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PubMed2004

Modeling and convergence analysis of distributed coevolutionary algorithms.

A theoretical foundation is presented for modeling and convergence analysis of a class of distributed coevolutionary algorithms applied to optimization problems in which the variables are partitioned among p nodes. An evolutionary algorithm at each of the p nodes performs a local evolutionary search based on its own set of primary variables, and the secondary variable set at each node is clamped during this phase. An infrequent intercommunication between the nodes updates the secondary variables at each node. The local search and intercommunication phases alternate, resulting in a cooperative search by the p nodes. First, we specify a theoretical basis for a class of centralized evolutionary algorithms in terms of construction and evolution of sampling distributions over the feasible space. Next, this foundation is extended to develop a model for a class of distributed coevolutionary algorithms. Convergence and convergence rate analyzes are pursued for basic classes of objective functions. Our theoretical investigation reveals that for certain unimodal and multimodal objectives, we can expect these algorithms to converge at a geometrical rate. The distributed coevolutionary algorithms are of most interest from the perspective of their performance advantage compared to centralized algorithms, when they execute in a network environment with significant local access and internode communication delays. The relative performance of these algorithms is therefore evaluated in a distributed environment with realistic parameters of network behavior.

Journal Article↗
PubMed2006

The evolution of imaging in advanced prostate cancer.

Medical advances will be driven by the enhancement of imaging for diagnosis, refinement of treatment, and evaluation of treatment efficacy. The convergence of technology in materials science, biology, and the computer industry has greatly advanced diagnostic imaging. Precision in control of the spatial and temporal properties of light and its heterogeneous scattering properties have extended our capability for imaging. Refinements in radioimmunoscintigraphy for image acquisition, fusion of images, and outcome data now suggest use for image-guided therapy. Novel MRI agents appear to provide significant imaging capabilities to detect malignant lymph nodes. Future applications of optical coherence tomography, electron paramagnetic resonance imaging, nanotechnology, molecular imaging, and hyperspectral spectroscopy promise further refinements to image tissues for diagnosis.

Diagnostic Imaging↗
PubMed2005

Elucidation of clathrin-mediated endocytosis in tetrahymena reveals an evolutionarily convergent recruitment of dynamin.

Ciliates, although single-celled organisms, contain numerous subcellular structures and pathways usually associated with metazoans. How this cell biological complexity relates to the evolution of molecular elements is unclear, because features in these cells have been defined mainly at the morphological level. Among these ciliate features are structures resembling clathrin-coated, endocytic pits associated with plasma membrane invaginations called parasomal sacs. The combination of genome-wide sequencing in Tetrahymena thermophila with tools for gene expression and replacement has allowed us to examine this pathway in detail. Here we demonstrate that parasomal sacs are sites of clathrin-dependent endocytosis and that AP-2 localizes to these sites. Unexpectedly, endocytosis in Tetrahymena also involves a protein in the dynamin family, Drp1p (Dynamin-related protein 1). While phylogenetic analysis of AP subunits indicates a primitive origin for clathrin-mediated endocytosis, similar analysis of dynamin-related proteins suggests, strikingly, that the recruitment of dynamin-family proteins to the endocytic pathway occurred independently during the course of the ciliate and metazoan radiations. Consistent with this, our functional analysis suggests that the precise roles of dynamins in endocytosis, as well as the mechanisms of targeting, differ in metazoans and ciliates.

Animals↗
PubMed2002

The evolution of monomeric and oligomeric betagamma-type crystallins. Facts and hypotheses.

The case of homologous monomeric gamma-type and oligomeric beta-type crystallins has been described and analyzed in evolutionary terms. Data and hypotheses from molecular genetics and structural investigations converge and suggest a novel three-phase model for the evolutionary history of crystallin-type proteins. In the divergent cascades of monomeric and oligomeric crystallins, a pivotal role was played by alterations in the gene segments encoding the C-terminal extensions and the intermotif or interdomain linker peptides. These were genomic hot spots where evolution experimented to produce the modern variety of betagamma-crystallin-type quaternary structures.

Animals↗
PubMed2004

Mitogenomic analyses provide new insights into cetacean origin and evolution.

The evolution of the order Cetacea (whales, dolphins, porpoises) has, for a long time, attracted the attention of evolutionary biologists. Here we examine cetacean phylogenetic relationships on the basis of analyses of complete mitochondrial genomes that represent all extant cetacean families. The results suggest that the ancestors of recent cetaceans had an explosive evolutionary radiation 30-35 million years before present. During this period, extant cetaceans divided into the two primary groups, Mysticeti (baleen whales) and Odontoceti (toothed whales). Soon after this basal split, the Odontoceti diverged into the four extant lineages, sperm whales, beaked whales, Indian river dolphins and delphinoids (iniid river dolphins, narwhals/belugas, porpoises and true dolphins). The current data set has allowed test of two recent morphological hypotheses on cetacean origin. One of these hypotheses posits that Artiodactyla and Cetacea originated from the extinct group Mesonychia, and the other that Mesonychia/Cetacea constitutes a sister group to Artiodactyla. The current results are inconsistent with both these hypotheses. The findings suggest that the claimed morphological similarities between Mesonychia and Cetacea are the result of evolutionary convergence rather than common ancestry.

Animals↗
PubMed1990

Evolution of sexual preferences in quantitative characters.

An analysis of equilibria and dynamics of the means, variances, and covariances of female mating preference for a quantitative male secondary sexual character following a Gaussian model is presented. For many combinations of viability and sexual selection parameters the evolving Gaussian distribution of phenotypes can diverge. The results on the cases of convergence and their limiting forms suggest some reinterpretations of Fisher's "runaway" process of sexual selection. One possibility is to interpret Fisher's postulated "initial advantage not due to female preference" as a shift in viability selection where runaway evolution occurs if the mean preferred trait evolves beyond its new viability optimum (due to sexual selection). This definition is contrasted with situations in which the new viability optimum is undershot. The quantitative and qualitative conclusions differ from models that approximate genetic covariance evolution involving a constant covariance.

Biological Evolution↗
PubMed1997

The evolution of vertebrate electrosensory systems.

Sensory systems that detect weak electric fields initially evolved as a primitive vertebrate character and have subsequently been lost and 're-evolved' a number of times in various taxa. As such, they provide unique examples of evolutionary parallelism and convergence in vertebrate sensory systems. Electrosensory systems have additionally proven to be admirable models for investigating the fundamental strategies by which nervous systems interpret environmental signals as the basis for organizing behaviors.

Animals↗
PubMed2003

A direct experimental test of founder-flush effects on the evolutionary potential for assortative mating.

Founder-flush speciation models propose that population bottlenecks can enhance evolutionary potential for reproductive isolation. To test this prediction, we subjected bottlenecked (three-pair founder-flush) and nonbottlenecked populations of the housefly to 18 generations of selection for assortative mating. After the selection regime, we analysed videotaped courtship bouts in these lines to identify correlated responses to the selection protocol. The realized heritabilities for assortative mating for both the bottlenecked and nonbottlenecked treatments were very low, but still significant. The founder-flush populations had thus responded to selection as well as the nonbottlenecked populations, although not significantly greater (i.e. total increases in assortative mating were 9.6 and 8.6%, respectively). Multivariate analyses on the courtship repertoires found that, although both bottlenecked and nonbottlenecked treatments attained similar levels of assortative mating, the treatments exhibited different evolutionary solutions in their correlated responses. Specifically, the bottlenecked lines demonstrated a significantly more diverse set of evolutionary trajectories (i.e. significant shifts along the second principal component for courtship). This suggests that the bottlenecked lines had greater potential for the evolution of novel phenotypes as predicted by founder-induced speciation models. Our results, however, cannot distinguish whether the more variable evolutionary responses resulted from increased heritabilities in courtship components, reduced potential to follow the convergent evolutionary trajectories noted for the nonbottlenecked lines, or some combination of both general processes in determining the resultant multivariate phenotype.

Animals↗
PubMed2003

Reducing the time complexity of the derandomized evolution strategy with covariance matrix adaptation (CMA-ES).

This paper presents a novel evolutionary optimization strategy based on the derandomized evolution strategy with covariance matrix adaptation (CMA-ES). This new approach is intended to reduce the number of generations required for convergence to the optimum. Reducing the number of generations, i.e., the time complexity of the algorithm, is important if a large population size is desired: (1) to reduce the effect of noise; (2) to improve global search properties; and (3) to implement the algorithm on (highly) parallel machines. Our method results in a highly parallel algorithm which scales favorably with large numbers of processors. This is accomplished by efficiently incorporating the available information from a large population, thus significantly reducing the number of generations needed to adapt the covariance matrix. The original version of the CMA-ES was designed to reliably adapt the covariance matrix in small populations but it cannot exploit large populations efficiently. Our modifications scale up the efficiency to population sizes of up to 10n, where n is the problem dimension. This method has been applied to a large number of test problems, demonstrating that in many cases the CMA-ES can be advanced from quadratic to linear time complexity.

Algorithms↗
PubMed2005

Estimation of linear mixed models with a mixture of distribution for the random effects.

The aim of this paper is to propose an algorithm to estimate linear mixed model when random effect distribution is a mixture of Gaussians. This heterogeneous linear mixed model relaxes the classical Gaussian assumption for the random effects and, when used for longitudinal data, can highlight distinct patterns of evolution. The observed likelihood is maximized using a Marquardt algorithm instead of the EM algorithm which is frequently used for mixture models. Indeed, the EM algorithm is computationally expensive and does not provide good convergence criteria nor direct estimates of the variance of the parameters. The proposed method also allows to classify subjects according to the estimated profiles by computing posterior probabilities of belonging to each component. The use of heterogeneous linear mixed model is illustrated through a study of the different patterns of cognitive evolution in the elderly. HETMIXLIN is a free Fortran90 program available on the web site: http://www.isped.u-bordeaux2.fr.

Aged↗
PubMed1977

Meiosis in perspective.

Our understanding of meiosis springs from two suggestions made by Weismann in 1887. One was that meiosis would be found to compensate for fertilization in the life cycles of both sexes and all organisms. The other was that the development of sexual reproduction in evolution depended on the value of meiosis in exposing the results of genetic recombination to natural selection. In confirming these propositions we were bound to discover that the properties of meiosis appear both as the causes and the consequences of evolution: it is the hinge on which turns the evolution of breeding method, reproductive habit, life cycle and hereditary structure, that is the genetic system, in all sexually reproducing species of organism. We have had three main fields of attack on our problem. First, there was the natural variation of meiosis including that of two-track hereditary within the species: here, animals took the lead. Secondly, there was the experimental field - both with genetic controls such as polyploidy and the sterilizing mutations of mitosis as well as meiosis, and with physical and chemical controls: here, the higher plants and micro-organisms have given us our great opportunities. Thirdly, we have the widening field where physicochemical knowledge and genetic control converge and collaborate. In all this work we have to be aware that meiosis works with chromosomes which always have the two functions of accomplishing evolution and of implementing its results in heredity. In consequence, the adaptation of meiosis is perpetually imperfect.

Biological Evolution↗
PubMed2006

Evolution of pathogens towards low R0 in heterogeneous populations.

Maximization of the basic reproduction ratio or R(0) is widely believed to drive the emergence of novel pathogens. The presence of exploitable heterogeneities in a population, such as high variance in the number of potentially infectious contacts, increases R(0) and thus pathogens that can exploit heterogeneities in the contact structure have an advantage over those that do not. However, exploitation of heterogeneities results in a more rapid depletion of the potentially susceptible neighbourhood for an infected host. Here a simple model of pathogen evolution in a heterogeneous environment is developed and placed in the context of HIV transmission. In this model, it is shown that pathogens may evolve towards lower R(0), even if this results in pathogen extinction. For sufficiently high transmissibility, two locally stable strategies exist for an evolving pathogen, one that exploits heterogeneities and results in higher R(0), and one that does not, and results in lower R(0). While the low R(0) strategy is never evolutionarily stable, invading strains with higher R(0) will also converge to the low R(0) strategy if not sufficiently different from the resident strain. Heterogenous transmission is increasingly recognized as fundamental to epidemiological dynamics and the evolution of pathogens; here, it is shown that the ability to exploit heterogeneity is a strategy that can itself evolve.

Disease Outbreaks↗
PubMed2004

Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons.

In human immunodeficiency virus type 1 (HIV-1), mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been documented, and sequence analyses have provided indirect support for the hypothesis that natural selection has favored CTL escape mutants within an infected host. In spite of such evidence for within-host selection by CTL, it has been more difficult to determine how natural selection by host CTL has influenced long-term evolution of HIV-1. We used statistical analysis of published HIV-1 genomic sequences to examine the role of natural selection in between-host evolution of CTL epitopes. Based on a phylogenetic analysis, we identified 21 pairs of closely related genomes isolated from different hosts and examined the pattern of nucleotide substitution in genomic regions encoding well-characterized CTL epitopes. The results revealed that certain CTL epitopes have been subject to repeated positive selection across the population, while others are generally conserved. Furthermore, evidence of positive selection was associated with divergence from the canonical epitope sequence and with an enhanced frequency of convergent amino acid sequence changes in CTL epitopes. The results support the hypothesis that CTL-driven selection has been a major factor in the long-term evolution of HIV-1.

Epitopes, T-Lymphocyte↗
PubMed1999

Natural history and behavioural homology.

Although similarities and differences among animals have long inspired ethologists, three misconceptions haunt the literature on behavioural evolution: the absence of 'ethofossils' seriously hampers detection of behavioural homology; behaviour is more variable and subject to experiential modification than morphology; and behaviour is especially subject to convergence. As a backdrop to address these issues, I briefly survey parental care by amniotes and antipredator mechanisms is non-avian reptiles. Although those behaviours remain inadequately sampled taxonomically, they clearly vary at several cladistic levels; they are conservative across some major groups, innovative within subclades, and exhibit apparent homoplasy among and within groups. These behavioural examples also illustrate contextual influences on the expression of traits, as well as how behavioural context can shape other aspects of development. Enhanced understanding of behavioural evolution will follow from greater emphasis on how developmental context, including behaviour itself, shapes phenotypes; from integration of data for fossil and recent organisms; and from much denser ethological sampling among taxa. Phylogenetic analyses of behavioural similarity should in turn provide exciting insights into the evolutionary roles of behavioural shifts and constraints, as well as inform our aesthetic appreciation for the richness of nature.

Adaptation, Biological↗
PubMed1997

Mapping homology between human and black and white colobine monkey chromosomes by fluorescent in situ hybridization.

We used in situ hybridization of chromosome specific DNA probes ("chromosome painting") of all human chromosomes to establish homologies between the human and the white and black colobus (Colobus guereza 2n = 44). The 24 human paints gave 31 signals on the autosomes (haploid male chromosomes homologus to human 14 and 15, 21 and 22, form colobine chromosomes 6 and 16, respectively. Reciprocal translocations were found between human chromosomes 1 and 10, 1 and 17, as well as 3 and 19. The alternating hybridization signals between human 3 and 19 on Colobus chromosome 12 show that in this case a reciprocal translocation was followed by a pericentric inversion. The hybridization data show that in spite of the same diploid number and similar Fundamental Numbers, the black and white colobine monkey differs from Presbytis cristata, an Asian colobine, by 6 reciprocal translocations. Comparisons with the hybridization patterns in other primates show that some Asian colobines have a more derived karyotype with respect to African colobines, macaques, great apes, and humans. Chromosome painting also clearly shows that similarities in diploid number and chromosome morphology both between colobines and gibbons are due to convergence.

Animals↗
PubMed1995

Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations.

Nanosecond molecular dynamics simulations of bovine pancreatic trypsin inhibitor and lysozyme in water are analyzed in terms of backbone atomic positional fluctuations and dynamical cross-correlations. It is found that although the molecular systems are stable, B-factors calculated over a time period as long as 500 ps are not representative for the motions within the proteins. This is especially true for the most mobile residues. On a nanosecond time-scale, the B-factors calculated from the simulations of the proteins in solution are considerably larger than those obtained by structure refinement of the proteins in crystals, based on X-ray data. The time evolution of the atomic fluctuations shows that for large portions of the proteins under study, atomic positional fluctuations are not yet converged after a nanosecond. Cross-correlations do not converge faster than the fluctuations themselves. Most display very erratic behavior if the sampling covers less than about 200 ps. It is also shown that inclusion of mobile atoms into the procedure used to remove rigid-body motion from the simulation can lead to spurious correlations between the motions of the atoms at the surface of the protein.

Animals↗
PubMed1990

Primary structure of a pheromone-binding protein from Antheraea pernyi: homologies with other ligand-carrying proteins.

An antennal cDNA clone encoding the complete sequence (163 amino acids) of a pheromone-binding protein precursor from the male silk moth, Antheraea pernyi, was isolated using oligonucleotide probes. The cloned cDNA was expressed and the translation product detected by specific antibodies. The deduced protein sequence consists of a signal peptide of 21 amino acids and a mature binding protein of 142 amino acid residues. The predicted structure of this protein is homologous to binding-proteins from different insect species which have previously been identified, but shows no similarities to odorant-binding proteins from vertebrates, suggesting that soluble odorant-binding proteins in insects and vertebrates represent an evolutionary convergence.

Amino Acid Sequence↗
PubMed2004

Effects of neighbourhood size and connectivity on the spatial Continuous Prisoner's Dilemma.

The Prisoner's Dilemma, a two-person game in which the players can either cooperate or defect, is a common paradigm for studying the evolution of cooperation. In real situations cooperation is almost never all or nothing. This observation is the motivation for the Continuous Prisoner's Dilemma, in which individuals exhibit variable degrees of cooperation. It is known that in the presence of spatial structure, when individuals "play against" (i.e. interact with) their neighbours, and "compare to" ("learn from") them, cooperative investments can evolve to considerable levels. Here, we examine the effect of increasing the neighbourhood size: we find that the mean-field limit of no cooperation is reached for a critical neighbourhood size of about five neighbours on each side in a Moore neighbourhood, which does not depend on the size of the spatial lattice. We also find the related result that in a network of players, the critical average degree (number of neighbours) of nodes for which defection is the final state does not depend on network size, but only on the network topology. This critical average degree is considerably (about 10 times) higher for clustered (social) networks, than for distributed random networks. This result strengthens the argument that clustering is the mechanism which makes the development and maintenance of the cooperation possible. In the lattice topology, it is observed that when the neighbourhood sizes for "interacting" and "learning" differ by more than 0.5, cooperation is not sustainable, even for neighbourhood sizes that are below the mean-field limit of defection. We also study the evolution of neighbourhood sizes, as well as investment level. Here, we observe that the series of the interaction and learning neighbourhoods converge, and a final cooperative state with considerable levels of average investment is achieved.

Animals↗