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PubMed2004

On the dependence of speciation rates on species abundance and characteristic population size.

The question of the potential importance for speciation of large/small population sizes remains open. We compare speciation rates in twelve major taxonomic groups that differ by twenty orders of magnitude in characteristic species abundance (global population number). It is observed that the twenty orders of magnitude's difference in species abundances scales to less than two orders of magnitude's difference in speciation rates. As far as species abundance largely determines the rate of generation of intraspecific endogenous genetic variation, the result obtained suggests that the latter rate is not a limiting factor for speciation. Furthermore, the observed approximate constancy of speciation rates in different taxa cannot be accounted for by assuming a neutral or nearly neutral molecular clock in subdivided populations. Neutral fixation is only relevant in sufficiently small populations with 4N(e)v < 1, which appears an unrealistic condition for many taxa of the smaller organisms. Further research is clearly needed to reveal the mechanisms that could equate the evolutionary pace in taxa with dramatically different population sizes

Animals↗
PubMed2006

Game theory and human evolution: a critique of some recent interpretations of experimental games.

Economists and psychologists have been testing Nash equilibrium predictions of game theory models of human behavior. In many instances, humans do not conform to the predictions. These results are of great interest to biologists because they also raise questions about well-known ESS models of cooperation. Cooperation in certain one-shot, anonymous interactions, and a willingness to punish others at a net cost to oneself are some of the most intriguing deviations from standard theory. One proposed explanation for these results that is receiving increasing attention invokes the cultural group selection of 'other regarding' social norms. We critically review this explanation. We conclude that experimental results reveal limits in two implicit models of cognitive structure commonly employed by economists and evolutionary biologists.

Altruism↗
PubMed2006

Heterogeneous colonization pattern of European Cyprinids, as highlighted by the dace complex (Teleostei: Cyprinidae).

The dace (Leuciscus leuciscus), with a very large geographic distribution all over Europe, represents an interesting species model for studies of the global mechanisms underlying aquatic system biodiversity. To assess the congruence with the past colonization process hypothesis of the freshwater fauna in Western Europe, we investigated the evolutionary history of this species, by integrating morphological variation (eight meristic characters), mitochondrial (cytochrome b, 16S rDNA and control region, over a total of 2169 bp) and nuclear (12 allozymes loci) phylogenetic relationships, and investigating population dynamics via expansion, migration, bottleneck, and divergence time analyses. We carried out nested clade phylogeographic analysis for a total of 663 specimens from 31 populations taken from all over the distribution area. Unlike previous studies, we found that L. leuciscus is currently constituted by five lineages belonging to two clades (yielding 6.3% of pairwise divergence). The relationships between these lineages were accounted for by complex biogeographical patterns due to Pliocene and Pleistocene paleoclimatic events, validating the identification of new glacial refuges for freshwater fish in Western Europe. Finally, we demonstrated hybridization between L. leuciscus and Leuciscus idus.

Animal Migration↗
PubMed2005

Multiple objective evolutionary algorithm for temporal linguistic rule extraction.

Autonomous temporal linguistic rule extraction is an application of growing interest for its relevance to both decision support systems and fuzzy controllers. In the presented work, rules are evaluated using three qualitative metrics based on their representation on the truth space diagram. Performance metrics are then treated as competing objectives and the multiple objective evolutionary algorithm is used to search for an optimal set of nondominant rules. Novel techniques for data pre-processing and rule set post-processing are designed that deal directly with the delays involved in dynamic systems. Data collected from a simulated hot and cold water mixer are used to validate the proposed procedure.

Algorithms↗
PubMed2005

Herbivores cause a rapid increase in hereditary symbiosis and alter plant community composition.

Microbial symbioses are ubiquitous in nature. Hereditary symbionts warrant particular attention because of their direct effects on the evolutionary potential of their hosts. In plants, hereditary fungal endophytes can increase the competitive ability, drought tolerance, and herbivore resistance of their host, although it is unclear whether or how these ecological benefits may alter the dynamics of the endophyte symbiosis over time. Here, we demonstrate that herbivores alter the dynamics of a hereditary symbiont under field conditions. Also, we show that changes in symbiont frequency were accompanied by shifts in the overall structure of the plant community. Replicated 25-m2 plots were enriched with seed of the introduced grass, Lolium arundinaceum at an initial frequency of 50% infection by the systemic, seed-transmitted endophyte Neotyphodium coenophialum. Over 54 months, there was a significantly greater increase in endophyte-infection frequency in the presence of herbivores (30% increase) than where mammalian and insect herbivory were experimentally reduced by fencing and insecticide application (12% increase). Under ambient mammalian herbivory, the above-ground biomass of nonhost plant species was reduced compared with the mammal-exclusion treatment, and plant composition shifted toward greater relative biomass of infected, tall fescue grass. These results demonstrate that herbivores can drive plant-microbe dynamics and, in doing so, modify plant community structure directly and indirectly.

Animals↗
PubMed2007

Rapid evolution of flowering time by an annual plant in response to a climate fluctuation.

Ongoing climate change has affected the ecological dynamics of many species and is expected to impose natural selection on ecologically important traits. Droughts and other anticipated changes in precipitation may be particularly potent selective factors, especially in arid regions. Here we demonstrate the evolutionary response of an annual plant, Brassica rapa, to a recent climate fluctuation resulting in a multiyear drought. Ancestral (predrought) genotypes were recovered from stored seed and raised under a set of common environments with descendant (postdrought) genotypes and with ancestorxdescendant hybrids. As predicted, the abbreviated growing seasons caused by drought led to the evolution of earlier onset of flowering. Descendants bloomed earlier than ancestors, advancing first flowering by 1.9 days in one study population and 8.6 days in another. The intermediate flowering time of ancestorxdescendant hybrids supports an additive genetic basis for divergence. Experiments confirmed that summer drought selected for early flowering, that flowering time was heritable, and that selection intensities in the field were more than sufficient to account for the observed evolutionary change. Natural selection for drought escape thus appears to have caused adaptive evolution in just a few generations. A systematic effort to collect and store propagules from suitable species would provide biologists with materials to detect and elucidate the genetic basis of further evolutionary shifts driven by climate change.

Biological Evolution↗
PubMed2003

A natural class of robust networks.

As biological studies shift from molecular description to system analysis we need to identify the design principles of large intracellular networks. In particular, without knowing the molecular details, we want to determine how cells reliably perform essential intracellular tasks. Recent analyses of signaling pathways and regulatory transcription networks have revealed a common network architecture, termed scale-free topology. Although the structural properties of such networks have been thoroughly studied, their dynamical properties remain largely unexplored. We present a prototype for the study of dynamical systems to predict the functional robustness of intracellular networks against variations of their internal parameters. We demonstrate that the dynamical robustness of these complex networks is a direct consequence of their scale-free topology. By contrast, networks with homogeneous random topologies require fine-tuning of their internal parameters to sustain stable dynamical activity. Considering the ubiquity of scale-free networks in nature, we hypothesize that this topology is not only the result of aggregation processes such as preferential attachment; it may also be the result of evolutionary selective processes.

Biophysical Phenomena↗
PubMed2004

Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans.

ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The approximately 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism.

ADP-Ribosylation Factors↗
PubMed2004

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Animals↗
PubMed1995

The population biology of suid herpesvirus 1.

Suid herpesvirus 1 (SHV-1) is the causative agent of Aujeszky's disease (AD, pseudorabies), known worldwide as a major economical threat to pig farming. Measures are taken in many countries to control or eradicate the disease and considerable effort therefore has been focused on the elucidation of the epizootiology of the infection. These studies were greatly facilitated by the possibilities, first reported in the early eighties, to identify SHV-1 strains by means of restriction fragment pattern (RFP) analysis. In the present thesis some molecular biological aspects of SHV-1 are reviewed. In addition, studies are reviewed focusing on three topics: (i) methodological aspects of molecular strain identification, (ii) various epizootiological features of the SHV-1 infection, and (iii) the population dynamics of coexisting virus particles comprising a field strain, tentatively defined as a transmissible entity. A systematization of the European isolates of SHV-1 was elaborated based on molecular characterization of various genome types and an evolutionary tree for some of the distinct types was suggested. For some of the types geographical niches could be identified indicating that the intertypic differences had been stable for decades. By the characterization of 5-10 isolates from each herd, in which a SHV-1 strain had been newly introduced, strain inherent non-intertypic genomic variations consistently could be demonstrated. Some strains appeared to consist of fairly homogeneous pools of genomic variants, while other strains appeared highly heterogeneous. Some exhibited hypervariable regions in the genome. The pool of genomic variants present in a strain was found to be a highly specific and most often a conservative characteristic of a strain. Yet, fluctuations in the proportions of subpopulations occasionally were seen. Thus, while one isolate from an outbreak might be a poor representative of the pool of variants comprising the causative strain, the analysis of 5-10 isolates from each outbreak might taken together provide the basis of an extremely fine resolving potential. Outbreaks of AD during the finishing stage of the Danish eradication campaign were subjected to intensive molecular epizootiological studies. The analysis of representative older isolates of SHV-1 revealed that only type III was present in Denmark prior to 1985. In 1985 type IIa isolates emerged in a border area, and since 1986 type IIp and IIa were the only types identified in Denmark. Severe epizootics have been recorded in border areas in Denmark since the winter of 1986/87.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1996

Comparison of low oxidoreduction potential cytochrome c553 from Desulfovibrio vulgaris with the class I cytochrome c family.

The cytochrome c553 from Desulfovibrio vulgaris (DvH c553) is of importance in the understanding of the relationship of structure and function of cytochrome c due to its lack of sequence homology with other cytochromes, and its abnormally low oxido-reduction potential. In evolutionary terms, this protein also represents an important reference point for the understanding of both bacterial and mitochondrial cytochromes c. Using the recently determined nuclear magnetic resonance (NMR) structure of the reduced protein we compare the structural, dynamic, and functional characteristics of DvH c553 with members of both the mitochondrial and bacterial cytochromes c to characterize the protein in the context of the cytochrome c family, and to understand better the control of oxide-reduction potential in electron transfer proteins. Despite the low sequence homology, striking structural similarities between this protein and representatives of both eukaryotic [cytochrome c from tuna (tuna c)] and prokaryotic [Pseudomonas aeruginosa c551 (Psa c551)] cytochromes c have been recognized. The previously observed helical core is also found in the DvH c553. The structural framework and hydrogen bonding network of the DvH c553 is most similar to that of the tuna c, with the exception of an insertion loop of 24 residues closing the heme pocket and protecting the propionates, which is absent in the DvH c553. In contrast, the Psa c551 protects the propionates from the solvent principally by extending the methionine ligand arm. The electrostatic distribution at the recognized encounter surface around the heme in the mitochondrial cytochrome is reproduced in the DvH c553, and corresponding hydrogen bonding networks, particularly in the vicinity of the heme cleft, exist in both molecules. Thus, although the cytochrome DvH c553 exhibits higher primary sequence homology to other bacterial cytochromes c, the structural and physical homology is significantly greater with respect to the mitochondrial cytochrome c. The major structural and functional difference is the absence of solvent protection for the heme, differentiating this cytochrome from both reference cytochromes, which have evolved different mechanisms to cover the propionates. This suggests that the abnormal redox potential of the DvH c553 is linked to the raised accessibility of the heme and supports the theory that redox potential in cytochromes is controlled by heme propionate solvent accessibility.

Amino Acid Sequence↗
PubMed1998

From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.

Because a large number of molecular mechanisms involved in gene regulation have been described during the last decades, it is now becoming possible to address questions about the global structure of gene regulatory networks, at least in the case of some of the best-characterized organisms. This paper presents a global characterization of the transcriptional regulation in Escherichia coli on the basis of the current data. The connectivity of the corresponding network was evaluated by analyzing the distribution of the number of genes regulated by a given regulatory protein, and the distribution of the number of regulatory genes regulating a given regulated gene. The mean connectivity found (between 2 and 3) shows a rather loosely interconnected structure. Special emphasis is given to circular sequences of interactions ("circuits") because of their critical dynamical properties. Only one-element circuits were found, in which negative autoregulation is the dominant architecture. These global properties are discussed in light of several pertinent theoretical approaches, as well as in terms of physiological and evolutionary considerations.

Bacterial Proteins↗
PubMed2006

Sexual conflict and the evolution of female preferences for indicators of male quality.

Males and females have opposing interests when it comes to the honesty of signals used in mate choice. The existence of this sexual conflict has long been acknowledged, but its consequences have not been fully investigated. By applying adaptive dynamics methods and individual-based computer simulations to a standard model for good-genes sexual selection, we show that sexual conflict over condition-dependent signaling can prevent the handicap process from ever attaining an evolutionary equilibrium. We outline the parameter conditions and properties of the underlying genetics conducive to nonequilibrium behavior and discuss the potential of such behavior to explain the elaboration and frequent phylogenetic loss of sexually selected traits. We also evaluate its consequences for well-established insights of sexual selection theory previously shown to apply when female mating preference and male ornament expression do converge on stable equilibrium levels. Contrary to equilibrium expectation, a continual change of condition-dependent signaling enables the evolution of a costly preference for a pure epistatic indicator and the evolution of preferences for redundant signals or a large number of independent ornaments. We thus conclude that seemingly general results of sexual selection theory, insofar as these are based on equilibrium considerations, do not extend to cases where nonequilibrium behavior occurs.

Adaptation, Biological↗
PubMed2000

Code-duality and the epistemic cut.

Howard Pattee has claimed that an epistemic cut separates the world from observers and therefore from organisms. The epistemic cut imputes a linguistic mode of operation to living systems. Among evolutionary systems-theorists on the other hand there seems to be a tendency to consider living systems as just one among many other kinds of evolutionary systems that, in principle, can all be described on the basis of thermodynamics or infodynamics. This paper searches a third position, in which the epistemic cut position is defended without adopting Pattee's distinction between a dynamic and a linguistic mode. It is observed that even the dynamic mode in living systems is always a semiotic mode although index- and analog-coded rather than symbolic and digitally coded. The analog-coded messages corresponds to a kind of tacit knowledge hidden in macromolecular structure and shape (e.g., molecular complementarity), and in organismic architecture and communication, that is, in the semiotic interactions of the body.

Biological Evolution↗
PubMed1998

Active nuclear pore complexes in Chironomus: visualization of transporter configurations related to mRNP export.

The Nuclear Pore Complex (NPC) regulates nucleocytoplasmic transport by providing small channels for passive diffusion and multiple docking surfaces that lead to a central translocation channel for active transport. In this study we have investigated by high resolution scanning and transmission electron microscopy the dynamics of NPC structure in salivary gland nuclei from Chironomus during Balbiani ring (BR) mRNP translocation, and present evidence of rearrangement of the transporter related to mRNP export. Analysis of the individual NPC components verified a strong evolutionary conservation of NPC structure between vertebrates and invertebrates. The transporter is an integral part of the NPC and is composed of a central short double cylinder that is retained within the inner spoke ring, and two peripheral globular assemblies which are tethered to the cytoplasmic and nucleoplasmic coaxial rings by eight conserved internal ring filaments. Distinct stages of BR mRNP nuclear export through the individual NPC components were directly visualized and placed in a linear transport sequence. The BR mRNP first binds to the NPC basket, which forms an expanded distal basket ring. In this communication we present stages of BR mRNP transport through the nucleoplasmic, central and cytoplasmic transporter subunits, which change their conformation during mRNP translocation, and the emergence of mRNP into the cytoplasm. We propose that the reorganization of the basket may be driven, in part, by an active translocation process at the transporter. Furthermore, the images provide dramatic evidence that the transporter functions as a central translocation channel with transiently open discrete gates in its globular assemblies. A model of NPC transporter reorganization accompanied with mRNP translocation is discussed.

Animals↗
PubMed1997

Continuous stability and evolutionary convergence.

A stochastic process of long-term evolution due to mutation and selection is defined over an asexually reproducing population, with selection according to a population game with a one-dimensional continuity of pure strategies. Limiting the analysis to mutations of small effect, it is shown that long-term dynamic stability in such a process is equivalent to continuous stability in the relevant population game. In the case of a one-dimensional strategy set (but not necessarily if the strategy set is multi-dimensional), this result is virtually independent of the distribution of mutations.

Animals↗
PubMed1996

Optimum superimposition of protein structures: ambiguities and implications.

BACKGROUND: Techniques for comparison and optimum superimposition of protein structures are indispensable tools, providing the basis for statistical analysis, modeling, prediction and classification of protein folds. Observed similarity of structures is frequently interpreted as an indication of evolutionary relatedness. A variety of advanced techniques are available, but so far the important issue of uniqueness of structural superimposition has been largely neglected. We set out to investigate this issue by implementing an efficient algorithm for structure superimposition enabling routine searches for alternative alignments. RESULTS: The algorithm is based on optimum superimposition of structures and dynamic programming. The implementation is tested and validated using published results. In particular, an automatic classification of all protein folds in a recent release of the protein data bank is performed. The results obtained are closely related to published data. Surprisingly, for many protein pairs alternative alignments are obtained. These alignments are indistinguishable in terms of number of equivalent residues and root mean square error of superimposition, but the respective sets of equivalent residue pairs are completely distinct. Alternative alignments are observed for all protein architectures, including mixed alpha/beta folds. CONCLUSIONS: Superimposition of protein folds is frequently ambiguous. This has several implications on the interpretation of structural similarity with respect to evolutionary relatedness and it restricts the range of applicability of superimposed structures in statistical analysis. In particular, studies based on the implicit assumption that optimum superimposition of structures is unique are bound to be misleading.

Algorithms↗