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PubMed2001

Emergence of memory-driven command neurons in evolved artificial agents.

Using evolutionary simulations, we develop autonomous agents controlled by artificial neural networks (ANNs). In simple lifelike tasks of foraging and navigation, high performance levels are attained by agents equipped with fully recurrent ANN controllers. In a set of experiments sharing the same behavioral task but differing in the sensory input available to the agents, we find a common structure of a command neuron switching the dynamics of the network between radically different behavioral modes. When sensory position information is available, the command neuron reflects a map of the environment, acting as a location-dependent cell sensitive to the location and orientation of the agent. When such information is unavailable, the command neuron's activity is based on a spontaneously evolving short-term memory mechanism, which underlies its apparent place-sensitive activity. A two-parameter stochastic model for this memory mechanism is proposed. We show that the parameter values emerging from the evolutionary simulations are near optimal; evolution takes advantage of seemingly harmful features of the environment to maximize the agent's foraging efficiency. The accessibility of evolved ANNs for a detailed inspection, together with the resemblance of some of the results to known findings from neurobiology, places evolved ANNs as an excellent candidate model for the study of structure and function relationship in complex nervous systems.

Biological Evolution↗
PubMed2006

Emergent neutrality.

Community ecology is in a current state of creative ferment, stimulated by the development of neutral models of community organization. Here, I reflect on recent papers by Scheffer and van Nes, and by Gravel et al., which illuminate how neutrality can emerge from ecological and evolutionary processes, thus suggesting ways to unify neutral and niche perspectives.

Adaptation, Physiological↗
PubMed1995

Population growth: a comparison of evolutionary views.

"Economists are divided about population growth: the pessimism of neo-Malthusians contrasts strongly with the optimism of cornucopians. Despite their differences, however, both schools of thought reject economic orthodoxy and prefer evolutionary forms of theory. Their interpretations of evolution are different: the neo-Malthusians appeal to the entropy law, whereas the cornucopians emphasize human creativity expressed through markets. [The author argues] that both schools are right to adopt an evolutionary outlook, but that they are too restrictive in their conception of evolution. A more complete evolutionary view, which allows properly for social institutions, could give a more balanced account of population growth."

Demography↗
PubMed2005

Comparative host-parasite population structures: disentangling prospecting and dispersal in the black-legged kittiwake Rissa tridactyla.

Although much insight is to be gained through the comparison of the population genetic structures of parasites and hosts, there are, at present, few studies that take advantage of the information on vertebrate life histories available through the consideration of their parasites. Here, we examined the genetic structure of a colonial seabird, the black-legged kittiwake (Rissa tridactyla) using seven polymorphic microsatellite markers to make inferences about population functioning and intercolony dispersal. We sampled kittiwakes from 22 colonies across the species' range and, at the same time, collected individuals of one of its common ectoparasites, the tick Ixodes uriae. Parasites were genotyped at eight microsatellite markers and the population genetic structure of host and parasite were compared. Kittiwake populations are only genetically structured at large spatial scales and show weak patterns of isolation by distance. This may be due to long-distance dispersal events that erase local patterns of population subdivision. However, important additional information is gained by comparing results with those of the parasite. In particular, tick populations are strongly structured at regional scales and show a stepping-stone pattern of gene flow. Due to the parasite's life history, its population structure is directly linked to the frequency and spatial extent of within-breeding season movements of kittiwakes. The comparison of host and parasite gene flow therefore helps us to disentangle the intercolony movements of birds from that of true dispersal events (movement followed by reproduction). In addition, such data can provide essential elements for predicting the outcome of local co-evolutionary interactions.

Animals↗
PubMed2005

The flexible evolutionary anchorage-dependent Pardee's restriction point of mammalian cells: how its deregulation may lead to cancer.

Living cells oscillate between the two states of quiescence and division that stand poles apart in terms of energy requirements, macromolecular composition and structural organization and in which they fulfill dichotomous activities. Division is a highly dynamic and energy-consuming process that needs be carefully orchestrated to ensure the faithful transmission of the mother genotype to daughter cells. Quiescence is a low-energy state in which a cell may still have to struggle hard to maintain its homeostasis in the face of adversity while waiting sometimes for long periods before finding a propitious niche to reproduce. Thus, the perpetuation of single cells rests upon their ability to elaborate robust quiescent and dividing states. This led yeast and mammalian cells to evolve rigorous Start [L.H. Hartwell, J. Culotti, J. Pringle, B.J. Reid, Genetic control of the cell division cycle in yeast, Science 183 (1974) 46-51] and restriction (R) points [A.B. Pardee, A restriction point for control of normal animal cell proliferation, Proc. Natl. Acad. Sci. U. S. A. 71 (1974) 1286-1290], respectively, that reduce deadly interferences between the two states by enforcing their temporal insulation though still enabling a rapid transition from one to the other upon an unpredictable change in their environment. The constitutive cells of multi-celled organisms are extremely sensitive in addition to the nature of their adhering support that fluctuates depending on developmental stage and tissue specificity. Metazoan evolution has entailed, therefore, the need for exceedingly flexible anchorage-dependent R points empowered to assist cells in switching between quiescence and division at various times, places and conditions in the same organism. Programmed cell death may have evolved concurrently in specific contexts unfit for the operation of a stringent R point that increase the risk of deadly interferences between the two states (as it happens notably during development). But, because of their innate flexibility, anchorage-dependent R points have also the ability to readily adjust to a changing structural context so as to give mutated cells a chance to reproduce, thereby encouraging tumor genesis. The Rb and p53 proteins, which are regulated by the two products of the Ink4a-Arf locus [C.J. Sherr, The INK4a/ARF network in tumor suppression, Nat. Rev., Mol. Cell Biol. 2 (2001) 731-737], govern separable though interconnected pathways that cooperate to restrain cyclin D- and cyclin E-dependent kinases from precipitating untimely R point transit. The expression levels of the Ink4a and Arf proteins are especially sensitive to changes in cellular shape and adhesion that entirely remodel at the time when cells shift between quiescence and division. The Arf proteins further display an extremely high translational sensitivity and can activate the p53 pathway to delay R point transit, but, only when released from the nucleolus, 'an organelle formed by the act of building a ribosome' [T. Mélèse, Z. Xue, The nucleolus: an organelle formed by the act of building a ribosome, Curr. Opin. Cell Biol. 7 (1995) 319-324]. In this way, the Ink4a/Rb and Arf/p53 pathways emerge as key regulators of anchorage-dependent R point transit in mammalian cells and their deregulation is, indeed, a rule in human cancers. Thus, by selecting the nucleolus to mitigate cell cycle control by the Arf proteins, mammalian cells succeeded in forging a highly flexible R point enabling them to match cell division with a growth rate imposed by factors controlling nucleolar assembling, such as nutrients and adhesion. It is noteworthy that nutrient control of critical size at Start in budding yeast has been shown recently to be governed by a nucleolar protein interaction network [P. Jorgensen, J.L. Nishikawa, B.-J. Breitkreutz, M. Tyers, Systematic identification of pathways that couple cell growth and division in yeast, Science 297 (2002) 395-400].

ADP-Ribosylation Factors↗
PubMed2001

A new method to model membrane protein structure based on silent amino acid substitutions.

The importance of accurately modeling membrane proteins cannot be overstated, in lieu of the difficulties in solving their structures experimentally. Often, however, modeling procedures (e.g., global searching molecular dynamics) generate several possible candidates rather then pointing to a single model. Herein we present a new approach to select among candidate models based on the general hypothesis that silent amino acid substitutions, present in variants identified from evolutionary conservation data or mutagenesis analysis, do not affect the stability of a native structure but may destabilize the non-native structures also found. The proof of this hypothesis has been tested on the alpha-helical transmembrane domains of two homodimers, human glycophorin A and human CD3-zeta, a component of the T-cell receptor. For both proteins, only one structure was identified using all the variants. For glycophorin A, this structure is virtually identical to the structure determined experimentally by NMR. We present a model for the transmembrane domain of CD3-zeta that is consistent with predictions based on mutagenesis, homology modeling, and the presence of a disulfide bond. Our experiments suggest that this method allows the prediction of transmembrane domain structure based only on widely available evolutionary conservation data.

Amino Acid Substitution↗
PubMed2005

Structure alignment via Delaunay tetrahedralization.

A novel protein structure alignment technique has been developed reducing much of the secondary and tertiary structure to a sequential representation greatly accelerating many structural computations, including alignment. Constructed from incidence relations in the Delaunay tetrahedralization, alignments of the sequential representation describe structural similarities that cannot be expressed with rigid-body superposition and complement existing techniques minimizing root-mean-squared distance through superposition. Restricting to the largest substructure superimposable by a single rigid-body transformation determines an alignment suitable for root-mean-squared distance comparisons and visualization. Restricted alignments of a test set of histones and histone-like proteins determined superpositions nearly identical to those produced by the established structure alignment routines of DaliLite and ProSup. Alignment of three, increasingly complex proteins: ferredoxin, cytidine deaminase, and carbamoyl phosphate synthetase, to themselves, demonstrated previously identified regions of self-similarity. All-against-all similarity index comparisons performed on a test set of 45 class I and class II aminoacyl-tRNA synthetases closely reproduced the results of established distance matrix methods while requiring 1/16 the time. Principal component analysis of pairwise tetrahedral decomposition similarity of 2300 molecular dynamics snapshots of tryptophanyl-tRNA synthetase revealed discrete microstates within the trajectory consistent with experimental results. The method produces results with sufficient efficiency for large-scale multiple structure alignment and is well suited to genomic and evolutionary investigations where no geometric model of similarity is known a priori.

Algorithms↗
PubMed2005

Biological anthropology and aging.

As the number of persons aged 65 and older is increasing dramatically in both developed and developing nations of the world, the health and well-being of elders has become a worldwide public health concern. Although older adults are now found in higher proportions across all cultures, the biology, behavior, and environment vary tremendously across older populations. Biomedical research largely follows a reductionist paradigm separating the domains of culture and biology. Even when health is examined in association with culture and behavior, biomedical researchers largely focus on static unidirectional associations instead of examining the dynamic multidirectional impact of culture, behavior, and the environment on physiology and ultimately health. Since aging and the processes of senescence clearly involve complex interactions among biological, environmental, and cultural domains, anthropologists with a bio-cultural and evolutionary perspective are well-equipped to study variation in aging and senescence. While relatively few biological anthropologists have focused their attention on aging, a growing literature has demonstrated the utility of biocultural approaches to aging. This paper serves as an introduction to a special issue that highlights the core of the biological anthropology of aging.

Aging↗
PubMed2004

Estimation of initial conditions and parameters of a chaotic evolution process from a short time series.

Tracing back to the initial state of a time-evolutionary process using a segment of historical time series may lead to many meaningful applications. In this paper, we present an estimation method that can detect the initial conditions, unobserved time-varying states and parameters of a dynamical (chaotic) system using a short scalar time series that may be contaminated by noise. The technique based on the Newton-Raphson method and the least-squares algorithm is tolerant to large mismatch between the initial guess and actual values. The feasibility and robustness of this method are illustrated via the numerical examples based on the Lorenz system and Rossler system corrupted with Gaussian noise.

Journal Article↗
PubMed2005

Multiple Alignment of protein structures and sequences for VMD.

Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and performing a variety of evolutionary and bioinformatic tasks, including the construction of structure-based phylogenetic trees and minimal basis sets of structures that best represent the topology of the phylogenetic tree. It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois.

Amino Acid Sequence↗
PubMed2005

On the choice of the offspring population size in evolutionary algorithms.

Evolutionary algorithms (EAs) generally come with a large number of parameters that have to be set before the algorithm can be used. Finding appropriate settings is a difficult task. The influence of these parameters on the efficiency of the search performed by an evolutionary algorithm can be very high. But there is still a lack of theoretically justified guidelines to help the practitioner find good values for these parameters. One such parameter is the offspring population size. Using a simplified but still realistic evolutionary algorithm, a thorough analysis of the effects of the offspring population size is presented. The result is a much better understanding of the role of offspring population size in an EA and suggests a simple way to dynamically adapt this parameter when necessary.

Algorithms↗
PubMed2006

Dispersal strategies of phytophagous insects at a local scale: adaptive potential of aphids in an agricultural environment.

BACKGROUND: The spread of agriculture greatly modified the selective pressures exerted by plants on phytophagous insects, by providing these insects with a high-level resource, structured in time and space. The life history, behavioural and physiological traits of some insect species may have evolved in response to these changes, allowing them to crowd on crops and to become agricultural pests. Dispersal, which is one of these traits, is a key concept in evolutionary biology but has been over-simplified in most theoretical studies. We evaluated the impact of the local-scale dispersal strategy of phytophagous insects on their fitness, using an individual-based model to simulate population dynamics and dispersal between leaves and plants, by walking and flying, of the aphid Aphis gossypii, a major agricultural pest, in a melon field. We compared the optimal values for dispersal parameters in the model with the corresponding observed values in experimental trials. RESULTS: We show that the rates of walking and flying disperser production on leaves were the most important traits determining the fitness criteria, whereas dispersal distance and the clustering of flying dispersers on the target plant had no effect. We further show that the effect of dispersal parameters on aphid fitness depended strongly on plant characteristics. CONCLUSION: Parameters defining the dispersal strategies of aphids at a local scale are key components of the fitness of these insects and may thus be essential in the adaptation to agricultural environments that are structured in space and time. Moreover, the fact that the effect of dispersal parameters on aphid fitness depends strongly on plant characteristics suggests that traits defining aphid dispersal strategies may be a cornerstone of host-plant specialization.

Adaptation, Physiological↗
PubMed2026

Assembly and comparative analysis of the mitochondrial genome of Pleione yunnanensis: genome structure and evolutionary insights.

BACKGROUND: Pleione yunnanensis a terrestrial or semi-epiphytic herbaceous plant belonging to the Orchidaceae family, is valued for both its medicinal uses and ornamental appeal. Although its chloroplast genomes have been sequenced, its complete mt genome had not previously been resolved, limiting genetic and evolutionary studies of the species. RESULTS: In this work, we assembled and characterized the first complete mt genome of P. yunnanensis, revealing a structurally complex, multibranched system composed of 14 circular-mapping molecules totaling 468,176 bp with a GC content of 44.32%. The genome encodes 44 annotated genes, including 28 protein-coding genes (PCGs), 15 tRNAs, and one rRNA. The multibranched architecture provides new evidence supporting the dynamic and recombinational nature of plant mt genomes. Repeat analysis uncovered 29 simple sequence repeats (SSRs), 19 tandem repeats, and 118 dispersed repeats, indicating a comparatively lower repeat abundance than that found in closely related orchids with similar mt genome sizes. Codon-usage profiling of PCGs showed a marked bias toward A/T-ending codons. Prediction of RNA editing sites identified 4,708 putative edits across mitochondrial PCGs. Most mitochondrial genes displayed Ka/Ks ratios close to 1.0, suggesting relaxed selective constraints or lineage-specific evolutionary patterns rather than strong positive selection. Moreover, we detected 69 chloroplast-derived homologous fragments, including 15 intact genes, suggesting ongoing plastid-mitochondrial DNA transfer. Phylogenetic reconstruction and collinearity comparisons demonstrated that P. yunnanensis clustered closely with Dendrobium species, including D. amplum and D. hancockii, within the Orchidaceae clade. CONCLUSIONS: This study provides the first complete mt genome of P. yunnanensis, providing a foundational genomic resource for the genus Pleione. The results not only improve our understanding of mt genome structure and evolution in Orchidaceae, but also offer valuable molecular evidence for phylogenetic inference, germplasm identification, and conservation of this endangered medicinal species.

Orchidaceae↗
PubMed2004

Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance.

'Hot zones' are areas that have >5% prevalence (or incidence) of multidrug-resistant tuberculosis (MDRTB). We present a new mathematical model (the amplifier model) that tracks the emergence and evolution of multiple (pre-MDR, MDR and post-MDR) strains of drug-resistant Mycobacterium tuberculosis. We reconstruct possible evolutionary trajectories that generated hot zones over the past three decades, and identify the key causal factors. Results are consistent with recently reported World Health Organization (WHO) data. Our analyses yield three important insights. First, paradoxically we found that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones. Second, some hot zones emerged even when MDR strains were substantially less fit (and thus less transmissible) than wild-type pansensitive strains. Third, levels of MDR are driven by case-finding rates, cure rates and amplification probabilities. To effectively control MDRTB in the hot zones, it is essential that the WHO specify a goal for minimizing the amplification probability.

Biological Evolution↗
PubMed1995

[Unpublished aspects of hominization. Fundamental ontogeny, chaotic aspects, harmonic aspects].

The recent discovery of a phenomenon of craniofacial growth, called craniofacial contraction, throws a new light on the process of hominization. The main interest of this discovery lies in a growth principle combining the different craniofacial units, that is to say, the neurocranium (neural skull), the chondrocranium (basal skull) and the splanchnocranium (visceral archs including the mandible). Until recent years, these different parts were considered as neighbouring element without any morphogenic or morphodynamic connection. But now, we know that the morphogenesis of the base of the skull governs that of the face. This basicranial morphogenesis is the occipital flexion. It generates morphogenic correlations with the face since embryogenesis. The ontogenic pathway of this phenomenon is the craniofacial contraction. It concerns embryonic dynamics connected with the spatial development of the embryonic neural system, the neural tube. These morphodynamics are common to each primate species, but they are differentiated by the amplitude of the embryonic contraction. We ask ourself the question: is hominization of the neurocephalic embryogenesis, that is the craniofacial contraction, plausible over a very long period, with gradual and chaotic evolutionary pathways, or, on the contrary, is the complexity of such an embryonic phenomenon, a limiting factor generating determined and predictable ontogenic thresholds? The study of extant and fossil primate skulls demonstrates that species are organized around 6 levels of embryonic contraction, which, starting from 60 millions years, evolve from the less to the most contracted skull. Among each ontogenic level, living and fossil species develop from the same embryonic system but between both levels, the embryos suddenly are reorganized. Therefore, I have defined an evolutive ontogenic unity, that is the fundamental ontogenesis. The cephalic pole has a fundamental ontogenesis, meaning that, beyond the diversities, we can see the same contraction in many living and extinct species. The ontogenic diversities are the result of the microevolution and are not predictable. In such a perspective, the ontogenic morphodynamics evolve with chaotic trajectories. But, between two embryonic levels, or two fundamental ontogeneses, evolutionary modalities are different. Eventually, from 60 millions years to XXth century, we observe the same phenomenon than during human ontogenesis; hominization of the cephalic pole is a craniofacial contraction. The evolutive pathway is stable, whatever the number of thresholds, the cranial shape changes but the ontogenic trajectory is preserved. This is a macroevolution because the embryonic system is reorganized.(ABSTRACT TRUNCATED AT 400 WORDS)

Biological Evolution↗
PubMedDate not supplied

Executive control emerging from dynamic interactions between brain systems mediating language, working memory and attentional processes.

In this theoretical paper, we review findings from a series of recent behavioral and functional neuroimaging studies of working memory and executive control which provide evidence for the following theses: 1. Working memory in humans is represented by two brain systems which differ from each other with respect to their functional-neuroanatomical organization and probably also with respect to their evolutionary origin. 2. One of these brain systems relies on prefronto-parietal and prefronto-temporal cortical networks that presumably also mediate attentional selection by the top-down modulation of domain-specific sensory association areas towards behaviorally relevant information. 3. The other system is implemented by mainly left-hemispheric premotor and parietal brain regions which to a greater part also underlie language functions and which may also be involved in the retrieval and maintenance of verbal goal representations during advance preparation for task switches. 4. Context-sensitive behavioral adaptation is supported by a complementary mechanism for the detection of conflicts and for the triggering of cognitive control processes that relies on parts of the medial frontal cortex. Based on these empirical results reported in the literature we propose a neurocognitive model of executive control according to which the human ability to flexibly adapt to changing behavioral requirements, i.e. executive control, depends on dynamic and context-sensitive interactions between these brain systems.

Attention↗
PubMed2005

A DNA polymerase V homologue encoded by TOL plasmid pWW0 confers evolutionary fitness on Pseudomonas putida under conditions of environmental stress.

Plasmids in conjunction with other mobile elements such as transposons are major players in the genetic adaptation of bacteria in response to changes in environment. Here we show that a large catabolic TOL plasmid, pWW0, from Pseudomonas putida carries genes (rulAB genes) encoding an error-prone DNA polymerase Pol V homologue which increase the survival of bacteria under conditions of accumulation of DNA damage. A study of population dynamics in stationary phase revealed that the presence of pWW0-derived rulAB genes in the bacterial genome allows the expression of a strong growth advantage in stationary phase (GASP) phenotype of P. putida. When rulAB-carrying cells from an 8-day-old culture were mixed with Pol V-negative cells from a 1-day-old culture, cells derived from the aged culture out-competed cells from the nonaged culture and overtook the whole culture. At the same time, bacteria from an aged culture lacking the rulAB genes were only partially able to out-compete cells from a fresh overnight culture of the parental P. putida strain. Thus, in addition to conferring resistance to DNA damage, the plasmid-encoded Pol V genes significantly increase the evolutionary fitness of bacteria during prolonged nutritional starvation of a P. putida population. The results of our study indicate that RecA is involved in the control of expression of the pWW0-encoded Pol V.

Adaptation, Physiological↗
PubMed2007

Analogy between language and biology: a functional approach.

We adopt here a functional approach to the classical comparison between language and biology. We first parallel events which have a functional signification in each domain, by matching the utterance of a sentence with the release of a protein. The meaning of a protein is then defined by analogy as "the constant contribution of the biochemical material composing the protein to the effects produced by any release of the protein". The proteome of an organism corresponds to an I-language (the idiolect of an individual), and the proteome of a species is equivalent to an E-language (a language in the common sense). Proteins and sentences are both characterized by a complex hierarchical structure, but the language property of 'double articulation' has no equivalent in the biological domain in this analogy, contrary to previous proposals centered on the genetic code. Besides, the same intimate relation between structure and meaning holds in both cases (syntactic structure for sentences and three-dimensional conformation for proteins). An important disanalogy comes from the combinatorial power of language which is not shared by the proteome as a whole, but it must be noted that the immune system possesses interesting properties in this respect. Regarding evolutionary aspects, the analogy still works to a certain extent. Languages and proteomes can be both considered as belonging to a general class of systems, that we call "productive self-reproductive systems", characterized by the presence of two dynamics: a fast dynamics in an external domain where functional events occur (productive aspect), and a slow dynamics responsible for the evolution of the system itself, driven by the feed-back of events related to the reproduction process.

Animals↗