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PubMed1989

Could natural selection account for molecular evolution and polymorphism?

A model of molecular evolution is presented that is based on the combined action of natural selection, genetic drift, and mutation. The mathematical description of the model uses strong-selection, weak-mutation limits to approximate the dynamics of multidimensional diffusion processes with one dimensional Markov chains. This approach leads to a great simplification of the dynamics and provides a unified method for describing many different mechanisms of natural selection. In this paper two models are examined, one based on selection in a randomly fluctuating environment, the other on overdominance. Both models exhibit similar dynamics, with a rapid buildup phase that introduces new alleles into the population, followed by a relatively quiescent phase where new alleles may enter and leave the population at a low rate. If occasional extreme environmental changes occur that favor particular alleles, the resulting dynamics turn out to be in remarkable agreement with many of the observations on molecular evolution and polymorphism. Thus the model is at least as successful as the neutral theory in accounting for evolutionary events at the molecular level.

Biological Evolution↗
PubMed2001

Convergence in evolutionary programs with self-adaptation.

Evolutionary programs are capable of finding good solutions to difficult optimization problems. Previous analysis of their convergence properties has normally assumed the strategy parameters are kept constant, although in practice these parameters are dynamically altered. In this paper, we propose a modified version of the 1/5-success rule for self-adaptation in evolution strategies (ES). Formal proofs of the long-term behavior produced by our self-adaptation method are included. Both elitist and non-elitist ES variants are analyzed. Preliminary tests indicate an ES with our modified self-adaptation method compares favorably to both a non-adapted ES and a 1/5-success rule adapted ES.

Algorithms↗
PubMed2004

Folding stabilizes the evolution of catalysts.

Sequence folding is known to determine the spatial structure and catalytic function of proteins and nucleic acids. We show here that folding also plays a key role in enhancing the evolutionary stability of the intermolecular recognition necessary for the prevalent mode of catalytic action in replication, namely, in trans, one molecule catalyzing the replication of another copy, rather than itself. This points to a novel aspect of why molecular life is structured as it is, in the context of life as it could be: folding allows limited, structurally localized recognition to be strongly sensitive to global sequence changes, facilitating the evolution of cooperative interactions. RNA secondary structure folding, for example is shown to be able to stabilize the evolution of prolonged functional sequences, using only a part of this length extension for intermolecular recognition, beyond the limits of the (cooperative) error threshold. Such folding could facilitate the evolution of polymerases in spatially heterogeneous systems. This facilitation is, in fact, vital because physical limitations prevent complete sequence-dependent discrimination for any significant-size biopolymer substrate. The influence of partial sequence recognition between biopolymer catalysts and complex substrates is investigated within a stochastic, spatially resolved evolutionary model of trans catalysis. We use an analytically tractable nonlinear master equation formulation called PRESS (McCaskill et al., Biol. Chem. 382: 1343-1363), which makes use of an extrapolation of the spatial dynamics down from infinite dimensional space, and compare the results with Monte Carlo simulations.

Catalysis↗
PubMed2006

MultiSeq: unifying sequence and structure data for evolutionary analysis.

BACKGROUND: Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. RESULTS: Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. CONCLUSION: MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/

Algorithms↗
PubMed1998

Mitochondrial DNA: a tool for populational genetics studies.

Mitochondria are cellular organelles that have the function of the oxidative phosphorilation and the formation of ATP. In humans, the mtDNA is a double-stranded, circular, covalent closed molecule of 16.5 kb. The mtDNA is inherited as a haploid from the mother and heteroplasmy has been found rarely. From a populational perspective, it could be considered as a system of small, sexually isolated demes, or clonal lineages, with an evolutionary rate 5 to 10 times faster than the nuclear genome. All these characteristics make this molecule ideal for evolutionary studies. We present two applications of this molecule in genetical studies. One of these is referred to the Balearic Islands populations, Majorca, Minorca, Ibiza, and Chuetas. The other example is the populational dynamics of the different mitochondrial haplotypes in Drosophila subobscura. We also discuss the importance of nuclear markers to complete these studies as well as the study of the Y chromosome to compensate the bias produced by the study of only the mtDNA.

Animals↗
PubMedDate not supplied

[Enzyme-substrate mode of action for bacteria survival in water biotic community].

The role of enzyme--substrate interactions for the survival of bacteria in natural biocenoses has been analyzed with the systems "lysozyme-antilysozyme", "histon-antihiston" used as models. The conception of a possible universal mechanism for supporting the circulation of pathogenic and opportunistic microorganisms among eukaryotes, irrespective of their evolutionary status and environment, has been formulated. This mechanism is ensured by the natural resistance of the eukaryotic cells and by persistence factors on the part of the pathogen; as a result, the dynamic system of interactions is formed which facilitates the survival of microorganisms due to their persistence potential. New knowledge thus obtained opens prospects in the study of sanitary and ecological aspects of water biocenoses.

Animals↗
PubMed2006

Emergence of asymmetry in evolution.

We investigate symmetry-breaking bifurcation patterns in evolution in the framework of adaptive dynamics (AD). We define weak and strong symmetry. The former applies for populations where only the simultaneous reflection of all individuals is an invariant transformation. The symmetry is strong in populations where reflection of some, but not all, individuals leaves the situation unchanged. We show that in case of weak symmetry evolutionary branching can lead to the emergence of two asymmetric variants, which are mirror images of each other, and the loss of the symmetric ancestor. We also show that in case of strong symmetry, evolutionary branching can occur into a symmetric and an asymmetric variant, both of which survive. The latter, asymmetric branching differs from the generic branching patterns of AD, which is always symmetric. We discuss biological examples for weak and strong symmetries and a specific model producing the new kind of branching.

Animals↗
PubMed2001

Evolution of East Asian ninespine sticklebacks as shown by mitochondrial DNA control region sequences.

Evolutionary processes in East Asian ninespine sticklebacks (Pungitius spp.), including both extremes of armor morphology in the genus, were demonstrated with mitochondrial DNA control region (CR) phylogeny. Entire CR sequences (830-930 bp long) were determined for three species: the most heavily armored (P. sinensis), the most reduced (P. tymensis), and an intermediate (P. pungitius). The former two species are endemic to East Asia, the latter being circumpolar. Three major lineages (A, B, and C) were revealed, whereas both the phylogenetic trees and the insertion sequence dynamics supported the polyphyly of P. sinensis. Haplotypes of the mainland populations of P. sinensis possessed lineage B, being the sister group of P. tymensis lineage A. Island populations of P. sinensis, however, possessed lineage C, along with all P. pungitius haplotypes. A molecular clock hypothesis was clearly rejected for the CR sequences, significantly slower evolutionary rates being observed in the P. tymensis lineage. The split of mainland P. sinensis and P. tymensis was considered to have preceded that of the lineage C colonization in East Asia. The contrasting morphology is probably attributable to adaptation of P. tymensis to island freshwater environments and an ecological interaction between P. tymensis and lineage C emigrants.

Animals↗
PubMed1996

Structural features of U6 snRNA and dynamic interactions with other spliceosomal components leading to pre-mRNA splicing.

In the spliceosome, the pre-mRNA, U2 and U6 snRNAs fold into a catalytic structure exhibiting striking similarities with domain V and VI of group II introns. Building of this tripartite structure implies that an evolutionary conserved base pairing between U4 and U6 snRNAs should be disrupted to allow potentially U6 catalytic residue to interact with U2 snRNAs and the pre-mRNA. The steps leading to U4/U6 disruption have been recently discovered and have been shown to involve a modification of the 3' end of U6 snRNA and the hnRNP C protein.

Base Composition↗
PubMed2005

Do telomere dynamics link lifestyle and lifespan?

Identifying and understanding the processes that underlie the observed variation in lifespan within and among species remains one of the central areas of biological research. Questions directed at how, at what rate and why organisms grow old and die link disciplines such as evolutionary ecology to those of cell biology and gerontology. One process now thought to have a key role in ageing is the pattern of erosion of the protective ends of chromosomes, the telomeres. Here, we discuss what is currently known about the factors influencing telomere regulation, and how this relates to fundamental questions about the relationship between lifestyle and lifespan.

Aging↗
PubMed2004

Evolutionary conserved role of ptf1a in the specification of exocrine pancreatic fates.

We have characterized and mapped the zebrafish ptf1a gene, analyzed its embryonic expression, and studied its role in pancreas development. In situ hybridization experiments show that from the 12-somite stage to 48 hpf, ptf1a is dynamically expressed in the spinal cord, hindbrain, cerebellum, retina, and pancreas of zebrafish embryos. Within the endoderm, ptf1a is initially expressed at 32 hpf in the ventral portion of the pdx1 expression domain; ptf1a is expressed in a subset of cells located on the left side of the embryo posteriorly to the liver primordium and anteriorly to the endocrine islet that arises from the posterodorsal pancreatic anlage. Then the ptf1a expression domain buds giving rise to the anteroventral pancreatic anlage that grows posteriorly to eventually engulf the endocrine islet. By 72 hpf, ptf1a continues to be expressed in the exocrine compartment derived from the anteroventral anlage. Morpholino-induced ptf1a loss of function suppresses the expression of the exocrine markers, while the endocrine markers in the islet are unaffected. In mind bomb (mib) mutants, in which delta-mediated notch signalling is defective [Dev. Cell 4 (2003) 67], ptf1a is normally expressed. In addition, the slow-muscle-omitted (smu) mutants that lack expression of endocrine markers because of a defective hedgehog signalling [Curr. Biol. 11(2001) 1358] exhibit normal levels of ptf1a. This indicates that hedgehog signaling plays a different genetic role in the specification of the anteroventral (mostly exocrine) and posterodorsal (endocrine) pancreatic anlagen.

Animals↗
PubMed2024

Extreme elevational migration spurred cryptic speciation in giant hummingbirds.

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Animals↗
PubMed1996

Topology prediction for helical transmembrane proteins at 86% accuracy.

Previously, we introduced a neural network system predicting locations of transmembrane helices (HTMs) based on evolutionary profiles (PHDhtm, Rost B, Casadio R, Fariselli P, Sander C, 1995, Protein Sci 4:521-533). Here, we describe an improvement and an extension of that system. The improvement is achieved by a dynamic programming-like algorithm that optimizes helices compatible with the neural network output. The extension is the prediction of topology (orientation of first loop region with respect to membrane) by applying to the refined prediction the observation that positively charged residues are more abundant in extra-cytoplasmic regions. Furthermore, we introduce a method to reduce the number of false positives, i.e., proteins falsely predicted with membrane helices. The evaluation of prediction accuracy is based on a cross-validation and a double-blind test set (in total 131 proteins). The final method appears to be more accurate than other methods published: (1) For almost 89% (+/-3%) of the test proteins, all HTMs are predicted correctly. (2) For more than 86% (+/-3%) of the proteins, topology is predicted correctly. (3) We define reliability indices that correlate with prediction accuracy: for one half of the proteins, segment accuracy raises to 98%; and for two-thirds, accuracy of topology prediction is 95%. (4) The rate of proteins for which HTMs are predicted falsely is below 2% (+/-1%). Finally, the method is applied to 1,616 sequences of Haemophilus influenzae. We predict 19% of the genome sequences to contain one or more HTMs. This appears to be lower than what we predicted previously for the yeast VIII chromosome (about 25%).

Algorithms↗
PubMed1999

PROFILE: Forest Landscape Management Revisited.

/ Over the last decade, forest management planning has shifted its focus from a production-oriented approach to an ecosystem-based approach. Forest landscape management has thus emerged as a new challenge to forest managers. In this paper we examine the evolutionary process of forest management leading to landscape management and compares and contrasts its concept and principles to its predecessor, the conventional forest resource management approach. It explains the conceptual framework, provides the principles and the improvements over conventional management planning, and discusses different design approaches towards the landscape management concept. However, the paper points out that the evolutionary process of forest management provides sustainable healthy forest ecosystems. Smarter use of information technology, such as geographic information systems and remote sensing, a comprehensive digital spatial database, better understanding of spatial forest ecosystem dynamics across spatial and temporal scales, effective public involvement, better decision-making tools, and development of workable management strategies towards sustainability are prerequisite to make the realization of holistic management approach on the ground happen.KEY WORDS: Forest landscape management; Holistic approach; Spatial structurehttp://link.springer-ny.com/link/service/journals/00267/bibs/24n4p437.html</HEA

Journal Article↗
PubMed2001

Ectopic transposition of a group II intron in natural bacterial populations.

Self-splicing group II introns are thought to be the evolutionary progenitors of eukaryotic spliceosomal introns. The invasion of novel (ectopic) sites by group II introns is considered to be a key mechanism by which spliceosomal introns may have become widely dispersed. However, the dynamics of these events in populations are unknown. In bacteria, only two group II introns have been shown to splice and to be mobile in vivo. One of these introns, RmInt1 from Sinorhizobium meliloti, which encodes a protein with no endonuclease domain, has been shown to invade the ectopic oxi1 site independently of recombinase. In this study, we analysed ectopic transposition of the RmInt1 intron in a natural population of S. meliloti. We characterized S. meliloti isolates by polymerase chain reaction amplification of a gene, dapB, which is found only on the pRmeGR4b plasmid diagnostic of GR4-type strains. The diversity within this specific field population of bacteria was analysed by restriction fragment length polymorphism using ISRm2011-2 (homing site of RmInt1) and RmInt1 as probes. We found that ectopic transposition of RmInt1 to the oxi1 site occurred in this natural bacterial population. This ectopic transposition was also the most frequent genetic event observed. This work provides further evidence that the ectopic transposition of group II introns is an important mechanism for their spread in natural bacterial populations.

DNA Transposable Elements↗
PubMed1996

New strategies to combat HIV drug resistance.

Recent insights into HIV dynamics argue strongly for early intervention with antiretroviral combinations designed to block resistant mutations. By using more potent agents and taking advantage of drug selective pressure to force the emergence of strains with reduced evolutionary fitness, investigators are attempting to bring HIV replication to a halt. And in many cases, they appear to be succeeding.

Anti-HIV Agents↗
PubMed2000

Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection.

Sexual reproduction presents significant challenges to formal treatment of evolutionary processes. A starting point for systematic treatments of ecological and evolutionary phenomena has been provided by the gene-centered view of evolution which assigns effective fitness to each allele instead of each organism. The gene-centered view can be formalized as a dynamic mean-field approximation applied to genes in reproduction and selection dynamics. We show that the gene-centered view breaks down for symmetry breaking and pattern formation within a population and show that spatial distributions of organisms with local mating neighborhoods in the presence of disruptive selection give rise to such symmetry breaking and pattern formation in the genetic composition of local populations. Global dynamics follows conventional coarsening of systems with nonconserved order parameters. The results have significant implications for the ecology of genetic diversity and species formation.

Alleles↗
PubMed2001

Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor.

A method based on neural networks is trained and tested on a nonredundant set of beta-barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane beta strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane beta-strands included in the training set, 93% are correctly assigned. The predictor includes an algorithm of model optimization, based on dynamic programming, that correctly models eight out of the 11 proteins present in the training/testing set. In addition, protein topology is assigned on the basis of the location of the longest loops in the models. We propose this as a general method to fill the gap of the prediction of beta-barrel membrane proteins.

Algorithms↗