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 1,765 records · Page 98Linked to original sources
PubMed2001

Competition at the mouse t complex: rare alleles are inherently favored.

We investigate the competition between alleles at a segregation distorter locus. The focus is on the invasion prospects of rare mutant distorter alleles in a population in which a wildtype and a resident distorter allele are present. The parameters are chosen to reflect the situation at the t complex of the house mouse, one of the best-studied examples of segregation distortion. By analyzing the invasion chances of rare alleles, we provide an analytical justification of earlier simulation results. We show that a new distorter allele can successfully invade even if it is inferior both at the gamete and at the individual level. In fact, newly arising distorter alleles have an inherent rareness advantage if their negative fitness consequences are restricted to homozygous condition. Likewise, rare mutant wildtype alleles may often invade even if their viability or fertility is reduced. As a consequence, the competition between alleles at a segregation distorter locus should lead to a high degree of polymorphism. We discuss the implications of this conclusion for the t complex of the house mouse and for the evolutionary stability of "honest" Mendelian segregation.

Alleles↗
PubMed2001

Stochastic population models with interacting species.

A stochastic model concerning the evolution of a multi-species population is presented assuming species competition for a habitat. The model takes into account colonization, death and replacement for all individuals. Two cases are treated: (i) colonizations follow the hierarchic rule by which species of lower rank are always outcompeted by those of higher rank and (ii) there are no privileged species. In both cases, under suitable assumptions, a thorough description of the evolution of the population is obtained. The two models are finally compared and the corresponding evolutionary behaviors of the populations are discussed.

Animals↗
PubMed2026

Genome-Wide Identification and Characterization of the TBL Gene Family and Temporal Expression Dynamics During Powdery Mildew Infection in Cucumber (Cucumis sativus).

Cell-wall polysaccharide O-acetylation contributes to cell-wall assembly, organ development, and plant-pathogen interactions, but the cucumber TBL gene family remains poorly characterized. Here, 37 CsTBL genes were identified genome-wide and analyzed using phylogenetic, syntenic, conserved-motif, gene-structure, promoter, protein-structure, Gene Ontology, and transcriptome approaches, followed by RT-qPCR analysis after powdery mildew inoculation. All CsTBL proteins contained the conserved GDS and DxxH motifs, whereas accessory motifs and predicted structural features varied among clades. Intraspecific analysis identified dispersed, WGD/segmental, and tandem duplication categories, and cross-species synteny was more extensive with melon than with Arabidopsis. Homology-derived annotations associated CsTBL genes with cell-wall polysaccharide metabolism, Golgi/endomembrane compartments, and O-acetyltransferase activity, including six genes assigned to xylan O-acetyltransferase-related annotations. Expression profiling revealed tissue- and developmental-stage-dependent patterns, whereas the publicly available powdery mildew RNA-seq dataset provided descriptive temporal expression profiles in Podosphaera xanthii-inoculated samples. Independent RT-qPCR analysis using time-matched mock controls revealed distinct post-inoculation responses among six selected genes. Relative to the corresponding mock controls, CsTBL2 was consistently repressed; CsTBL15 showed transient induction at 1 dpi followed by repression; CsTBL24 exhibited a biphasic response; CsTBL25 was induced at all sampled post-inoculation time points; CsTBL26 showed progressive induction; and CsTBL30 reached its highest observed expression level at 3 dpi. Integrated functional annotation and expression evidence highlighted CsTBL26 as a priority candidate for further functional characterization, while CsTBL24 and CsTBL25 represented fruit-associated candidates with distinct powdery mildew responses; CsTBL30 remained an additional strongly infection-responsive candidate. These findings provide an evolutionary and expression-based framework for the functional characterization of the cucumber TBL gene family.

O-acetylation↗
PubMed2026

Genome-Wide Analysis of the PYL Gene Family and Its Expression Dynamics in Response to Abscisic Acid in Tomato.

The plant hormone abscisic acid (ABA) plays a crucial role throughout the plant life cycle and in adaptive responses to environmental stresses. The pyrabactin resistance 1-like (PYR/PYL/RCAR) proteins act as key regulators in the ABA signal transduction pathway by functioning as direct receptors for ABA. Although PYL genes have been identified in a variety of plant species, their evolutionary and structural characteristics in tomatoes (Solanum lycopersicum) remain elusive. To address this gap, we identified nine SlPYL genes, which were classified into three subfamilies: I (two genes), II (three genes), and III (four genes), and their encoded proteins were predicted to be primarily localized in the cytosol and chloroplast. Structural analysis revealed diverse exon-intron organizations along with five conserved motifs. All identified SlPYLs contained the START domain (PF10604), validating their identity as actual PYL proteins. Prediction of cis-acting regulatory elements in SlPYL's promoter regions was found to be associated with light responsiveness, hormone signaling, stress responses, and plant growth and development. Prediction of post-translational modification sites indicated that SlPYLs are predominantly phosphorylated and acetylated at serine and lysine residues, respectively. Tertiary structure modeling demonstrated conserved three-dimensional architectures among SlPYL proteins, supporting their functional conservation. Expression profiling revealed that specific SlPYL genes exhibit distinct expression patterns across different tissues (root, leaf, and bud) following ABA treatment, indicating functional diversification. Considering the well-established negative correlation between ABA accumulation and bud outgrowth, the ABA-induced differential expression (3~5-fold) of some SlPYL genes (SlPYL3, SlPYL4, SlPYL7, and SlPYL8), particularly in bud tissues after 24 hpt, suggests a potential role in ABA-mediated suppression of bud outgrowth. However, these functional inferences are primarily based on genome-wide computational analyses and expression profiling and therefore require further experimental validation.

Solanum lycopersicum↗
PubMedDate not supplied

Actor-critic models of the basal ganglia: new anatomical and computational perspectives.

A large number of computational models of information processing in the basal ganglia have been developed in recent years. Prominent in these are actor-critic models of basal ganglia functioning, which build on the strong resemblance between dopamine neuron activity and the temporal difference prediction error signal in the critic, and between dopamine-dependent long-term synaptic plasticity in the striatum and learning guided by a prediction error signal in the actor. We selectively review several actor-critic models of the basal ganglia with an emphasis on two important aspects: the way in which models of the critic reproduce the temporal dynamics of dopamine firing, and the extent to which models of the actor take into account known basal ganglia anatomy and physiology. To complement the efforts to relate basal ganglia mechanisms to reinforcement learning (RL), we introduce an alternative approach to modeling a critic network, which uses Evolutionary Computation techniques to 'evolve' an optimal RL mechanism, and relate the evolved mechanism to the basic model of the critic. We conclude our discussion of models of the critic by a critical discussion of the anatomical plausibility of implementations of a critic in basal ganglia circuitry, and conclude that such implementations build on assumptions that are inconsistent with the known anatomy of the basal ganglia. We return to the actor component of the actor-critic model, which is usually modeled at the striatal level with very little detail. We describe an alternative model of the basal ganglia which takes into account several important, and previously neglected, anatomical and physiological characteristics of basal ganglia-thalamocortical connectivity and suggests that the basal ganglia performs reinforcement-biased dimensionality reduction of cortical inputs. We further suggest that since such selective encoding may bias the representation at the level of the frontal cortex towards the selection of rewarded plans and actions, the reinforcement-driven dimensionality reduction framework may serve as a basis for basal ganglia actor models. We conclude with a short discussion of the dual role of the dopamine signal in RL and in behavioral switching.

Animals↗
PubMed2004

Radiocarbon evidence of mid-Holocene mammoths stranded on an Alaskan Bering Sea island.

Island colonization and subsequent dwarfing of Pleistocene proboscideans is one of the more dramatic evolutionary and ecological occurrences, especially in situations where island populations survived end-Pleistocene extinctions whereas those on the nearby mainland did not. For example, Holocene mammoths have been dated from Wrangel Island in northern Russia. In most of these cases, few details are available about the dynamics of how island colonization and extinction occurred. As part of a large radiocarbon dating project of Alaskan mammoth fossils, I addressed this question by including mammoth specimens from Bering Sea islands known to have formed during the end-Pleistocene sea transgression. One date of 7,908 +/- 100 yr bp (radiocarbon years before present) established the presence of Holocene mammoths on St Paul Island, a first Holocene island record for the Americas. Four lines of evidence--265 accelerator mass spectrometer (AMS) radiocarbon dates from Alaskan mainland mammoths, 13 new dates from Alaskan island mammoths, recent reconstructions of bathymetric plots and sea transgression rates from the Bering Sea--made it possible to reconstruct how mammoths became stranded in the Pribilofs and why this apparently did not happen on other Alaskan Bering Sea islands.

Alaska↗
PubMed2003

Competition and coexistence: exploring mechanisms that restrict and maintain diversity within mutualist guilds.

Mutualistic interactions are diverse and widespread and often involve multispecies guilds of mutualists competing for access to one or more partner species. Despite the ubiquity of these interactions, we know little about the dynamics of competition and coexistence within these guilds or how interactions between mutualists and their shared resource (the partner species) may influence these dynamics. In this article, we review the evidence for interspecific competition for partners within mutualist guilds in both plant-pollinator and ant-myrmecophyte systems. We then review evidence for the operation of different coexistence mechanisms within these guilds and discuss how the dynamics of competition and coexistence may be uniquely shaped by multispecies mutualist interactions. In particular, we note that adaptive and plastic responses by mutualists to variation in partner quality are likely to play an important role in determining these dynamics. We summarize by considering the ecological conditions that are likely to restrict or promote species coexistence within mutualist guilds. We suggest that these guilds may provide powerful model systems for exploring multiple mechanisms of species coexistence, and we discuss how these mechanisms may be modified by evolutionary adaptation.

Adaptation, Biological↗
PubMed2005

Community epidemiology framework for classifying disease threats.

Recent evidence suggests that most parasites can infect multiple host species and that these are primarily responsible for emerging infectious disease outbreaks in humans and wildlife. However, the ecologic and evolutionary factors that constrain or facilitate such emergences are poorly understood. We propose a conceptual framework based on the pathogen's between- and within-species transmission rates to describe possible configurations of a multihost-pathogen community that may lead to disease emergence. We establish 3 dynamic thresholds separating 4 classes of disease outcomes, spillover, apparent multi-host, true multihost, and potential emerging infectious disease; describe possible disease emergence scenarios; outline the population dynamics of each case; and clarify existing terminology. We highlight the utility of this framework with examples of disease threats in human and wildlife populations, showing how it allows us to understand which ecologic factors affect disease emergence and predict the impact of host shifts in a range of disease systems.

Animals↗
PubMed1994

Dynamics of emergence.

I have touched briefly here on the complex matrix of social, economic, political, and ecologic factors that have played a major role in the emergence of microbial diseases. But beyond these factors that contribute to the emergence of new infectious diseases, we must also recognize changes in microbial agents, human populations, insect vectors, and the ecologic relationships among them. Microbes and vectors swim in the evolutionary stream and they swim much faster than we do. Bacteria reproduce every 30 min; for them a millennium is compressed into a fortnight. Microbes were here, learning every trick for survival, 2 billion years before humans arrived, and it is likely that they will be here 2 billion years after we depart. Furthermore, science cannot halt the future occurrence of new microbes, which emerge from the evolutionary stream as a consequence of genetic events and selective pressures that favor the new over the old. It is nature's way. For all of these reasons, old and new infections will occur in the future as they have in the past. Surveillance efforts, both in the United States and other regions of the world, will be needed to blunt the emergence of such infections and to forestall epidemics and pandemics. But surveillance alone cannot detect the unexpected emergence of future microbes or prepare the defense against them. That will require a broadly based research effort to devise new methods of diagnosis, treatment, and prevention. We must swim with the microbes and study their survival and adaptation to new habitats.(ABSTRACT TRUNCATED AT 250 WORDS)

Acquired Immunodeficiency Syndrome↗
PubMed2003

Selection-driven evolution of emergent dengue virus.

In the last four decades the incidence of dengue fever has increased 30-fold worldwide, and over half the world's population is now threatened with infection from one or more of four co-circulating viral serotypes (DEN-1 through DEN-4). To determine the role of viral molecular evolution in emergent disease dynamics, we sequenced 40% of the genome of 82 DEN-4 isolates collected from Puerto Rico over the 20 years since the onset of endemic dengue on the island. Isolates were derived from years with varying levels of DEN-4 prevalence. Over our sampling period there were marked evolutionary shifts in DEN-4 viral populations circulating in Puerto Rico; viral lineages were temporally clustered and the most common genotype at a particular sampling time often arose from a previously rare lineage. Expressed changes in structural genes did not appear to drive this lineage turnover, even though these regions include primary determinants of viral antigenic properties. Instead, recent dengue evolution can be attributed in part to positive selection on the nonstructural gene 2A (NS2A), whose functions may include replication efficiency and antigenicity. During the latest and most severe DEN-4 epidemic in Puerto Rico, in 1998, viruses were distinguished by three amino acid changes in NS2A that were fixed far faster than expected by drift alone. Our study therefore demonstrates viral genetic turnover within a focal population and the potential importance of adaptive evolution in viral epidemic expansion.

Communicable Diseases, Emerging↗
PubMed2004

A likelihood-based approach to estimating and testing for isolation by distance.

Simple regression of genetic similarities between pairs of populations on their corresponding geographic distances is frequently used to detect the presence of isolation by distance (IBD). However, these pairwise values are obviously not independent and there is no parametric procedure for estimating and testing for the IBD intercepts and slopes based on standard regression theory. Nonparametric tests, such as the Mantel test, and resampling techniques, such as bootstrapping, have been exploited with limited success. Here, I describe a likelihood-based analysis to allow for simultaneously detecting patterns of correlated residuals and estimating and testing for the presence of IBD. It is shown, through the analysis of two molecular datasets in pine species, that different covariance structures of the residuals exist. More over, the likelihood ratio tests under these covariance structures are less sensitive to the presence of IBD than the Mantel test and the simple regression analysis but more sensitive than the bootstrap and jackknife samples over independent populations or population pairs. Because the likelihood analysis directly models and accounts for nonindependence of residuals, it should legitimately detect the presence of IBD, thereby allowing for accurate inferences about evolutionary and demographic processes influencing the extent and patterns of IBD.

Analysis of Variance↗
PubMed2005

Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae).

Besides showing an extraordinary degree of phenotypic variability, Capsella bursa-pastoris (Brassicaceae) is also one of the world's most common plant species and a serious weed in many countries. We have employed a coalescent-based Bayesian analysis of chloroplast microsatellite data to infer demographic and evolutionary parameters of this species. Two different demographic models applied to data from seven chloroplast microsatellite loci among 59 accessions show that the effective population size of C. bursa-pastoris is very small indicating a rapid expansion of the species, a result that is in accordance with fossil and historical data. Against this background, analysis of flowering time variation among accessions suggests that ecotypic differentiation in flowering time has occurred recently in the species' history. Finally, our results also indicate that mononucleotide repeat loci in the chloroplast genome can deteriorate in relatively short periods of evolutionary time.

Base Sequence↗
PubMed2004

Cope's rule, hypercarnivory, and extinction in North American canids.

Over the past 50 million years, successive clades of large carnivorous mammals diversified and then declined to extinction. In most instances, the cause of the decline remains a puzzle. Here we argue that energetic constraints and pervasive selection for larger size (Cope's rule) in carnivores lead to dietary specialization (hypercarnivory) and increased vulnerability to extinction. In two major clades of extinct North American canids, the evolution of large size was associated with a dietary shift to hypercarnivory and a decline in species durations. Thus, selection for attributes that promoted individual success resulted in progressive evolutionary failure of their clades.

Animals↗
PubMed1996

Plant and animal profilins are functionally equivalent and stabilize microfilaments in living animal cells.

We have analyzed the degree of functional similarity between birth and mammalian profilins, two members of the profilin family which show only a moderate sequence homology (22%) in living animal cells. The plant profilin, derived from birch pollen, was stably expressed in BHK-21 cells. Plant and endogenous profilin synthesis and cellular distribution were monitored by specific monoclonal antibodies. Quantitation of profilin and actin on calibrated immunoblots showed that two stable clones contained in total 1.4 and 2.0 times as much profilin as the parental cells. Using double fluorescence and confocal laser scanning microscopy, it was seen that the endogenous and the plant profilin colocalized with dynamic microfilaments, in particular with F-actin-rich foci and cortical microfilament webs of spreading cells, with dynamic microfilament bundles induced by serum deprival, and with cytochalasin D- and latrunculin-induced transient F-actin aggregates. The increase in the overall profilin concentration correlated with a significantly higher resistance of actin filaments to these drugs. Our data indicate that even profilins of highly distant evolutionary origin can functionally substitute for each other and support the hypothesis that in animal cells, profilins are engaged in regulating either the stability or the kinetic properties of actin filaments.

Actin Cytoskeleton↗
PubMed2005

Rapid evolutionary escape by large populations from local fitness peaks is likely in nature.

Fitness interactions between loci in the genome, or epistasis, can result in mutations that are individually deleterious but jointly beneficial. Such epistasis gives rise to multiple peaks on the genotypic fitness landscape. The problem of evolutionary escape from such local peaks has been a central problem of evolutionary genetics for at least 75 years. Much attention has focused on models of small populations, in which the sequential fixation of valley genotypes carrying individually deleterious mutations operates most quickly owing to genetic drift. However, valley genotypes can also be subject to mutation while transiently segregating, giving rise to copies of the high fitness escape genotype carrying the jointly beneficial mutations. In the absence of genetic recombination, these mutations may then fix simultaneously. The time for this process declines sharply with increasing population size, and it eventually comes to dominate evolutionary behavior. Here we develop an analytic expression for N(crit), the critical population size that defines the boundary between these regimes, which shows that both are likely to operate in nature. Frequent recombination may disrupt high-fitness escape genotypes produced in populations larger than N(crit) before they reach fixation, defining a third regime whose rate again slows with increasing population size. We develop a novel expression for this critical recombination rate, which shows that in large populations the simultaneous fixation of mutations that are beneficial only jointly is unlikely to be disrupted by genetic recombination if their map distance is on the order of the size of single genes. Thus, counterintuitively, mass selection alone offers a biologically realistic resolution to the problem of evolutionary escape from local fitness peaks in natural populations.

Biological Evolution↗
PubMed1980

[The glider. Postural kinetic behavior during the pre-locomotor period in infants].

Soaring movements-in an opisthotonic posture-which appear between 3 and 10 months when the infant is in a prone position, have been observed with cinematographic recordings. This is a postural and kinetic activity which takes place during the first year's development; i is a transitional stage leading to intentional propulsive movements. This activity may become a repetitive one for some children, especially between 4 and 7 months; at this peak period, it takes on an unusual aspect, not only because of the "aerial" attitude but also because of the rhythmicity of the postural changes which characterize it. This behavior has been studied in its evolutionary forms, its individual characteristics, and its emotional expressions. Hovering movements are localized in the neuro-psychological evolution of the infant (tonico-postural evolution, acquisition of balance in a prone position, alternating postures, propulsive movements). The conditions which set off and quieten this activity explain the dynamics of its functioning between movements to which the baby is submitted and deliberate ones, between constraint and pleasure.

Child Development↗
PubMed1993

Is morphogenesis an intrinsically robust process?

Because morphogenesis is dynamically complex, involving many processes operating over different spatial and temporal scales, it is generally assumed that the stability and repeatability of development depends primarily upon accurate control over parameter values i.e. a precise genetic program. However, it is possible that the dynamic coupling between the different mechanisms involved in development reduces the choices available to the system because of bias in successive symmetry-breaking events. Evidence for such stable cascades in morphogenetic processes is described, and a general argument is presented for morphogenesis as an intrinsically robust process. The evolutionary implications of the hypothesis are considerable.

Acetabularia↗
PubMed2006

Recognition of flowers by pollinators.

The flowers of angiosperm plants present us with a staggering diversity of signal designs, but how did this diversity evolve? Answering this question requires us to understand how pollinators analyze these signals with their visual and olfactory sense organs, and how the sensory systems work together with post-receptor neural wiring to produce a coherent percept of the world around them. Recent research on the dynamics with which bees store, manage and retrieve memories all have fundamental implications for how pollinators choose between flowers, and in turn for floral evolution. New findings regarding how attention, peak-shift phenomena, and speed-accuracy tradeoffs affect pollinator choice between flower species show that analyzing the evolutionary ecology of signal-receiver relationships can substantially benefit from knowledge about the neural mechanisms of visual and olfactory information processing.

Animals↗