repeat diseases such as Huntington chorea, where a marked periodicity of 3 bp could be observed. Fourier transform analysis applied to a DNA sequence offers a great new avenue for extracting information on the evolution of a DNA sequence.

Animals↗

PubMed1998

Maize as a model system for investigating the molecular basis of morphological evolution in plants.

The genetic and molecular bases of morphological evolution in plants are largely unknown. To address questions surrounding this issue, my laboratory has been investigating the evolution of maize from its wild ancestor, teosinte. Our research suggests that a few gene changes of large effect were involved in the evolution of several different traits including plant and ear architecture and kernel color. In cases where gene function could be identified, the genes involved in maize evolution were regulatory in nature. Additional evidence suggests that changes in cis regulatory elements of the regulatory genes rather than changes in protein function underlie the evolution of the traits analyzed. Future work with other plant species, especially wild plants, will be required to test the generality of our observations with maize.

Biological Evolution↗

PubMed2000

Molecular evolution of the chalcone synthase multigene family in the morning glory genome.

Plant genomes appear to exploit the process of gene duplication as a primary means of acquiring biochemical and developmental flexibility. Thus, for example, most of the enzymatic components of plant secondary metabolism are encoded by small families of genes that originated through duplication over evolutionary time. The dynamics of gene family evolution are well illustrated by the genes that encode chalcone synthase (CHS), the first committed step in flavonoid biosynthesis. We review pertinent facts about CHS evolution in flowering plants with special reference to the morning glory genus, Ipomoea. Our review shows that new CHS genes are recruited recurrently in flowering plant evolution. Rates of nucleotide substitution are frequently accelerated in new duplicate genes, and there is clear evidence for repeated shifts in enzymatic function among duplicate copies of CHS genes. In addition, we present new data on expression patterns of CHS genes as a function of tissue and developmental stage in the common morning glory (I. purpurea). These data show extensive differentiation in gene expression among duplicate copies of CHS genes. We also show that a single mutation which blocks anthocyanin biosynthesis in the floral limb is correlated with a loss of expression of one of the six duplicate CHS genes present in the morning glory genome. This suggests that different duplicate copies of CHS have acquired specialized functional roles over the course of evolution. We conclude that recurrent gene duplication and subsequent differentiation is a major adaptive strategy in plant genome evolution.

Acyltransferases↗

PubMed2002

Experimental life-history evolution: selection on the allocation to sexual reproduction and its plasticity in a clonal plant.

Allocation to sexual reproduction is an important life-history trait in clonal plants. Different selection pressures between competitive and competition-free environments are likely to result in the evolution of specialized genotypes and to maintain genetic variation in reproductive allocation. Moreover, selection may also result in the evolution of plastic allocation strategies. The necessary prerequisite for evolution, heritable genetic variation, can best be studied with selection experiments. Starting from a base population of 102 replicated genotypes of the clonal herb Ranunculus reptans, we imposed selection on the proportion of flowering rosettes in the absence of competition (base population: mean = 0.391, broad-sense heritability = 0.307). We also selected on the plasticity in this trait in response to competition with a naturally coexisting grass in a parallel experiment (base population: 14% lower mean in the presence of competition, broad-sense heritability = 0.072). After two generations of bidirectional selection, the proportion of flowering rosettes was 26% higher in the high line than in the low line (realized heritability +/- SE = 0.205 +/- 0.017). Moreover, genotypes of the high line had 11% fewer carpels per flower, a 22% lower proportion of rooted rosettes, and a 39% smaller average distance between rosettes within a clone. In the second experiment, we found no significant responses to selection for high and low plasticity in the proportion of flowering rosettes (realized heritability +/- SE = -0.002 +/- 0.013). Our study indicates a high heritability and potential for further evolution of the proportion of flowering rosettes in R. reptans, but not for its plasticity, which may have been fixed by past evolution at its current level. Moreover, our results demonstrate strong genetic correlations between allocation to sexual reproduction and other clonal life-history characteristics.

Biological Evolution↗

PubMed2003

The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose.

The EBG system of E. coli has served as a model for the evolution of novel functions. This paper reviews the experimental evolution of the catabolism of beta-galactoside sugars in strains of E. coli that carry deletions of the classical lacZ beta-galactosidase gene. Evolution of the ebgA encoded Ebg beta-galactosidase for an expanded substrate range, evolution of the ebgR encoded Ebg repressor for sensitivity to an expanded range of inducers, the amino acid replacements responsible for those changes, and the evolutionary potential of the system are discussed. The EBG system has also served as a model for studying the detailed catalytic consequences of experimental evolution at the physical-chemical level. The analysis of free-energy profiles for the wildtype and all of the various evolved Ebg enzymes has permitted rejection of the Albery-Knowles hypothesis that relates likely changes in free-energy profiles to evolutionary change.

Crosses, Genetic↗

PubMed2003

Evolution of phenylalanyl-tRNA synthetase by domain losing.

The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs). However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing. Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryote are obviously less than those in bacteria. The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity.

Archaea↗

PubMed2004

Evolution of multihost parasites.

Multihost parasites can infect different types of hosts or even different host species. Epidemiological models have shown the importance of the diversity of potential hosts for understanding the dynamics of infectious disease (e.g., the importance of reservoirs), but the consequences of this diversity for virulence and transmission evolution remain largely overlooked. Here, I present a general theoretical framework for the study of life-history evolution of multihost parasites. This analysis highlights the importance of epidemiology (the relative quality and quantity of different types of infected hosts) and between-trait constraints (both within and between different hosts) to parasite evolution. I illustrate these effects in different transmission scenarios under the simplifying assumption that parasites can infect only two types of hosts. These simple but contrasted evolutionary scenarios yield new insights into virulence evolution and the evolution of transmission routes among different hosts. Because many of the pathogens that have large public-health and agricultural impacts have complex life cycles, an understanding of their evolutionary dynamics could hold substantial benefits for management.

Animals↗

PubMed2004

Implications of the evolution pattern of human T-cell leukemia retroviruses on their pathogenic virulence (Review).

Simian retroviruses pose a serious threat to public health, as two human pathogenic retroviruses, HIV and HTLV, have been already proved to originate from such non-human viruses. Therefore, studying their natural prevalence among wild non-human primates is important for planning strategies to prevent the emergence of additional human retroviral pathogens. This article is focused on tracing the origin and evolution of the human T-cell leukemia viruses HTLV-I and HTLV-II in comparison to that of the simian lymphotropic viruses STLV-I, STLV-II and STLV-L, which are phylo-genically classified into a common group called primate T-lymphotropic viruses (PTLV). Thus, HTLV-I and STLV-I are referred to as PTLV-I and HTLV-II and STLV-II as PTLV-II, whereas STLV-L, which is highly divergent from both HTLV types, comprises a third subgroup called PTLV-L. The phylogeny of PTLV indicates that both, HTLV-I and HTLV-II emerged from a simian origin, but their subsequent evolution continued in different patterns. HTLV-I includes 6 subtypes which evolved from STLV-I through several times of different geographic interspecies transmission between simian and human hosts. These repeated invasions to new primate species are likely to give rise to viral strains with increasing pathogenic potential. On the other hand, HTLV-II includes 4 subtypes which appear to originate from a common human ancestor virus that emerged from only one simian to human transmission, whereas the subsequent evolution of HTLV-II and STLV-II strains continued separately only within the Homo sapiens and Pan paniscus species respectively, without repeated interspecies jumps. Such evolution pattern likely involves less genetic changes and selection of viral strains with low pathogenic virulence that could co-exist with their hosts for long time. These different evolution patterns can explain the much wider implication of HTLV-I with human clinical disorders than HTLV-II. Of note, however, more recently HTLV-II started spreading much more rapidly through intravenous drug users to many geographical regions, with a 150-350 fold higher mutation rate than that of its previous strictly endemic strains. This change in the mode of the virus spread creates a serious risk for emergence of HTLV-II strains with higher virulence.

Animals↗

PubMed2004

[Evolution of language: attempt at synthesis].

There are at least three traits that distinguish modern Homo sapiens from his closest relatives: bipedal locomotion, the unusual size of his brain and the ability to use symbolic language. To this day the emergence and evolution of these traits have not been explained sufficiently. New research in anthropology, linguistics, cognitive science and other disciplines shows, that the evolution of the human language faculty is a complex field that was influenced by a wide variety of factors. This paper tries to show the width of these factors and to work out the demands that are to be met by a theory of language evolution. After the introduction, in Section 2 the evolutionary principles and their role in the evolution of symbolic communication will be reviewed. Section 3 gives an overview of the results and controversies of brain evolution research, while Section 4 introduces our current knowledge of the neuronal basis of language. In Section 5 the controversies that had the greatest impact on the field and development of ways to solve them are reviewed before Section 6 summarizes the most important preadaptations for the evolving language faculty.

Animals↗

PubMed2005

Evolution of coadaptation in a two-locus epistatic system.

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.

Biological Evolution↗

PubMedDate not supplied

[The evolution of plant life span: facts and hypotheses].

There are two different views on the evolution of life forms in Cormophyta: from woody plants to herbaceous ones or in opposite direction - from herbs to trees. In accordance with these views it is supposed that life span in plants changed in the course of evolution from many years (perennials) to few years (annuals, biennials), or went in reverse - from few years to many years. The author discusses the problems of senescence and longevity in Cormophyta in the context of various hypotheses of ageing (programmed death theory, mutation accumulation, antagonistic pleiotropy, disposable soma, genes of ageing, genes of longevity). Special attention is given to bio-morphological aspects of longevity and cases of non-ageing plants ("negative senescence", "potential immortality"). It is proposed to distinguish seven models of simple ontogenesis in Cormophyta that can exemplify the diversity of mechanisms of ageing and longevity. The evolution of life span in plants is considered as an indirect result of natural selection of other characteristics of organisms or as a consequence of fixation of modifications (episelectional evolution). It seems that short life span could emerge several times during evolution of one group of plants, thus favoring its adaptive radiation.

Biological Evolution↗

PubMed2006

A model of the evolution of dichogamy incorporating sex-ratio selection, anther-stigma interference, and inbreeding depression.

Historically, explanations for the evolution of floral traits that reduce self-fertilization have tended to focus on selection to avoid inbreeding depression. However, there is growing support for the hypothesis that such traits also play a role in promoting efficient pollen dispersal by reducing anther-stigma interference. The relative importance of these two selective pressures is currently a popular topic of investigation. To date, there has been no theoretical exploration of the relative contributions of selection to avoid the genetic costs of self-fertilization and selection to promote efficient pollen dispersal on the evolution of floral traits. We developed a population genetic model to examine the influence of these factors on the evolution of dichogamy: the temporal separation of anther maturation and stigma receptivity. Our analysis indicates that anther-stigma interference can favor dichogamy even in the absence of in-breeding depression. Although anther-stigma interference and inbreeding depression are the key forces driving the initial evolution of dichogamy, selection to match the timing of pollen dispersal to the availability of ovules at the population level becomes a more potent force opposing the further evolution of dichogamy as the extent of temporal separation increases. This result may help to explain otherwise puzzling phenomena such as why dichogamy is rarely complete in nature and why dichogamy tends to be associated with asynchronous flower presentation.

Biological Evolution↗

PubMed2006

Population demography and the evolution of helping behaviors.

Limited dispersal may favor the evolution of helping behaviors between relatives as it increases their relatedness, and it may inhibit such evolution as it increases local competition between these relatives. Here, we explore one way out of this dilemma: if the helping behavior allows groups to expand in size, then the kin-competition pressure opposing its evolution can be greatly reduced. We explore the effects of two kinds of stochasticity allowing for such deme expansion. First, we study the evolution of helping under environmental stochasticity that may induce complete patch extinction. Helping evolves if it results in a decrease in the probability of extinction or if it enhances the rate of patch recolonization through propagules formed by fission of nonextinct groups. This mode of dispersal is indeed commonly found in social species. Second, we consider the evolution of helping in the presence of demographic stochasticity. When fecundity is below its value maximizing deme size (undersaturation), helping evolves, but under stringent conditions unless positive density dependence (Allee effect) interferes with demographic stochasticity. When fecundity is above its value maximizing deme size (oversaturation), helping may also evolve, but only if it reduces negative density-dependent competition.

Altruism↗

PubMed1996

[Calculation of specific evolution rate of proteins based on phylogenetic].

A method of calculating specific protein evolution distance and evolution rate is presented. This is based on the reconstruction of the phylogenetic tree and on the deduction of ancestral sequences according to temporally homologous protein sequences. The evolution distance and evolution rate are calculated from the difference percentage of the sequence between the temporal and deduced ancestral sequences. A comparison with Dayoff simulation method and an example of using it to calculate the specific evolution rates of mammalian erythropoietin. The method presented here would be specially useful under certain circumstances.

Amino Acid Sequence↗