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PubMed2005

Genetic variation in response to an indirect ecological effect.

Indirect ecological effects (IEEs) are widespread and often as strong as the phenotypic effects arising from direct interactions in natural communities. Indirect effects can influence competitive interactions, and are thought to be important selective forces. However, the extent that selection arising from IEEs results in long-term evolutionary change depends on genetic variation underlying the phenotypic response-that is, a genotype-by-IEE interaction. We provide the first data on genetic variation in the response of traits to an IEE, and illustrate how such genetic variation might be detected and analysed. We used a model tri-trophic system to investigate the effect of host plants on two populations of predatory ladybirds through a clonal aphid herbivore. A split-family experimental design allowed us to estimate the effects of aphid host plant on ladybird traits (IEE) and the extent of genetic variation in ladybird predators for response to these effects (genotype-by-indirect environmental effect interaction). We found significant genetic variation in the response of ladybird phenotypes to the indirect effect of host plant of their aphid prey, demonstrating the potential for evolutionary responses to selection arising from the prey host.

Animals↗
PubMed2006

Genotype x environment interaction for male attractiveness in an acoustic moth: evidence for plasticity and canalization.

The lek paradox arises when choosy females deplete the genetic variance for male display traits from a population, yet substantial additive genetic variation (V(A)) in male traits persists. Thus, the lek paradox can be more generally stated as one of the most fundamental evolutionary questions: What maintains genetic variation in natural populations? One solution to this problem may be found in the condition-dependent nature of many sexually selected traits. Genotype x environment (G x E) interactions can maintain V(A) under conditions of environmental heterogeneity provided certain restrictions are met, although antagonistic pleiotropy has also been proposed as a mechanism. Here, we provide evidence for G x E interactions and against the role of antagonistic pleiotropy in the maintenance of V(A) for sexually selected traits. Using inbred lines of the lesser waxmoth Achroia grisella, we measured V(A) for song attractiveness, condition and development rate under different competitive environments and found that genotypes differed in their plasticity. We argue that variation persists in natural populations because G x E interactions prevent any one variant from producing the optimal phenotype across all environments.

Animals↗
PubMed2003

Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift.

Quantitative genetics theory provides a framework that predicts the effects of selection on a phenotype consisting of a suite of complex traits. However, the ability of existing theory to reconstruct the history of selection or to predict the future trajectory of evolution depends upon the evolutionary dynamics of the genetic variance-covariance matrix (G-matrix). Thus, the central focus of the emerging field of comparative quantitative genetics is the evolution of the G-matrix. Existing analytical theory reveals little about the dynamics of G, because the problem is too complex to be mathematically tractable. As a first step toward a predictive theory of G-matrix evolution, our goal was to use stochastic computer models to investigate factors that might contribute to the stability of G over evolutionary time. We were concerned with the relatively simple case of two quantitative traits in a population experiencing stabilizing selection, pleiotropic mutation, and random genetic drift. Our results show that G-matrix stability is enhanced by strong correlational selection and large effective population size. In addition, the nature of mutations at pleiotropic loci can dramatically influence stability of G. In particular, when a mutation at a single locus simultaneously changes the value of the two traits (due to pleiotropy) and these effects are correlated, mutation can generate extreme stability of G. Thus, the central message of our study is that the empirical question regarding G-matrix stability is not necessarily a general question of whether G is stable across various taxonomic levels. Rather, we should expect the G-matrix to be extremely stable for some suites of characters and unstable for others over similar spans of evolutionary time.

Analysis of Variance↗
PubMed2005

Effective sizes of macroparasite populations: a conceptual model.

Effective population size (N(e)) is a crucial parameter in evolutionary biology because it controls genetic drift and the response to selection. Thus, N(e) influences evolutionary processes in parasites, such as speciation, host-race formation, local host adaptation and the evolution of drug resistance. However, N(e) is a parameter that is ignored almost completely in parasitology. Our goal is to provide a conceptual framework that facilitates future studies of the N(e) of macroparasites. The key feature of macroparasite populations is that breeders are subdivided into infrapopulations. We use a model of subdivided breeders to show how some basic demographic factors that control N(e) in all species could be estimated for macroparasites. An important conclusion is that several features of parasite life cycles probably function in concert to reduce N(e) below that expected in a single free-living population of equivalent census size.

Animals↗
PubMedDate not supplied

Evolutionary robots with on-line self-organization and behavioral fitness.

We address two issues in Evolutionary Robotics, namely the genetic encoding and the performance criterion, also known as the fitness function. For the first aspect, we suggest to encode mechanisms for parameter self-organization, instead of the parameters themselves as in conventional approaches. We argue that the suggested encoding generates systems that can solve more complex tasks and are more robust to unpredictable sources of change. We support our arguments with a set of experiments on evolutionary neural controllers for physical robots and compare them to conventional encoding. In addition, we show that when also the genetic encoding is left free to evolve, artificial evolution will select to exploit mechanisms of self-organization. For the second aspect, we shall discuss the role of the performance criterion, als known as fitness function, and suggest Fitness Space as a framework to conceive fitness functions in Evolutionary Robotics. Fitness Space can be used as a guide to design fitness functions as well as to compare different experiments in Evolutionary Robotics.

Evolution, Molecular↗
PubMed1993

[The genetic language: grammar, semantics, evolution].

The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics. There is a review of these general attributes of genetic language, including also the problems of synonymy and evolution. The main directions of theoretical investigations of genetic language and neighbouring questions are formulated: (1) cryptographic problems, (2) analysis of genetic texts, (3) theoretical-linguistic problems, (4) evolutionary linguistic questions. The problem of genetic language becomes one of the key ones of molecular genetics, molecular biology and gene engineering.

Codon↗
PubMed1994

Transfer RNA mutation and the malleability of the genetic code.

We propose that evolutionary reassignment of codons is facilitated by a translationally ambiguous intermediate. For example, recently discovered tRNA mutations that allow relatively efficient simultaneous cognate and near-cognate coding (sharing 2 contiguous nt) in vivo may speed reassignment of the near-cognate codon. As predicted by this notion, characterized codon reassignments are strikingly non-random, and half can be immediately explained by unusual tRNA activities already demonstrated. In addition, sequences of reassigned tRNAs contain sequences that promote ambiguity. tRNA structural change may provide a transitional pathway that allows rapid selection of a new specificity, rather than slow mutation toward a new codon-amino acid association.

Biological Evolution↗
PubMedDate not supplied

[The modelling of the initiation of genetic damages from low doses of ionizing radiation in eukaryotic cells based on the concept of the existence of evolutionary reserve cells].

The model predicting quantitatively a dose response for genetic lesions in low dose range is presented. The model is based on the concept of programmed initiation of the genetic damage in the subpopulation of specific cells of "evolutionary reserve" (CER). It is demonstrated that complex shape of dose-response curve results from superposition of processes in different subpopulations within exposed cell population, mainly in CER. The model allows us to explain the minimum observed in the dose-response curve at doses corresponding to one (on the average) event of energy deposition per CER with spontaneous aberrations. The equation for dose-response function for dicentrics describes satisfactory experimental observations. Advantage of proposed equation is that it does not deal with free parameters to fit the data. They are determined independently by using known physical and biological characteristics. The data described allow us to suggest that sensitive body for CER is a cell as a whole. Probably, programmed initiation of genetic lesions in CER requires both two hits at cell membrane and radiation effect on cell nucleus.

Animals↗
PubMed2002

Directed evolution of a genetic circuit.

The construction of artificial networks of transcriptional control elements in living cells represents a new frontier for biological engineering. However, biological circuit engineers will have to confront their inability to predict the precise behavior of even the most simple synthetic networks, a serious shortcoming and challenge for the design and construction of more sophisticated genetic circuitry in the future. We propose a combined rational and evolutionary design strategy for constructing genetic regulatory circuits, an approach that allows the engineer to fine-tune the biochemical parameters of the networks experimentally in vivo. By applying directed evolution to genes comprising a simple genetic circuit, we demonstrate that a nonfunctional circuit containing improperly matched components can evolve rapidly into a functional one. In the process, we generated a library of genetic devices with a range of behaviors that can be used to construct more complex circuits.

DNA↗
PubMed2005

Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis.

The level of genetic differentiation within and between evolutionary lineages of the common vole (Microtus arvalis) in Europe was examined by analyzing mitochondrial sequences from the control region (mtDNA) and 12 nuclear microsatellite loci (nucDNA) for 338 voles from 18 populations. The distribution of evolutionary lineages and the affinity of populations to lineages were determined with additional sequence data from the mitochondrial cytochrome b gene. Our analyses demonstrated very high levels of differentiation between populations (overall FST: mtDNA 70%; nucDNA 17%). The affinity of populations to evolutionary lineages was strongly reflected in mtDNA but not in nucDNA variation. Patterns of genetic structure for both markers visualized in synthetic genetic maps suggest a postglacial range expansion of the species into the Alps, as well as a potentially more ancient colonization from the northeast to the southwest of Europe. This expansion is supported by estimates for the divergence times between evolutionary lineages and within the western European lineage, which predate the last glacial maximum (LGM). Furthermore, all measures of genetic diversity within populations increased significantly with longitude and showed a trend toward increase with latitude. We conclude that the detected patterns are difficult to explain only by range expansions from separate LGM refugia close to the Mediterranean. This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species.

Animals↗
PubMed2006

Concealed female external genitals: possible morpho-psychological clue to unique emotional and cognitive evolutionary matrix of man.

Despite genetic similarities between man and other anthropoids, the cognitive abilities of man are distinct. Inaccessible and concealed external female genitals are one of the morphological characteristics distinguishing humans from other higher primates. External female sexual organs in subhuman primates are visible and accessible in the habitual quadrupedal and occasional bipedal posture, whereas these organs in the human female are inaccessible and concealed in any posture. A prospective consequence of gradual bipedalism of hominids during evolution was a shifting of the external female genitals in an anterior direction. In the completely bipedal Homo sapiens, this resulted in the vulvo-cryptic phenomenon, i.e. concealed female genitals in humans. The unique morphology of the human female pelvis served as an obstacle to easy access of the male in the process of copulation, necessitating the female's conscious decision for sexual intercourse. This circumstance might have created a psychological basis for female propellant psychosexual manipulation of the male as a natural consequence. Also, through the process of positive selection it could have formed a basis for linking reproductive success with the development of cognitive and emotional capacities. Female consent to copulation is a conscious and complex act that would be impossible without the involvement of highly developed emotional-cognitive and memoric brain systems. Thus the extraordinary evolutionary strategy might imply a teleological link between concealed female genitals and the emotional-cognitive characteristics of man, creating a permanent promoter of further development of emotional and cognitive brain systems with an impact on all domains of everyday life.

Animals↗
PubMed1997

Multilocus genotypes, a tree of individuals, and human evolutionary history.

Our goal is to infer, from human genetic data, general patterns as well as details of human evolutionary history. Here we present the results of an analysis of genetic data at the level of the individual. A tree relating 144 individuals from 12 human groups of Africa, Asia, Europe, and Oceania, inferred from an average of 75 DNA polymorphisms/individual, is remarkable in that most individuals cluster with other members of their regional group. In order to interpret this tree, we consider the factors that influence the tree pattern, including the number of genetic loci examined, the length of population isolation, the sampling process, and the extent of gene flow among groups. Understanding the impact of these factors enables us to infer details of human evolutionary history that might otherwise remain undetected. Our analyses indicate that some recent ancestor(s) of each of a few of the individuals tested may have immigrated. In general, the populations within regional groups appear to have been isolated from one another for <25,000 years. Regional groups may have been isolated for somewhat longer.

Biological Evolution↗
PubMed1998

Evolutionary epidemiology and manic depression.

The reformulation of epidemiological prevalence rates as evolutionary frequency rates puts medical genetics within an explicit framework of Darwinian theory. Yet an enduring and still current assumption of genomic medicine is that genes associated with disease are necessarily maladapted. Indeed, it seems it could hardly be otherwise. However, evolutionary epidemiology has begun to uncover important and surprising counter-exemplary case-studies. Thus, the present aim is to first outline this emerging sub-discipline of 'evolutionary epidemiology'. Then, a major psychopathological syndrome--manic-depression--is examined in some detail within the purview of evolutionary epidemiology. Its medical genetics are those of an adaptive polymorphism in the human genome. Hence, genes associated with what is now a major public health problem accrued as they conferred selective advantage in phylogeny. Why should manic-depressive etiogenes have been selected? A preliminary anatomic-functional model, assembled from facts of human paleoneuropsychiatry, more adequately contextualises manic-depressive genomics and phenotypy. In this model, manic-depression finds its heuristic origins in a hierarchy of behavioural strategies stabilised in phylogeny and embedded at serial levels in the brain (Hawk-Dove ESS). A proportion of the population has variant genotypy which appears to have been favoured in social competition phylogenetically but express more pathogenic phenotypy in the current environment. The paper closes with a brief consideration of clinical practices and ethical issues as alternative considerations emerge with the syndrome recast in a more positive Darwinian light.

Adaptation, Physiological↗
PubMed2005

Evolutionary dynamics of human retroviruses investigated through full-genome scanning.

To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the human immunodeficiency virus type 1 (HIV-1) group M and the primate T-cell lymphotropic virus (PTLV) using a full-genome analysis. Evolutionary rates and nonsynonymous/synonymous substitution rate ratios were estimated across the genome using a maximum likelihood sliding window approach, and molecular clock properties were investigated. We confirm a remarkable difference in genetic stability and selective pressure at the interhost level. While there is evidence for adaptive evolution in HIV-1, the evolution of PTLV is almost exclusively characterized by negative selection or nearly neutral processes. For both retroviruses, evolutionary rate estimates across the genome reflect the differential selective constraints. However, based on the relationship between evolutionary rate and selective pressure and based on the comparison of synonymous substitution rates, the differences in rate between HIV-1 and PTLV cannot be explained by selective forces only. Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference.

Bayes Theorem↗
PubMed1978

On the physical basis for ambiguity in genetic coding interactions.

We report the relative stabilities, in the form of complex lifetimes, of complexes between the tRNAs complementary, or nearly so, in their anticodons. The results show striking parallels with the genetic coding rules, including the wobble interaction and the role of modified nucleotides S2U and V (a 5-oxyacetic acid derivative of U). One important difference between the genetic code and the pairing rules in the tRNA-tRNA interaction is the stability in the latter of the short wobble pairs, which the wobble hypothesis excludes. We stress the potential of U for translational errors, and suggest a simple stereochemical basis for ribosome-mediated discrimination against short wobble pairs. Surprisingly, the stability of anticodon-anticodon complexes does not vary systematically on base sequence. Because of the close similarity to the genetic coding rules, it is tempting to speculate that the interaction between two RNA loops may have been part of the physical basis for the evolutionary origin of the genetic code, and that this mechanism may still be utilized by folding the mRNA on the ribosome into a loop similar to the anticodon loop.

Base Sequence↗
PubMed1998

Genetic control of murine limb morphogenesis: relationships with human syndromes and evolutionary relevance.

Over the past ten years, the discovery and functional characterisation of murine Hox genes has led to a better understanding of some of the molecular mechanisms underlying limb development. It has also shed some light on the potential genetic events which have accompanied the fin-to-limb transition, an evolutionary step of critical importance which opened the way to the evolution of higher vertebrates. This convergence between developmental biology and the sciences of evolution is one of the synergistic interface that has been established recently thanks to the use of genetic engineering and transgenic animals. The increasing number of human genetic syndromes which are derived from mutations in developmental control genes remind us that many human genetic diseases are nothing else but alterations in our developmental programme. Here, we illustrate these various issues by discussing the function of Hox genes during limb development.

Animals↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗
PubMed2026

Dissecting fluctuating selection: A unified population and quantitative genetics framework.

One of the longstanding debates in evolutionary biology is the effect of fluctuating selection on genetic changes in populations. However, the extent to which these periodic forces influence organisms at both genomic and phenotypic levels remains unclear. Despite the compelling evidence of fluctuating selection from recent studies, there is a disconnect between empirical and theoretical findings concerning the underlying mechanisms due to the limited evidence regarding the scale and processes that generate genome-wide oscillations. This study aims to elucidate how both genetic factors (e.g. heritability, number of causative loci) and ecological factors (e.g. season length, the difference in the phenotypic optima between seasons, population size dynamics) drive fluctuating selection and to identify the parameters that produce consistent oscillatory patterns. We developed a modeling framework integrating quantitative and population genetics to simulate a population under various selection regimes. We applied spectral analysis to detect periodicity, indicating cyclical selective environments. Our simulations highlight the conditions sustaining oscillations in allele frequencies over time. Spectral analysis successfully identifies the periodic patterns from allele frequency trajectories, even under highly complex selection regimes. Not only does our study clarify the conditions that yield oscillatory behaviors, but these parameters can also potentially be estimated in natural populations, providing a possibility of empirically testing these models.

Fluctuating selection↗