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PubMed1994

Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.

We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.

Adaptation, Physiological↗
PubMed2003

Linking dynamical and population genetic models of persistent viral infection.

This article develops a theoretical framework to link dynamical and population genetic models of persistent viral infection. This linkage is useful because, while the dynamical and population genetic theories have developed independently, the biological processes they describe are completely interrelated. Parameters of the dynamical models are important determinants of evolutionary processes such as natural selection and genetic drift. We develop analytical methods, based on coupled differential equations and Markov chain theory, to predict the accumulation of genetic diversity within the viral population as a function of dynamical parameters. These methods are first applied to the standard model of viral dynamics and then generalized to consider the infection of multiple host cell types by the viral population. Each cell type is characterized by specific parameter values. Inclusion of multiple cell types increases the likelihood of persistent infection and can increase the amount of genetic diversity within the viral population. However, the overall rate of gene sequence evolution may actually be reduced.

Biological Evolution↗
PubMed2001

Evolutionary stability concepts for N-species frequency-dependent interactions.

The classical static concept of an evolutionarily stable strategy (ESS) for a single species gives rise to two new notions when there are more than two species (called an N-species ESS and RL-stability). The paper relates these to the dynamic stability of monomorphic and polymorphic evolutionary systems. It is shown that RL-stability implies the global asymptotic stability of either system with or without mutations. However, the N-species ESS only implies stability of the monomorphic system.

Animals↗
PubMed1998

The foot-and-mouth disease RNA virus as a model in experimental phylogenetics.

Phylogenetic reconstruction methods are subject to two types of limitations: our knowledge about the true history of organisms and the gross simplification implied in the numerical simulation models of the relationships between them. In such a situation, experimental phylogenetics provides a way to assess the accuracy of the phylogenetic reconstruction methods. Nonetheless, this capacity is only feasible for organisms in which replication and mutation rates are high enough to provide valuable data. On the other hand, experimental phylogenetics also provides insights on the main evolutionary processes acting on viral variability under different population dynamics. Our study with the foot-and-mouth disease virus (FMDV) strongly suggests that the phylogenetic reconstruction methods can infer erroneous phylogenies due to nucleotide convergences between isolates belonging to different experimental lineages. We also point out that the diverse evolutionary mechanisms acting in different experimental dynamics generate alterations and change the frequencies of genetic variants, which can lead to the misinterpretation of the real evolutionary history.

Animals↗
PubMed2002

Cryptic lineages in a small frog: the post-glacial history of the spring peeper, Pseudacris crucifer (Anura: Hylidae).

The spring peeper (Pseudacris crucifer) is believed to have been a primary herpetological invader of eastern North America following the most recent period of glacial retreat. We examined the phylogeographic pattern and population structure of P. crucifer to determine whether the distribution of haplotypic variants reflect post-Pleistocene recolonization dynamics. A number of geographically isolated evolutionary lineages were supported by both maximum parsimony and neighbor-joining analyses, and by coalescence approaches applied to mtDNA. South-western Ontario represents a high level of genotypic diversity (pi) due to the presence of two divergent lineages. The geographic distribution of these lineages are interpreted as reflecting post-glacial recolonization dynamics from separate, isolated refugia during the late Pleistocene that have come into secondary contact in SW Ontario. The phylogenetic placement of haplotypes from the range of P. crucifer bartramiana (Florida and South Carolina) does not allow for monophyly of P. crucifer crucifer, and therefore the bartramiana subspecies designation does not reflect a separate evolutionary lineage.

Animals↗
PubMed2005

The role of log-normal dynamics in the evolution of biochemical pathways.

The study of the scale-free topology in non-biological and biological networks and the dynamics that can explain this fascinating property of complex systems have captured the attention of the scientific community in the last years. Here, we analyze the biochemical pathways of three organisms (Methanococcus jannaschii, Escherichia coli, Saccharomyces cerevisiae) which are representatives of the main kingdoms Archaea, Bacteria and Eukaryotes during the course of the biological evolution. We can consider two complementary representations of the biochemical pathways: the enzymes network and the chemical compounds network. In this article, we propose a stochastic model that explains that the scale-free topology with exponent in the vicinity of gamma approximately 3/2 found across these three organisms is governed by the log-normal dynamics in the evolution of the enzymes network. Precisely, the fluctuations of the connectivity degree of enzymes in the biochemical pathways between evolutionary distant organisms follow the same conserved dynamical principle, which in the end is the origin of the stationary scale-free distribution observed among species, from Archaea to Eukaryotes. In particular, the log-normal dynamics guarantees the conservation of the scale-free distribution in evolving networks. Furthermore, the log-normal dynamics also gives a possible explanation for the restricted range of observed exponents gamma in the scale-free networks (i.e., gamma > or = 3/2). Finally, our model is also applied to the chemical compounds network of biochemical pathways and the Internet network.

Biological Evolution↗
PubMed1999

Dynamic evolution of genomes and the concept of genome space.

A new era in the elucidation of genome evolution has been heralded with the availability of numerous genome sequences. With these data, it has been possible to study evolutionary processes at a greater level of detail in order to characterize features such as gene shuffling, genome rearrangements, base bias composition, and horizontal gene transfer. In this paper, we discuss the evolutionary implications of significant rearrangements within genomes as well as characteristic genomic regions that have been conserved across genomes. This is based on our analysis of orthologous and paralogous genes. We argue that genome plasticity has most likely contributed substantially to the dynamic evolution of genomes. We also describe the characteristic mosaic features of an archaea genome that is comprised of both bacterial and eukaryal elements. Here we investigate base compositional differences as well as the similarity of this species' genes to either bacteria or eukarya. We conclude that these features can be largely explained by the mechanism of horizontal gene transfer. Finally, we introduce the concept of genome space which is defined as the entire set of genomes of all living organisms. We explain its usefulness to describe as well as to gain deeper insight into the general features of the dynamic genomic evolutionary process.

Archaea↗
PubMed2006

Dynamics of mutation and recombination in a replicating population of complementing, defective viral genomes.

In a previous study, we documented that serial passage of a biological clone of foot-and-mouth disease virus (FMDV) at high multiplicity of infection (moi) in cell culture resulted in viral populations dominated by defective genomes that included internal in-frame deletions, affecting the L and capsid-coding regions, and were infectious by complementation. In the present study, analyses of the defective genomes present in individual viral plaques, and of consensus nucleotide sequences determined for the entire genomes of sequential samples, have revealed a continuous dynamics of mutation and recombination. At some points of high genetic instability, multiple minority genomes with different internal deletions co-existed in the population. At later passages, a new defective RNA arose and displaced a related, previously dominant RNA. Nucleotide sequences of the different genomic forms found in sequential isolates have revealed an accumulation of mutations at an average rate of 0.12 substitutions per genome per passage. At the regions around the deletion sites, substantial, minor or no nucleotide sequence identity is found, suggesting relaxed sequence requirements for the occurrence of internal deletions. Competition experiments indicate a selective advantage of late phase defective genomes over their precursor forms. The defective genome-based FMDV retained an expansion of host cell tropism, undergone by the standard virus at a previous stage of the same evolutionary lineage. Thus, despite a complex dynamics of mutation and recombination, and phases of high genetic instability, a biologically relevant phenotypic trait was stably maintained after the evolutionary transition towards a primitive genome segmentation. The results extend the concept of a complex spectrum of mutant genomes to a complex spectrum of defective genomes in some evolutionary transitions of RNA viruses.

Animals↗
PubMed1997

Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes.

The time of spread of human immunodeficiency virus type 1 (HIV-1) from lymphoid to nonlymphoid tissues in the course of infection was investigated by sequence comparisons of variants infecting a range of lymphoid and nonlymphoid tissues from three individuals with AIDS in the pl7gag gene and regions flanking the V1/V2 hypervariable regions. Phylogenetic analysis in both regions revealed several lineages in each individual that contained sequences from both lymphoid and nonlymphoid tissues such as the brain. This observation contrasts strongly with the previously described organ-specific sequences in the V3 region in this study population and other investigations. Although individual pairwise comparisons of relatively short sequences such as p17gag are subject to considerable stochastic error, we found that the diversity of gag sequences in variants from lymphoid tissue was consistently lower than that found among variants amplified from the brain. By estimating mean synonymous pairwise distances in the p17gag region, we were able to make an approximate calculation of the ages of populations in different tissues. Those from lymphoid tissue ranged from 2.65 to 5.6 years in the three study subjects, compared with 4.1 to 6.2 years for variants in the brain. Indeed, variants infecting the brain were no more closely related to each other than they were to variants infecting other tissues in the body. In two of the three individuals, these times of divergence indicate that infection of the brain may have occurred as an early event in the progression to disease, preceding the onset of AIDS by several years. This study is the first in which it was possible to estimate times of diversification in different tissues in vivo and is of importance in understanding the dynamics of the spread of HIV-1 into nonlymphoid tissues and its possible adaptation for replication in different cell types.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Geographic range size and evolutionary age in birds.

Together with patterns of speciation and extinction, post-speciation transformations in the range sizes of individual species determine the form of contemporary species range-size distributions. However, the methodological problems associated with tracking the dynamics of a species' range size over evolutionary time have precluded direct study of such range-size transformations, although indirect evidence has led to several models being proposed describing the form that they might take. Here, we use independently derived molecular data to estimate ages of species in six monophyletic groups of birds, and examine the relationship between species age and global geographic range size. We present strong evidence that avian range sizes are not static over evolutionary time. In addition, it seems that, with the regular exception of certain taxa (for example island endemics and some threatened species), range-size transformations are non-random in birds. In general, range sizes appear to expand relatively rapidly post speciation; subsequently; and perhaps more gradually, they then decline as species age. We discuss these results with reference to the various models of range-size dynamics that have been proposed.

Animals↗
PubMed2003

Kramers problem in evolutionary strategies.

We calculate the escape rates of different dynamical processes for the case of a one-dimensional symmetric double-well potential. In particular, we compare the escape rates of a Smoluchowski process, i.e., a corresponding overdamped Brownian motion dynamics in a metastable potential landscape, with the escape rates obtained for a biologically motivated model known as the Fisher-Eigen process. The main difference between the two models is that the dynamics of the Smoluchowski process is determined by local quantities, whereas the Fisher-Eigen process is based on a global coupling (nonlocal interaction). If considered in the context of numerical optimization algorithms, both processes can be interpreted as archetypes of physically or biologically inspired evolutionary strategies. In this sense, the results discussed in this work are utile in order to evaluate the efficiency of such strategies with regard to the problem of surmounting various barriers. We find that a combination of both scenarios, starting with the Fisher-Eigen strategy, provides a most effective evolutionary strategy.

Journal Article↗
PubMed2001

Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.

MOTIVATION: Current growth in the field of genomics has provided a number of exciting approaches to the modeling of evolutionary mechanisms within the genome. Separately, dynamical and statistical analyses of networks such as the World Wide Web and the social interactions existing between humans have shown that these networks can exhibit common fractal properties-including the property of being scale-free. This work attempts to bridge these two fields and demonstrate that the fractal properties of molecular networks are linked to the fractal properties of their underlying genomes. RESULTS: We suggest a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks. This model generates networks that share important statistical properties (so-called scale-free behavior) with real molecular networks. In particular, the frequency of vertices connected to exactly k other vertices follows a power-law distribution. The shape of this distribution remains invariant to changes in network scale: a small subgraph has the same distribution as the complete graph from which it is derived. Furthermore, the model correctly predicts that the frequencies of distinct DNA and protein domains also follow a power-law distribution. Finally, the model leads to a simple equation linking the total number of different DNA and protein domains in a genome with both the total number of genes and the overall network topology. AVAILABILITY: MatLab (MathWorks, Inc.) programs described in this manuscript are available on request from the authors. CONTACT: ar345@columbia.edu.

Biological Evolution↗
PubMed2002

Evolutionary conservation of microtubule-capture mechanisms.

The dynamic nature of microtubules allows them to search the three-dimensional space of the cell. But what are they looking for? During cellular morphogenesis, microtubules are captured at sites just under the plasma membrane, and this polarizes the microtubule array and associated organelles. Recent data indicate that the signalling pathways that are involved in regulating the different microtubule cortical interactions are not only conserved between species, but also that they function in diverse processes.

Animals↗
PubMed1997

Memory, sleep and the evolution of mechanisms of synaptic efficacy maintenance.

The origin of both sleep and memory appears to be closely associated with the evolution of mechanisms of enhancement and maintenance of synaptic efficacy. The development of activity-dependent synaptic plasticity apparently was the first evolutionary adaptation of nervous systems beyond a capacity to respond to environmental stimuli by mere reflexive actions. After the origin of activity-dependent synaptic plasticity, whereby single activations of synapses led to short-term efficacy enhancement, lengthy maintenance of enhancements probably was achieved by repetitive activations ("dynamic stabilization"). One source of selective pressure for the evolutionary origin of neurons and neural circuits with oscillatory firing capacities may have been a need for repetitive spontaneous activations to maintain synaptic efficacy in circuits that were in infrequent use. This process is referred to as "non-utilitarian" dynamic stabilization. Dynamic stabilization of synapses in "simple" invertebrates occurs primarily through frequent use. In complex, locomoting forms, it probably occurs through both frequent use and non-utilitarian activations during restful waking. With the evolution of increasing repertories and complexities of behavioral and sensory capabilities--with vision usually being the vastly pre-eminent sense brain complexity increased markedly. Accompanying the greater complexity, needs for storage and maintenance of hereditary and experiential information (memories) increased greatly. It is suggested that these increases led to conflicts between sensory input processing during restful waking and concomitant non-utilitarian dynamic stabilization of infrequently used memory circuits. The selective pressure for the origin of primitive sleep may have been a resulting need to achieve greater depression of central processing of sensory inputs largely complex visual information than occurs during restful waking. The electrical activities of the brain during sleep (aside from those that subserve autonomic activities) may function largely to maintain sleep and to dynamically stabilize infrequently used circuitry encoding memories. Sleep may not have been the only evolutionary adaptation to conflicts between dynamic stabilization and sensory input processing. In some ectothermic vertebrates, sleep may have been postponed or rendered unnecessary by a more readily effected means of resolution of the conflicts, namely, extensive retinal processing of visual information during restful waking. By this means, processing of visual information in central regions of the brain may have been maintained at a sufficiently low level to allow adequate concomitant dynamic stabilization. As endothermy evolved, the skeletal muscle hypotonia of primitive sleep may have become insufficient to prevent sleep-disrupting skeletal muscle contractions during non-utilitarian dynamic stabilization of motor circuitry at the accompanying higher body temperatures and metabolic rates. Selection against such disruption during dynamic stabilization of motor circuitry may have led to the inhibition of skeletal muscle tone during a portion of primitive sleep, the portion designated as rapid-eye-movement sleep. Many marine mammals that are active almost continuously engage only in unihemispheric non-rapid-eye-movement sleep. They apparently do not require rapid-eye-movement sleep and accompanying non-utilitarian dynamic stabilization of motor circuitry, because this circuitry is in virtually continuous use. Studies of hibernation by arctic ground squirrels suggest that each hour of sleep may stabilize brain synapses for as long as 4 h. Phasic irregularities in heart and respiratory rates during rapid-eye-movement sleep may be a consequence of superposition of dynamic stabilization of motor circuitry on the rhythmic autonomic control mechanisms. Some information encoded in circuitry being dynamically stabilized during sleep achieves unconscious awareness in authentic and var

Animals↗
PubMed2005

Modeling gene and genome duplications in eukaryotes.

Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.

Arabidopsis↗
PubMed2006

Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution.

Hemiascomycetous yeasts have the greatest number of sequenced species for a single phylum, and are at the forefront of evolutionary genomics of eukaryotes. Yeast genomes show the dynamic interplay between the formation and loss of genes and help to characterize the mechanisms involved and their functional and evolutionary consequences. These mechanisms have equivalents in the genomes of multicellular organisms. Yeast genomes show extensive loss of introns and a reduced role of transposable elements, and so probably have a more limited potential to form novel genes and functions than multicellular organisms, possibly explaining their conserved biological and morphological properties despite their considerable evolutionary range.

DNA Transposable Elements↗
PubMed2004

Habitat selection and population regulation in temporally fluctuating environments.

Understanding and predicting the distribution of organisms in heterogeneous environments lies at the heart of ecology, and the theory of density-dependent habitat selection (DDHS) provides ecologists with an inferential framework linking evolution and population dynamics. Current theory does not allow for temporal variation in habitat quality, a serious limitation when confronted with real ecological systems. We develop both a stochastic equivalent of the ideal free distribution to study how spatial patterns of habitat use depend on the magnitude and spatial correlation of environmental stochasticity and also a stochastic habitat selection rule. The emerging patterns are confronted with deterministic predictions based on isodar analysis, an established empirical approach to the analysis of habitat selection patterns. Our simulations highlight some consistent patterns of habitat use, indicating that it is possible to make inferences about the habitat selection process based on observed patterns of habitat use. However, isodar analysis gives results that are contingent on the magnitude and spatial correlation of environmental stochasticity. Hence, DDHS is better revealed by a measure of habitat selectivity than by empirical isodars. The detection of DDHS is but a small component of isodar theory, which remains an important conceptual framework for linking evolutionary strategies in behavior and population dynamics.

Animals↗
PubMed2001

Understanding hierarchical protein evolution from first principles.

We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved across protein families. Due to its dynamic nature, the model sheds light on the evolutionary time-scales. By studying the relaxation of the correlation function between consecutive mutations at a given position in proteins, we observe separation of the evolutionary time-scales: at short time intervals families of proteins with similar sequences and structures are formed, while at long time intervals the families of structurally similar proteins that have low sequence similarity are formed. We discuss the evolutionary implications of our model. We provide a "profile" solution to our model and find agreement between predicted patterns of conserved amino acids and those actually observed in nature.

Amino Acid Sequence↗