Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “evolutionary dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,747 records · Page 97Linked to original sources
PubMed2005

Mode-focusing in molecules by feedback-controlled shaping of femtosecond laser pulses.

The feasibility of mode-selective excitation with broadband femtosecond laser pulses is demonstrated for toluene in liquid phase. A learning-loop optimal control scheme was applied to a stimulated Raman excitation process. Modifications of the phase shape of one of the exciting pulses resulted in dramatic changes of the mode distribution reflected in coherent anti-Stokes Raman spectra. An evolutionary algorithm guided the coherent excitation process to a selective enhancement or suppression of one or more vibrational modes over the complete coherence lifetime spanning several picoseconds. New ways of spectral filtering as well as exciting possibilities of mode-selective studying of chemical reaction dynamics are indicated.

Feedback↗
PubMed1999

Linguistic diversity of the Americas can be reconciled with a recent colonization.

The Americas harbor a very great diversity of indigenous language stocks, many more than are found in any other continent. J. Nichols [(1990) Language 66, 475-521] has argued that this diversity indicates a great time depth of in situ evolution. She thus infers that the colonization of the Americas must have begun around 35,000 years ago. This estimate is much earlier than the date for which there is strong archaeological support, which does not much exceed 12,000 years. Nichols' assumption is that the diversity of linguistic stocks increases linearly with time. This paper compares the major continents of the world to show that this assumption is not correct. In fact, stock diversity is highest in the Americas, which are by consensus the youngest continents, intermediate in Australia and New Guinea, and lowest in Africa and Eurasia where the time depth is greatest. If anything, then, after an initial radiation, stock diversity decreases with time. A simple model is outlined that predicts these dynamics. It assumes that early in the peopling of continents, there are many unfilled niches for communities to live in, and so fissioning into new lineages is frequent. As the habitat is filled up, the rate of fissioning declines and lineage extinction becomes the dominant evolutionary force.

Americas↗
PubMed1998

Genetic subtypes of HIV-1 in the Philippines.

OBJECTIVES: To determine the genetic variability of HIV-1 amongst infected Filipinos and to analyze phylogenetic relationships, temporal introductions and transmission dynamics of identified variants. METHODS: Polymerase chain reaction amplification and direct sequencing of a 204 base-pair fragment of the env C2-V3 region from uncultured peripheral blood mononuclear cells obtained from 51 HIV-1-positive Filipinos infected from 1987 to mid-1996. Evolutionary distance and phylogenetic relationships among the DNA sequences were estimated. RESULTS: The 51 Philippine strains were classified into five env V3 subtypes, namely subtype B (n = 37), subtype E (n = 8), subtype A (n = 3), subtype C (n = 2) and subtype D (n = 1). The overall env nucleotide divergence ranged from 11.7 to 32.2%. The nucleotide variation appeared to be random and no temporal ordering was observed. The variation of the sequences at the tip of the V3 loop was very broad. Subtypes B and C isolates did not show close genetic relationship to other Asian variants. Only three of the subtype E strains had close affinity to known Asian sequences. The majority (94%) of the subjects acquired the infection by sexual transmission. About two-thirds were presumably infected outside the Philippines, whereas the remaining were infected indigenously. Information was limited to allow segregation of the identified subtypes by mode of transmission or risk groups. CONCLUSION: Our findings demonstrate the presence of multiple genetic subtypes of HIV-1 in the Philippines. The apparent geographic range of previously reported genotypes in South and South-east Asia was extended and has obvious implications for env-based antiviral interventions.

Adult↗
PubMed2002

Time-dependent extinction rate and species abundance in a tangled-nature model of biological evolution.

We present a model of evolutionary ecology consisting of a web of interacting individuals, a tangle-nature model. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and the macroevolutionary mode of the dynamics are emergent properties. The macrodynamics exhibit intermittent two-mode switching with a gradually decreasing extinction rate. The generated ecologies become gradually better adapted as well as more complex in a collective sense. The form of the species abundance curve compares well with observed functional forms. The model's error threshold can be understood in terms of the characteristics of the two dynamical modes of the system.

Biological Evolution↗
PubMed2025

Comparative phylogeographic patterns in three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria).

We examined DNA sequences of 328 individuals of three lineages (species or species complexes) of Amazonian antwrens to evaluate their degree of geographical and historical concordance. All lineages (Myrmotherula longipennis, M. menetriesii, and the Isleria guttata-hauxwelli species complex) consist of small insectivorous birds that occupy understory or midstory of terra firme forest and are widely distributed across the Amazon Basin. Individuals of each of the three lineages grouped into genetic clades mainly separated by the Amazon and some major tributaries, although members of different clades of both M. menetriesii and I. hauxwelli were documented in the Madeira-Tapajós interfluvium. Branching patterns differed among taxa, but all taxa were highly differentiated across the lower or upper Amazon. Despite the morphological, ecological, and phylogenetic similarities among lineages, and despite the fact that nearly all taxa are bounded by rivers, the effect of the other major rivers as biogeographic barriers was highly variable. The Marañón, Ucayali, Madeira, Tapajós, Xingu, Napo, Negro, and Branco all separated main clades in one or two lineages but not in the others. Levels of genetic differentiation along the Teles Pires were substantially higher than those across the Tapajós in M. menetriesii and I. hauxwelli, consistent with a proposed historical change of river course for the Tapajós. Genetic units in this study were comparable for the most part to taxonomic units delineated by analyses of vocal and morphological variation, and identical, with one exception, to units defined solely by vocal variation in a companion paper (Isler et al. 2025). These results, in conjunction with those of Isler et al. (2025), provide additional instances of the variability of responses to the historical dynamism of Amazonia, in this case in closely related and ecologically similar species; highlight the consistency of genetic differentiation with vocal differentiation in additional species of Neotropical suboscine birds; support the importance of Amazonian rivers in creating conditions that result in the differentiation of independent evolutionary lineages; and demonstrate that species richness in two of the lineages studied (M. longipennis and M. menetriesii) was previously underestimated.

Passeriformes↗
PubMed2006

Gene regulatory network models for plant development.

Accumulated genetic data are stimulating the use of mathematical and computational tools for studying the concerted action of genes during cell differentiation and morphogenetic processes. At the same time, network theory has flourished, enabling analyses of complex systems that have multiple elements and interactions. Reverse engineering methods that use genomic data or detailed experiments on gene interactions have been used to propose gene network architectures. Experiments on gene interactions incorporate enough detail for relatively small developmental modules and thus allow dynamical analyses that have direct functional interpretations. Generalities are beginning to emerge. For example, biological genetic networks are robust to environmental and genetic perturbations. Such dynamical studies also enable novel predictions that can lead to further experimental tests, which might then feedback to the theoretical analyses. This interplay is proving productive for understanding plant development. Finally, both experiments on gene interactions and theoretical analyses allow the identification of frequent or fixed evolutionary solutions to developmental problems, and thus are contributing to an understanding of the genetic basis of the evolution of development and body plan.

Biological Evolution↗
PubMed2005

Do disparate mechanisms of duplication add similar genes to the genome?

Gene duplication is the fundamental source of new genes. Biases in duplication have profound implications for the dynamics of gene content during evolution. In this article, we compare genes arising from whole gene duplication (WGD), smaller scale duplication (SSD) and singletons in Saccharomyces cerevisiae. Our results demonstrate that genes duplicated by WGD and SSD are similarly biased with respect to codon bias and evolutionary rate, although differing significantly in their functional constituency.

Codon↗
PubMed1991

The evolution of viruses. Competition between horizontal and vertical transmission of mobile genes.

The transmission dynamics of viruses in a replicating cell population is investigated, assuming that viral mutants differ in their efficiencies of horizontal and vertical transmission. As a genetic result we find that competition between such different viral strategies need not select for increasing basic reproductive rates. We illustrate evolutionary trajectories that lead to increased viral latency even at the expense of lower basic reproductive rates and lower equilibrium abundance. In some cases oscillations in the prevalence of different mutants are obtained.

Biological Evolution↗
PubMed1993

A symmetric inhibitor binds HIV-1 protease asymmetrically.

Potential advantages of C2-symmetric inhibitors designed for the symmetric HIV-1 protease include high selectivity, potency, stability, and bioavailability. Pseudo-C2-symmetric monools and C2-symmetric diols, containing central hydroxymethylene and (R,R)-dihydroxyethylene moieties flanked by a variety of hydrophobic P1/P1' side chains, were studied as HIV-1 protease inhibitors. The monools and diols were synthesized in 8-10 steps from D-(+)-arabitol and D-(+)-mannitol, respectively. Monools with ethyl or isobutyl P1/P1' side chains were weak inhibitors of recombinant HIV-1 protease (Ki > 10 microM), while benzyl P1/P1' side chains afforded a moderately potent inhibitor (apparent Ki = 230 nM). Diols were 100-10,000x more potent than analogous monools, and a wider range of P1/P1' side chains led to potent inhibition. Both classes of compounds exhibited lower apparent Ki values under high-salt conditions. Surprisingly, monool and diol HIV-1 protease inhibitors were potent inhibitors of porcine pepsin, a prototypical asymmetric monomeric aspartic protease. These results were evaluated in the context of the pseudosymmetric structure of monomeric aspartic proteases and their evolutionary kinship with the retroviral proteases. The X-ray crystal structure of HIV-1 protease complexed with a symmetric diol was determined at 2.6 A. Contrary to expectations, the diol binds the protease asymmetrically and exhibits 2-fold disorder in the electron density map. Molecular dynamics simulations were conducted beginning with asymmetric and symmetric HIV-1 protease/inhibitor model complexes. A more stable trajectory resulted from the asymmetric complex, in agreement with the observed asymmetric binding mode. A simple four-point model was used to argue more generally that van der Waals and electrostatic force fields can commonly lead to an asymmetric association between symmetric molecules.

Alcohols↗
PubMed2026

Convergence and conflict among telomere-specialized transposons across 60 million years of Drosophilid evolution.

The Drosophila telomere is one of the best-studied examples of active transposable elements (TEs) benefiting, rather than harming, the host genome. All Drosophila species lack telomerase, and most species instead have telomeres composed of head-to-tail arrays of specialized retrotransposons. These TEs ostensibly act as mutualists by elongating chromosome ends, but evidence from species closely related to Drosophila melanogaster suggests that telomeric transposons may also antagonize their host genome. Importantly, the limited number of Drosophila species characterized thus far has precluded our ability to delineate idiosyncrasies from universal evolutionary forces and genetic mechanisms that shape the history of these TEs. Here, we have surveyed long-read genome assemblies of more than 100 species of Drosophila, identifying a total of 396 telomeric TE families. Our findings show that these telomere-specialized elements evolve dynamically and also undergo striking convergent evolution: The complete loss of telomeric TEs has occurred repeatedly across the genus, whereas individual telomeric TE lineages have repeatedly lost one of their two protein-coding genes. These elements have also repeatedly undergone horizontal transfer between distantly related Drosophila lineages and have repeatedly captured host gene fragments that promote their selfish suppression of host TE-silencing systems. Furthermore, telomere specialization itself appears to have evolved convergently, as some nontelomeric families have gained the ability to target their insertions to telomeres. These results provide unprecedented resolution into the evolution of these unusual TEs and highlight several novel mechanisms by which they evolve in conflict both with each other and their host genome despite the essential telomere function they provide.

Animals↗
PubMed2026

Spatially resolved single-cell atlas reveals the macroevolutionary trajectory of animal hearts.

Animal hearts display diverse anatomical structures during adaptive evolution. Here, we present a multiomics atlas of adult hearts from 27 species across chordates, arthropods, and mollusks. Joint analysis indicates that Bilateria hearts share a core gene repertoire, taking a stepwise "add-on" approach as a universal evolutionary strategy. The "proto-heart" is populated by key cell types, including cardiomyocytes, fibroblasts, endothelial cells, and neural cells, which maintained core signatures while evolving with shifts in living environments and corresponding adaptations in the cardiovascular system. Additionally, we reveal an evolutionarily conserved cardiomyocyte state dynamic potentially linked to cardiac development and stress responses. Finally, we identify a common molecular program underpinning chamber evolution from a ventricular foundation. This work establishes a resource for understanding the intrinsic mechanisms of heart evolution.

Animals↗
PubMed1997

Modern thoughts on an ancyent marinere: function, evolution, regulation.

The mariner/Tc1 superfamily of transposable elements is one of the most diverse and widespread Class II transposable elements. Within the larger assemblage, the mariner-like elements (MLEs) and the Tc1-like elements (TLEs) are distinct families differing characteristically in the composition of the "D,D(35)E" cation-binding domain. Based on levels of sequence similarity, the elements in each family can be subdivided further into several smaller subfamilies. MLEs and TLEs both have an extraordinarily wide host range. They are abundant in insect genomes and other invertebrates and are found even in some vertebrate species including, in the case of mariner, humans, in which one element on chromosome 17p has been implicated as a hotspot of recombination. In spite of the extraordinary evolutionary success of the elements, virtually nothing is known about their mode of regulation within genomes. There is abundant evidence that the elements are disseminated to naive host genomes by horizontal transmission, and there is a substantial base of evidence for inference about the subsequent population dynamics. Studies of engineered mariner elements and induced mutations in the transposase have identified two mechanisms that may be operative in mariner regulation. One mechanism is overproduction inhibition, in which excessive wild-type transposase reduces the rate of excision of a target element. A second mechanism is dominant-negative complementation, in which certain mutant transposase proteins antagonize the activity of the wild-type transposase. The latter process may help explain why the vast majority of MLEs in nature undergo "vertical inactivation" by multiple mutations and, eventually, stochastic loss. There is also evidence that mariner/Tc1 elements can be mobilized in hybrid dysgenesis; in particular, certain dysgenic crosses in Drosophila virilis result in mobilization of a TLE designated Paris as well as the mobilization of other unrelated transposable elements.

Animals↗
PubMed2000

Exploring the relationship between neutral and selective mutations in cancer.

The transformation of normal cells into cancerous cells is an evolutionary process. Populations of precancerous cells reproduce, mutate, and compete for resources. Some of these mutations eventually lead to cancer. We calculate the probability of developing cancer under a set of simplifying assumptions and then elaborate these calculations, culminating in a simple simulation of the cell dynamics. The agent-based model allows us to examine the interactions of mutations critical for the development of cancer that are either evolutionarily neutral or selective. We can also examine the interaction of these mutations with a "mutator phenotype" derived from mutations that raise the mutation rate for the entire cell. The simulations suggest that there must be at least two selectively neutral mutations necessary for the development of cancer and that preventive treatments will be most effective when they increase this number. The model also suggests that selective mutations facilitate the development of cancer, so that the more selective mutations necessary for the development of cancer, the greater the chance of developing it.

Adenocarcinoma↗
PubMed1993

Transient expression of the intermediate filament nestin during skeletal muscle development.

It has previously been established that skeletal muscle development is accompanied by changes in the composition of intermediate filaments: vimentin is expressed predominantly in myoblasts and desmin in adult myotubes. We show that the intermediate filament transitions during muscle development are more complex, and involve a transient expression of the recently discovered intermediate filament nestin. Nestin RNA is expressed predominantly early, in a biphasic pattern, and is markedly downregulated in adult rat muscle, whereas desmin RNA becomes more abundant throughout development. Nestin protein was found up to the postnatal myotube stage, where it colocalized with desmin in Z bands. The intracellular distribution of nestin, vimentin and desmin was analysed in the human myogenic cell line G6 before and after in vitro differentiation. Despite its more distant evolutionary and structural relationship to the other two intermediate filaments, nestin formed a cytoplasmic filamentous network indistinguishable from that of desmin and vimentin, both in undifferentiated myoblasts and after differentiation to multinuclear myotubes. In conclusion, our data suggest that nestin is an integrated component of the dynamic intermediate filament network during muscle development and that nestin copolymerizes with desmin and vimentin at stages of coexpression.

Animals↗
PubMed2006

Synthetic gene recruitment reveals adaptive reprogramming of gene regulation in yeast.

The recruitment of a gene to a foreign regulatory system is a major evolutionary event that can lead to novel phenotypes. However, the evolvability potential of cells depends on their ability to cope with challenges presented by gene recruitment. To study this ability, we combined synthetic gene recruitment with continuous culture and online measurements of the metabolic and regulatory dynamics over long timescales. The gene HIS3 from the histidine synthesis pathway was recruited to the GAL system, responsible for galactose utilization in the yeast S. cerevisiae. Following a switch from galactose to glucose--from induced to repressed conditions of the GAL system--in histidine-lacking chemostats (where the recruited HIS3 is essential), the regulatory system reprogrammed to adaptively tune HIS3 expression, allowing the cells to grow competitively in pure glucose. The adapted state was maintained for hundreds of generations in various environments. The timescales involved and the reproducibility of separate experiments render spontaneous mutations an unlikely underlying mechanism. Essentially all cells could adapt, excluding selection over a genetically variable population. The results reveal heritable adaptation induced by the exposure to glucose. They demonstrate that genetic regulatory networks have the potential to support highly demanding events of gene recruitment.

Adaptation, Biological↗
PubMed2002

Sperm competition and the dynamics of X chromosome drive: stability and extinction.

Several empirical studies of sperm competition in populations polymorphic for a driving X chromosome have revealed that Sex-ratio males (those carrying a driving X) are at a disadvantage relative to Standard males. Because the frequency of the driving X chromosome determines the population-level sex ratio and thus alters male and female mating rates, the evolutionary consequences of sperm competition for sex chromosome meiotic drive are subtle. As the SR allele increases in frequency, the ratio of females to males also increases, causing an increase in the male mating rate and a decrease in the female mating rate. While the former change may exacerbate the disadvantage of Sex-ratio males during sperm competition, the latter change decreases the incidence of sperm competition within the population. We analyze a model of the effects of sperm competition on a driving X chromosome and show that these opposing trends in male and female mating rates can result in two coexisting locally stable equilibria, one corresponding to a balanced polymorphism of the SR and ST alleles and the second to fixation of the ST allele. Stochastic fluctuations of either the population sex ratio or the SR frequency can then drive the population away from the balanced polymorphism and into the basin of attraction for the second equilibrium, resulting in fixation of the SR allele and extinction of the population.

Animals↗
PubMed2002

Self-segregation versus clustering in the evolutionary minority game.

Complex adaptive systems have been the subject of much recent attention. It is by now well established that members ("agents") tend to self-segregate into opposing groups characterized by extreme behavior. However, the study of such adaptive systems has mostly been restricted to simple situations in which the prize-to-fine ratio R equals unity. In this Letter we explore the dynamics of evolving populations with various different values of the ratio R, and demonstrate that extreme behavior is in fact not a generic feature of adaptive systems. In particular, we show that "confusion" and "indecisiveness" take over in times of depression, in which case cautious agents perform better than extreme ones.

Adaptation, Psychological↗
PubMed2005

Sex ratio bias, male aggression, and population collapse in lizards.

The adult sex ratio (ASR) is a key parameter of the demography of human and other animal populations, yet the causes of variation in ASR, how individuals respond to this variation, and how their response feeds back into population dynamics remain poorly understood. A prevalent hypothesis is that ASR is regulated by intrasexual competition, which would cause more mortality or emigration in the sex of increasing frequency. Our experimental manipulation of populations of the common lizard (Lacerta vivipara) shows the opposite effect. Male mortality and emigration are not higher under male-biased ASR. Rather, an excess of adult males begets aggression toward adult females, whose survival and fecundity drop, along with their emigration rate. The ensuing prediction that adult male skew should be amplified and total population size should decline is supported by long-term data. Numerical projections show that this amplifying effect causes a major risk of population extinction. In general, such an "evolutionary trap" toward extinction threatens populations in which there is a substantial mating cost for females, and environmental changes or management practices skew the ASR toward males.

Aggression↗