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 595 records · Page 33Linked to original sources
PubMed1999

Selection for intermediate mortality and reproduction rates in a spatially structured population.

How local interactions influence both population and evolutionary dynamics is currently a key topic in theoretical ecology. We use a 'well-mixed' analytical model and spatially explicit individual-based models to investigate a system where a population is subject to rare disturbance events. The disturbance can only propagate through regions of the population where the density of individuals is sufficiently high and individuals affected by the disturbance die shortly after. We find that populations where individuals are sessile often exhibit very different dynamic behaviour when compared to populations where individuals are mobile and spatially well mixed. When mutations are allowed which affect either offspring birth rates or mortality rates, the well-mixed populations always evolve to a state where a single disturbance event leads to extinction. Populations often persist substantially longer if individuals are sessile and they disperse their offspring locally. We also find that for sessile populations selection may favour short-lived individuals with limited offspring production. Population dynamics are found to be strongly influenced by the host characters that are evolving and the rate at which host variation is introduced into the system.

Animals↗
PubMed1999

Joint effects of feeding and breeding behaviour on trophic dimorphism in hummingbirds

A survey of 166 hummingbird species reveals novel associations of bill-length sexual dimorphism (BLSD) with plumage and breeding behaviours. Across all species, female bills become proportionately longer than male bills (higher female-to-male BLSD ratio) as sexual dichromatism increases. However, male bills are proportionately longer (lower female-to-male BLSD ratio) in both lekkers (traditional group display) and clustered breeders (female harems or colonial nests) compared with dispersed breeders. The overall positive association of plumage with BLSD suggests that social status determines priority of access to nectar-providing flowers. Furthermore, the distinctive BLSD associated with breeding aggregations may arise from behaviours that impose constraints on the usual male priority at flowers: female dominance over males around nest colonies and male residence on lek-mating territories. These various factors appear to alter plumage and bill characters of both sexes to produce the range of dimorphisms within the various dispersed and aggregated breeding system categories. Feedback loops caused by ecological consequences of breeding behaviour may alter the evolutionary dynamics of breeding systems, bird-plant interactions, and competing pollinators, as well as help explain the lek paradox.

Journal Article↗
PubMed2001

Language as an evolving word web.

Human language may be described as a complex network of linked words. In such a treatment, each distinct word in language is a vertex of this web, and interacting words in sentences are connected by edges. The empirical distribution of the number of connections of words in this network is of a peculiar form that includes two pronounced power-law regions. Here we propose a theory of the evolution of language, which treats language as a self-organizing network of interacting words. In the framework of this concept, we completely describe the observed word web structure without any fitting. We show that the two regimes in the distribution naturally emerge from the evolutionary dynamics of the word web. It follows from our theory that the size of the core part of language, the 'kernel lexicon', does not vary as language evolves.

Humans↗
PubMed2002

Procedures for reliable estimation of viral fitness from time-series data.

In order to develop a better understanding of the evolutionary dynamics of HIV drug resistance, it is necessary to quantify accurately the in vivo fitness costs of resistance mutations. However, the reliable estimation of such fitness costs is riddled with both theoretical and experimental difficulties. Experimental fitness assays typically suffer from the shortcoming that they are based on in vitro data. Fitness estimates based on the mathematical analysis of in vivo data, however, are often questionable because the underlying assumptions are not fulfilled. In particular, the assumption that the replication rate of the virus population is constant in time is frequently grossly violated. By extending recent work of Marée and colleagues, we present here a new approach that corrects for time-dependent viral replication in time-series data for growth competition of mutants. This approach allows a reliable estimation of the relative replicative capacity (with confidence intervals) of two competing virus variants growing within the same patient, using longitudinal data for the total plasma virus load, the relative frequency of the two variants and the death rate of infected cells. We assess the accuracy of our method using computer-generated data. An implementation of the developed method is freely accessible on the Web (http://www.eco.ethz.ch/fitness.html).

Anti-HIV Agents↗
PubMed2003

The evolution of mate choice and mating biases.

We review the current status of three well-established models (direct benefits, indirect benefits and sensory drive) and one newcomer (antagonistic chase-away) of the evolution of mate choice and the biases that are expressed during choice. We highlight the differences and commonalities in the underlying genetics and evolutionary dynamics of these models. We then argue that progress in understanding the evolution of mate choice is currently hampered by spurious distinctions among models and a misguided tendency to test the processes underlying each model as mutually exclusive alternatives. Finally, we suggest potentially fruitful directions for future theoretical and empirical research.

Animals↗
PubMed2003

Disease evolution on networks: the role of contact structure.

Owing to their rapid reproductive rate and the severe penalties for reduced fitness, diseases are under immense evolutionary pressure. Understanding the evolutionary response of diseases in new situations has clear public-health consequences, given the changes in social and movement patterns over recent decades and the increased use of antibiotics. This paper investigates how a disease may adapt in response to the routes of transmission available between infected and susceptible individuals. The potential transmission routes are defined by a computer-generated contact network, which we describe as either local (highly clustered networks where connected individuals are likely to share common contacts) or global (unclustered networks with a high proportion of long-range connections). Evolution towards stable strategies operates through the gradual random mutation of disease traits (transmission rate and infectious period) whenever new infections occur. In contrast to mean-field models, the use of contact networks greatly constrains the evolutionary dynamics. In the local networks, high transmission rates are selected for, as there is intense competition for susceptible hosts between disease progeny. By contrast, global networks select for moderate transmission rates because direct competition between progeny is minimal and a premium is placed upon persistence. All networks show a very slow but steady rise in the infectious period.

Biological Evolution↗
PubMed2005

Tasting the difference: do multiple defence chemicals interact in Müllerian mimicry?

Müllerian mimicry, where two unpalatable species share a warning pattern, is classically believed to be a form of mutualism, where the species involved share the cost of predator education. The evolutionary dynamics of Müllerian mimicry have recently become a controversial subject, after mathematical models have shown that if minor alterations are made to assumptions about the way in which predators learn and forget about unpalatable prey, this textbook case of mutualism may not be mutualistic at all. An underlying assumption of these models is that Müllerian mimics possess the same defence chemical. However, some Müllerian mimics are known to possess different defence chemicals. Using domestic chicks as predators and coloured crumbs flavoured with either the same or different unpalatable chemicals as prey, we provide evidence that two defence chemicals can interact to enhance predator learning and memory. This indicates that Müllerian mimics that possess different defence chemicals are better protected than those that share a single defence chemical. These data provide insight into how multiple defence chemicals are perceived by birds,and how they influence the way birds learn and remember warningly coloured prey. They highlight the importance of considering how different toxins in mimicry rings can interact in the evolution and maintenance of Müllerian mimicry and could help to explain the remarkable variation in chemical defences found within and between species.

Adaptation, Physiological↗
PubMed2005

Resource partitioning among flower visitors and evolution of nectar concealment in multi-species communities.

The plant community within which flower evolution takes place has largely been ignored. We develop two models for the evolution of nectar concealment when flowers are visited by legitimate pollinators and flower parasites. When there is a single plant species, no level of nectar concealment is evolutionarily stable: any population can be invaded by mutants exhibiting a higher level of nectar concealment. However, the presence of a second flower species with exposed nectar and not subject to evolution breaks the runaway process. In the presence of open flowers, depending on the fitness function there may be an evolutionarily stable level of nectar concealment, or more complex evolutionary dynamics, with nectar concealment fluctuating within a bounded range. Concealment of nectar from flower parasites can evolve even if it implies decreasing the accessibility of nectar to legitimate pollinators.

Animals↗
PubMed2005

Pathogen adaptation under imperfect vaccination: implications for pertussis.

Mass vaccination campaigns have drastically reduced the burden of infectious diseases. Unfortunately, in recent years several infectious diseases have re-emerged. Pertussis poses a well-known example. Inspired by pertussis, we study, by means of an epidemic model, the population and evolutionary dynamics of a pathogen population under the pressure of vaccination. A distinction is made between infection in immunologically naive individuals (primary infection) and infection in individuals whose immune system has been primed by vaccination or infection (secondary infection). The results show that (i) vaccination with an imperfect vaccine may not succeed in reducing the infection pressure if the transmissibility of secondary infections is higher than that of primary infections; (ii) pathogen strains that are able to evade the immunity induced by vaccination can only spread if escape mutants incur no or only a modest fitness cost and (iii) the direction of evolution depends crucially on the distribution of the different types of susceptibles in the population. We discuss the implications of these results for the design and use of vaccines that provide temporary immunity.

Adaptation, Biological↗
PubMed2006

Individual advantages to ecological specialization: insights on cognitive constraints from three conspecific taxa.

The information-processing hypothesis (IPH) posits that specialist herbivores should make host-associated decisions more effectively than generalists and thus enjoy associated fitness advantages that may help explain the evolutionary prevalence of host-specific insects. This is because generalists must evaluate a greater diversity of host plants/cues than specialists and thus face a cognitive challenge that is predicted to constrain the efficiency and accuracy of their choices. Here, we present the first individual-level evaluation of this hypothesis. This involved experimentally quantifying the specificity, efficiency, and accuracy of host selection, as both larvae and adults, for many individuals representing each of three 'host forms' of Neochlamisus bebbianae leaf beetles. These experiments provided several significant findings: host forms differed in larval specificity, with the more specialized host forms more efficiently and accurately selecting optimal hosts as both larvae and adults. Positive correlations between larval specificity and both efficiency and accuracy across test individuals provided the most direct evidence to date for a biological association between these variables. Our results thus provide strong and consistent support for the IPH at the level of both populations and individuals. Because individual N. bebbianae make many host-associated decisions in nature, our results suggest that cognitive constraints may play a major role in the evolutionary dynamics of ongoing ecological specialization and diversification in this species.

Analysis of Variance↗
PubMed2000

Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens.

Recent innovations have increased enormously the opportunities for investigating the molecular basis of bacterial pathogenicity, including the availability of whole-genome sequences, techniques for identifying key virulence genes, and the use of microarrays and proteomics. These methods should provide powerful tools for analysing the patterns of gene expression and function required for investigating host-microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reductionist approach does not adequately address the eclectic and variable outcomes of host-microbe interactions, including evolutionary dynamics and ecological factors. There are difficulties in distinguishing bacterial 'virulence' factors from the many determinants that are permissive for pathogenicity, for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and discuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies available to us, we are still struggling to come to grips with the question of 'What is a pathogen?'

Animals↗
PubMed2000

Evolutionary biology of language.

Language is the most important evolutionary invention of the last few million years. It was an adaptation that helped our species to exchange information, make plans, express new ideas and totally change the appearance of the planet. How human language evolved from animal communication is one of the most challenging questions for evolutionary biology The aim of this paper is to outline the major principles that guided language evolution in terms of mathematical models of evolutionary dynamics and game theory. I will discuss how natural selection can lead to the emergence of arbitrary signs, the formation of words and syntactic communication.

Animals↗
PubMed2006

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution.

To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed 'community phylogeny' approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.

Bacteria↗
PubMed2025

Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback.

Antiviral resistance evolution poses a major obstacle for controlling viral infections. A promising strategy is to target shared viral proteins that allow drug susceptible viruses to sensitize resistant ones during cellular coinfection, muting selection for resistance. Pocapavir, a poliovirus capsid inhibitor, employs this sociovirological strategy. While susceptible viruses significantly suppressed resistance in the presence of pocapavir in cell culture, a pocapavir clinical trial observed widespread resistance evolution and limited improvements to clearance times. To reconcile these findings, we present an intra-host eco-evolutionary model of poliovirus in the presence of pocapavir, which reproduces both the potent interference observed in vitro and the resistance emergence seen in patients. In the short term, our model predicts that a high density of susceptible viruses sensitizes resistant ones to pocapavir, mirroring cell culture results. However, over multiple replication cycles, pocapavir's high potency collapses viral density, which reduces coinfection and allows resistance to evolve as observed in the clinical trial. Since coinfection is essential to suppress resistance, enabling greater survival of susceptible viruses could offer therapeutic advantages. Counterintuitively, we demonstrate that this can be achieved by lessening antiviral potency, which can limit resistance evolution while also maintaining a low viral load. These findings suggest that antivirals that rely on viral intracellular interaction must balance immediate neutralization with the preservation of future coinfection, yielding more sustained inhibition. Explicitly considering the eco-evolutionary feedback encompassing viral density, shared phenotypes and absolute fitness not only provides new insights into designing effective therapies but also illuminates viral evolutionary dynamics more broadly.

Journal Article↗
PubMed2000

The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses.

The srh family of chemoreceptors in the nematode Caenorhabditis elegans is very large, containing 214 genes and 90 pseudogenes. It is related to the str, stl, and srd families of seven-transmembrane or serpentine receptors. Like these three families, most srh genes are concentrated on chromosome V, and mapping of their chromosomal locations on a phylogenetic tree reveals 27 different movements of genes to other chromosomes. Mapping of intron gains and losses onto the phylogenetic tree reveals that the last common ancestral gene of the family had five introns, which are inferred to have been lost 70 times independently during evolution of the family. In addition, seven intron gains are revealed, three of which are fairly recent. Comparisons with 20 family members in the C. briggsae genome confirms these patterns, including two intron losses in C. briggsae since the species split. There are 14 clear C. elegans orthologs for these 20 genes, whose average amino acid divergence of 68% allows estimation of 85 gene duplications in the C. elegans lineage since the species split. The absence of six orthologs in C. elegans also indicates that gene loss occurs; consideration of all deletions and terminal truncations of srh pseudogenes reveals that large deletions are common. Together these observations provide insight into the evolutionary dynamics of this compact animal genome.

Amino Acid Sequence↗
PubMed2001

Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22.

Human chromosomes 1q21-q25, 6p21.3-22.2, 9q33-q34, and 19p13.1-p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21-25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCERIA belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21-q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, IFI-16, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides.

Antigens, CD1↗
PubMed2004

A global view of the selection forces in the evolution of yeast cis-regulation.

The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.

Binding Sites↗
PubMed2026

Nuclear mitochondrial sequences in great ape telomere-to-telomere genomes.

Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology with extant mitochondrial DNA (mtDNA), termed NUMTs, confound mtDNA sequence analysis. Here, we use great ape telomere-to-telomere (T2T) genomes to study NUMTs in bonobo, chimpanzee, human, gorilla, and Bornean and Sumatran orangutans. A phylogeny based on shared and lineage-specific NUMTs accurately recapitulates the great ape species tree topology. NUMTs are enriched at nonfunctional nonrepetitive regions of the nuclear genome and depleted within enhancers and coding sequences, suggesting negative selection. We validate the presence of a 76-kb-long heterozygous NUMT in chimpanzee, which is larger than any other NUMT observed in great apes, and find that dozens of NUMTs on the Pan Y Chromosome expanded together with palindromes. Finally, by analyzing intra-specific variation, we confirm that the vast majority of species-specific NUMTs identified in T2T assemblies are fixed or present at high frequencies in each species. Our study highlights NUMTs as a dynamic evolutionary force contributing to shaping ape genomes and is valuable for characterizing mtDNA in great apes.

Journal Article↗