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PubMed1996

Collapsing a coevolutionary process into a computable function.

It is shown how the entire dynamics of a class of evolutionary systems can be used to perform a computation. The argument is constructive by presenting a Turing-machine-based set-up implemented in Enact, an artificial-life world embedded in a family of cellular automata; in this system, a population of agents move about in a two-dimensional space, interacting with their environment, reproducing and undergoing developmental and coevolutionary processes. As a byproduct, the paper also serves to characterise the main model of computation underlying Enact. This model is essentially parallel, and relies upon the machinery defined by the artificial-life processes. According to the model, a particular computation is considered to have been performed, if and only if, for some initial population and environmental configuration, at least one agent has developed into a state configuration that is insensitive to any further environmental interactions; in this situation, if the computation involved is a function, this individual has the result. If the population ever vanishes, or if the environment becomes short of the resources needed for development, the cellular space has to be re-initialized, and the process iterated. The presentation relies on the implementation of a function that recognises a particular context-free language. Implications of the model of computation are then discussed, in particular the model of coupled computations suggested by it.

Algorithms↗
PubMed2005

Equivalence-set genes partitioning using an evolutionary-DP approach.

Computation of transitive-closure equivalence sets has recently emerged as an important step for building static and dynamic models of gene network from DNA sequences. We present an evolutionary-DP approach in which dynamic programming (DP) is embedded into a genetic algorithm (GA) for fitness function evaluation of small equivalence sets (with m genes) within a large-scale genetic network of n genes, where n > m. This approach reduces a computation-intensive optimal problem of high dimension into a heuristic search problem on nCm candidates. The DP computation of transitive closure forms the basic fitness evaluation for selecting candidate chromosomes generated by GA operators. By introducing bounded mutation and conditioned crossover operators to constrain the feasible solution domain, small transitive-closure equivalence sets for large genetic networks can be found with much reduced computational effort. Empirical results have successfully demonstrated the feasibility of our GA-DP approach for offering highly efficient solutions to large scale equivalence gene-set partitioning problem. We also describe dedicated GA-DP hardware using field programmable gate arrays (FPGAs), in which significant speedup could be obtained over software implementation.

Algorithms↗
PubMed2006

Cognitive conflict without explicit conflict monitoring in a dynamical agent.

We examine mechanisms for resolving cognitive conflict in an embodied, situated, and dynamic agent, developed through an evolutionary learning process. The agent was required to solve problems of response conflict in a dual-target "catching" task, focusing response on one of the targets while ignoring the other. Conflict in the agent was revealed at the behavioral level in terms of increased latencies to the second target. This behavioral interference was correlated to peak violations of the network's stable state equation. At the level of the agent's neural network, peak violations were also correlated to periods of disagreement in source inputs to the agent's motor effectors. Despite observing conflict at these numerous levels, we did not find any explicit conflict monitoring mechanisms within the agent. We instead found evidence of a distributed conflict management system, characterized by competitive sources within the network. In contrast to the conflict monitoring hypothesis [Botvinick, M. M., Braver, T. S., Barch, D. M., Carter, C. S., & Cohen, J. D. (2001). Conflict monitoring and cognitive control. Psychological Review, 108(3), 624-652], this agent demonstrates that resolution of cognitive conflict does not require explicit conflict monitoring. We consider the implications of our results for the conflict monitoring hypothesis.

Attention↗
PubMed2004

The lack of recombination drives the fixation of transposable elements on the fourth chromosome of Drosophila melanogaster.

In regions of suppressed recombination, where selection is expected to be less efficient in removing slightly deleterious mutations, transposable element (TE) insertions should be more likely to drift to higher frequencies, and even to reach fixation. In the absence of excision events, once a TE is fixed it cannot be eliminated from the population, and accumulation of elements thus should become an irreversible process. In the long term, this can drive the degeneration of large non-recombining fractions of the genomes. Chromosome 4 of Drosophila melanogaster has very low levels of recombination, if any, and this could be causing its degeneration. Here we report the results of a PCR-based analysis of the population frequencies of TE insertions in a sample from three African natural populations. We investigated 27 insertions from 12 TE families, located in regions of either suppressed or free recombination. Our results suggest that TE insertions tend to be fixed in the non-recombining regions, particularly on the fourth chromosome. We have also found that this involves all types of elements, and that fixed insertions are significantly shorter and more divergent from the canonical sequence than those segregating in the sample (28.1% vs 86.3% of the canonical length, and average nucleotide divergence (D(XY)) = 0.082 vs 0.008, respectively). Finally, DNA-based elements seem to show a greater tendency to reach fixation than retrotransposons. Implications of these findings for the population dynamics of TEs, and the evolutionary forces that shape the patterns of genetic variation in regions of reduced recombination, are discussed.

Animals↗
PubMed1995

Temporal fluctuations in coherence of brain waves.

As a measure of dynamical structure, short-term fluctuations of coherence between 0.3 and 100 Hz in the electroencephalogram (EEG) of humans were studied from recordings made by chronic subdural macroelectrodes 5-10 mm apart, on temporal, frontal, and parietal lobes, and from intracranial probes deep in the temporal lobe, including the hippocampus, during sleep, alert, and seizure states. The time series of coherence between adjacent sites calculated every second or less often varies widely in stability over time; sometimes it is stable for half a minute or more. Within 2-min samples, coherence commonly fluctuates by a factor up to 2-3, in all bands, within the time scale of seconds to tens of seconds. The power spectrum of the time series of these fluctuations is broad, extending to 0.02 Hz or slower, and is weighted toward the slower frequencies; little power is faster than 0.5 Hz. Some records show conspicuous swings with a preferred duration of 5-15s, either irregularly or quasirhythmically with a broad peak around 0.1 Hz. Periodicity is not statistically significant in most records. In our sampling, we have not found a consistent difference between lobes of the brain, subdural and depth electrodes, or sleeping and waking states. Seizures generally raise the mean coherence in all frequencies and may reduce the fluctuations by a ceiling effect. The coherence time series of different bands is positively correlated (0.45 overall); significant nonindependence extends for at least two octaves. Coherence fluctuations are quite local; the time series of adjacent electrodes is correlated with that of the nearest neighbor pairs (10 mm) to a coefficient averaging approximately 0.4, falling to approximately 0.2 for neighbors-but-one (20 mm) and to < 0.1 for neighbors-but-two (30 mm). The evidence indicates fine structure in time and space, a dynamic and local determination of this measure of cooperativity. Widely separated frequencies tending to fluctuate together exclude independent oscillators as the general or usual basis of the EEG, although a few rhythms are well known under special conditions. Broad-band events may be the more usual generators. Loci only a few millimeters apart can fluctuate widely in seconds, either in parallel or independently. Scalp EEG coherence cannot be predicted from subdural or deep recordings, or vice versa, and intracortical microelectrodes show still greater coherence fluctuation in space and time. Widely used computations of chaos and dimensionality made upon data from scalp or even subdural or depth electrodes, even when reproducible in successive samples, cannot be considered representative of the brain or the given structure or brain state but only of the scale or view (receptive field) of the electrodes used. Relevant to the evolution of more complex brains, which is an outstanding fact of animal evolution, we believe that measures of cooperativity are likely to be among the dynamic features by which major evolutionary grades of brains differ.

Brain↗
PubMed2000

The Discovery of a Companion to the Very Cool Dwarf Gliese 569B with the Keck Adaptive Optics Facility.

We report observations obtained with the Keck adaptive optics facility of the nearby (d=9.8 pc) binary Gl 569. The system was known to be composed of a cool primary (dM2) and a very cool secondary (dM8.5) with a separation of 5&arcsec; (49 AU). We have found that Gl 569B is itself double with a separation of only 0&farcs;101+/-0&farcs;002 (1 AU). This detection demonstrates the superb spatial resolution that can be achieved with adaptive optics at Keck. The difference in brightness between Gl 569B and the companion is approximately 0.5 mag in the J, H, and K&arcmin; bands. Thus, both objects have similarly red colors and very likely constitute a very low mass binary system. For reasonable assumptions about the age (0.12-1.0 Gyr) and total mass of the system (0.09-0.15 M middle dot in circle), we estimate that the orbital period is approximately 3 yr. Follow-up observations will allow us to obtain an astrometric orbit solution and will yield direct dynamical masses that can constrain evolutionary models of very low mass stars and brown dwarfs.

Journal Article↗
PubMed2000

Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis.

An information theoretic approach is used to examine the magnitude and origin of associations among amino acid sites in the basic helix-loop-helix (bHLH) family of transcription factors. Entropy and mutual information values are used to summarize the variability and covariability of amino acids comprising the bHLH domain for 242 sequences. When these quantitative measures are integrated with crystal structure data and summarized using helical wheels, they provide important insights into the evolution of three-dimensional structure in these proteins. We show that amino acid sites in the bHLH domain known to pack against each other have very low entropy values, indicating little residue diversity at these contact sites. Noncontact sites, on the other hand, exhibit significantly larger entropy values, as well as statistically significant levels of mutual information or association among sites. High levels of mutual information indicate significant amounts of intercorrelation among amino acid residues at these various sites. Using computer simulations based on a parametric bootstrap procedure, we are able to partition the observed covariation among various amino acid sites into that arising from phylogenetic (common ancestry) and stochastic causes and those resulting from structural and functional constraints. These results show that a significant amount of the observed covariation among amino acid sites is due to structural/functional constraints, over and above the covariation arising from phylogenetic constraints. These quantitative analyses provide a highly integrated evolutionary picture of the multidimensional dynamics of sequence diversity and protein structure.

Amino Acids↗
PubMed1991

Ancestral transfer of symbionts between cockroaches and termites: an alternative hypothesis.

Closely related cellulolytic protozoa reside in the hindguts of extant woodroaches (Cryptocercidae) and termites (Isoptera). The evolutionary origin of these symbiotic relationships in the two lineages is uncertain. Transfer of protozoa between ancestors of modern Cryptocercus and termites remains a valid alternative theory to the established hypothesis of symbiont inheritance from a common ancestor. Nalepa's (Proc. R. Soc. Lond. B 246, 185 (1991] concerns regarding the protozoan transfer hypothesis focus on the biology of modern species, and neglect to consider the evolutionary framework of an ancestral dynamic postulated to occur among Palaeozoic insects. Legitimacy of the symbiont transfer theory removes the constraint of interpreting presence of cellulolytic protozoa as a synapomorphy between Cryptocercidae and Isoptera, with potential impact on objective resolution of dictyopteran phylogeny.

Animals↗
PubMed2001

Natural selection of the critical period for language acquisition.

The language acquisition period in humans lasts about 13 years. After puberty it becomes increasingly difficult to learn a language. We explain this phenomenon by using an evolutionary framework. We present a dynamical system describing competition between language acquisition devices, which differ in the length of the learning period. There are two selective forces that play a role in determining the critical learning period: (i) having a longer learning period increases the accuracy of language acquisition; (ii) learning is associated with certain costs that affect fitness. As a result, there exists a limited learning period which is evolutionarily stable. This result is obtained analytically by means of a Nash equilibrium analysis of language acquisition devices. Interestingly, the evolutionarily stable learning period does not maximize the average fitness of the population.

Biological Evolution↗
PubMed2006

Self-harm caused by an insect's innate immunity.

It has been a long-held assumption that the innate immune system of insects causes self-harm when used to combat an immune insult. We show empirically that this assumption is correct. Invertebrate innate immunity relies heavily on effector systems which, on activation, produce cytotoxins that kill pathogens. Reliance on these robust, fast-acting, generic killing mechanisms ensures a potent and rapid response to pathogen invasion, but has the potential disadvantage of causing self-damage. We show that the innate immune response against an immune insult produces measurable phenotypic and functional damage to self-tissue in the beetle Tenebrio molitor. This type of self-harm (autoreactivity) and the life-history implications that arise from it are important to understand evolutionary phenomena such as the dynamics between hosts and parasites as well as the nature of immune system costs.

Animals↗
PubMed2025

The effects of cryptic diversity on diversification dynamics analyses in Crocodylia.

Incomplete taxon sampling due to underestimation of present-day biodiversity biases diversification analysis by favouring slowdowns in speciation rates towards the recent time. For instance, in diversification dynamics studies in Crocodylia, long-term low net-diversification rates and slowdowns in speciation rates have been suggested to characterize crocodylian evolution. However, crocodylian cryptic diversity has never been considered. Here, we explore the effects of incorporating cryptic diversity into a diversification dynamics analysis of extant crocodylians. We inferred a time-calibrated cryptic-species-level phylogeny using cytochrome b sequences of 45 lineages compared with the formally recognized 26 crocodylian species. Diversification rate estimates using the cryptic-species-level phylogeny show increasing speciation and net-diversification rates towards the present time, which contrasts with previous findings. Cryptic diversity should be considered in future macroevolutionary analyses; however, the representation of cryptic extinct taxa represents a major challenge. Additionally, further investigation of crocodylian diversification dynamics under different underlying genomic data is encouraged upon advances in population genetics. Our case study adds to the diversification dynamics knowledge of extant taxa and demonstrates that cryptic species and robust taxonomic assessment are essential to study recent biodiversity dynamics with broad implications for evolutionary biology and ecology.

Animals↗
PubMed2025

Recent rapid radiation of apex predators suggests dramatic biodiversity turnover in an ancient lake.

Top predators have oversized influence on food webs and ecosystem dynamics, and introducing a novel predator to a naive environment can have dramatic consequences for endemic biodiversity. Using genomic data, we find that the colonization of Lake Tanganyika by Lates fishes-the top predators in this ancient lake-occurred more recently than other diverse clades within the lake. Diversification into four endemic Lates species occurred within the lake during a time of dramatic changes in lake levels driven by glacial-interglacial cycles, supporting the hypothesis that these fluctuations were a "species pump" for lacustrine taxa. These lake level fluctuations also likely contributed to multiple admixture events among Lates species during the Pleistocene (~90-500 Kya). Together, our findings suggest a dynamic and environmentally-linked evolutionary history of this predator radiation, and that their colonization of the lake and subsequent diversification likely had dramatic ecosystem consequences for taxa already present in Lake Tanganyika.

Journal Article↗
PubMed2025

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability.

Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 &#xd7; 10-9 and an indel mutation rate of 2.75 &#xd7; 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 de novo loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene conversion events. The genome-wide gene conversion rate was estimated at 2.62 &#xd7; 10-5 per heterozygous site per generation. These findings provide a comprehensive view of the mutation spectrum, selective pressures, and mechanisms underlying genome stability in D. obtusa.

Daphnia obtusa↗
PubMed2006

Microsatellite analysis reveals strong but differential impact of a social parasite on its two host species.

The speed and the dynamics of the co-evolutionary process strongly depend on the relative strengths of reciprocal selection pressures exerted by the interacting species. Here, we investigate the influence of an obligate social parasite, the slave-making ant Harpagoxenus sublaevis, on populations of the two main host species Leptothorax acervorum and Leptothorax muscorum from a German ant community. A combination of genetic and demographic data allowed us to analyse the consequences of raiding pressure on the hosts' life history and possible host preferences of the parasite. We can demonstrate that slave raids during which the social parasite pillages brood from neighbouring host colonies are both frequent and extremely destructive for both host species. Microsatellite analysis showed that, on average, a single slave-maker colony conducts more than three raids per year and that host colonies mostly perish in the aftermath of these parasite attacks. Only in few cases, surviving nests of previously raided host colonies were found in the surroundings of slave-maker colonies. As a consequence of the high prevalence of parasites and their recurrent and devastating slave raids on host colonies, the life expectancy of host colonies was severely reduced. Combining our results on host-specific parasitic colony founding and raiding frequencies with the post-raid survival rate, we can demonstrate an overall higher mortality rate for the smaller host species L. muscorum. This might be caused by a preference of H. sublaevis for this secondary host species as demographic data on host species usage indicate.

Animals↗
PubMed2000

Identification and psychic closure. A dynamic structuralist approach of the psyche

In this paper, the emergence of psychic structures is conceived within a dynamic structuralist framework, developed in dialogue with the semiotic and dynamic viewpoint on levels from evolutionary systems theory. If psychic structures emerge, it is because they are particular kinds of organizationally closed systems that interpret the variety from below (the biological level) for the level above (the social level). The mechanism of psychic closure is presented as the key mechanism for the constitution of psychic structures, and is interpreted in terms of identification: an identificatory judgment is a self-referential, closing judgment that involves a reinterpretation of the level below (the organic body) and is addressed to the level above (the fellow human being). The way in which identification has worked determines the kinds of psychic structures that are formed and also leads to different kinds of signifying practices. Different types of identification are discussed and a brief presentation of clinical arguments serves to illustrate the determinative role of identification in the formation of psychic structures.

Journal Article↗
PubMed2002

How host-microbial interactions shape the nutrient environment of the mammalian intestine.

Humans and other mammals are colonized by a vast, complex, and dynamic consortium of microorganisms. One evolutionary driving force for maintaining this metabolically active microbial society is to salvage energy from nutrients, particularly carbohydrates, that are otherwise nondigestible by the host. Much of our understanding of the molecular mechanisms by which members of the intestinal microbiota degrade complex polysaccharides comes from studies of Bacteroides thetaiotaomicron, a prominent and genetically manipulatable component of the normal human and mouse gut. Colonization of germ-free mice with B. thetaiotaomicron has shown how this anaerobe modifies many aspects of intestinal cellular differentiation/gene expression to benefit both host and microbe. These and other studies underscore the importance of understanding precisely how nutrient metabolism serves to establish and sustain symbiotic relationships between mammals and their bacterial partners.

Animals↗
PubMed2005

The transmembrane oligomers of coronavirus protein E.

We have tested the hypothesis that severe acute respiratory syndrome (SARS) coronavirus protein E (SCoVE) and its homologs in other coronaviruses associate through their putative transmembrane domain to form homooligomeric alpha-helical bundles in vivo. For this purpose, we have analyzed the results of molecular dynamics simulations where all possible conformational and aggregational space was systematically explored. Two main assumptions were considered; the first is that protein E contains one transmembrane alpha-helical domain, with its N- and C-termini located in opposite faces of the lipid bilayer. The second is that protein E forms the same type of transmembrane oligomer and with identical backbone structure in different coronaviruses. The models arising from the molecular dynamics simulations were tested for evolutionary conservation using 13 coronavirus protein E homologous sequences. It is extremely unlikely that if any of our assumptions were not correct we would find a persistent structure for all the sequences tested. We show that a low energy dimeric, trimeric and two pentameric models appear to be conserved through evolution, and are therefore likely to be present in vivo. In support of this, we have observed only dimeric, trimeric, and pentameric aggregates for the synthetic transmembrane domain of SARS protein E in SDS. The models obtained point to residues essential for protein E oligomerization in the life cycle of the SARS virus, specifically N15. In addition, these results strongly support a general model where transmembrane domains transiently adopt many aggregation states necessary for function.

Binding Sites↗
PubMed1998

The Role of Weak Interactions in Biological Systems: the Dual Dynamics Model.

The dual dynamics model is a random autonomous network of nodes whose dynamical behavior is determined by both strong and weak interactions. The model combines discrete decision-making features reflective of logical operations with arithmetic features that represent graded influences. Dual dynamics abstracts the ubiquitous fact that biological systems at all levels of organization consist of components that respond both to specific (strong) signals and to the cumulative effect of numerous weak interactions. We have thoroughly studied the dynamical characteristics of three-valued dual dynamics networks in the range from four to 14 nodes and have compared these characteristics to those of non-boolean three-valued networks (without weak interaction) and to Kauffman boolean networks. Properties studied include: attractor length, number of attractors, basin sizes, orbital stability, and evolutionary transformability in response both to individual and cumulative mutations (where mutations are implemented as random changes in the response of a node to the pattern of strong influences impinging on it). The introduction of weak interactions and their manner of coupling to strong interactions has major altering effects on these properties. With suitable coupling it is possible to significantly enhance equifinality and evolutionary transformability. The model demonstrates that self-organizing dynamics are compatible with evolutionary plasticity when weak interactions are taken into account.Copyright 1998 Academic Press

Journal Article↗