SEARCH · PubMed Health

Results for “evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 1,135 records · Page 63Linked to original sources

PubMed2025

Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution.

Computational multi-scale pandemic modelling remains a major and timely challenge. Here we identify specific requirements for a new class of models simulating pandemics across three scales: (1) pathogen evolution, often punctuated by the rapid emergence of new variants, (2) human interactions within a heterogeneous population, and (3) public health responses which constrain individual actions to control the disease transmission. We then present a pandemic modelling framework satisfying these requirements and capable of simulating feedback loops between dynamics unfolding at these different scales. The developed framework comprises a stochastic agent-based model of pandemic spread, coupled with a phylodynamic model that incorporates within-host pathogen evolution. It is validated with a case study, modelling the punctuated evolution of SARS-CoV-2, based on global and contemporary genomic surveillance data, which captures a large heterogeneous population. We demonstrate that the model replicates the essential features of the COVID-19 pandemic and virus evolution, while retaining computational tractability and scalability.

SARS-CoV-2↗

PubMed2006

Sexual selection and the evolution of brain size in primates.

Reproductive competition among males has long been considered a powerful force in the evolution of primates. The evolution of brain size and complexity in the Order Primates has been widely regarded as the hallmark of primate evolutionary history. Despite their importance to our understanding of primate evolution, the relationship between sexual selection and the evolutionary development of brain size is not well studied. The present research examines the evolutionary relationship between brain size and two components of primate sexual selection, sperm competition and male competition for mates. Results indicate that there is not a significant relationship between relative brain size and sperm competition as measured by relative testis size in primates, suggesting sperm competition has not played an important role in the evolution of brain size in the primate order. There is, however, a significant negative evolutionary relationship between relative brain size and the level of male competition for mates. The present study shows that the largest relative brain sizes among primate species are associated with monogamous mating systems, suggesting primate monogamy may require greater social acuity and abilities of deception.

Animals↗

PubMed2000

Evolution of urate-degrading enzymes in animal peroxisomes.

The end product of purine metabolism varies from species to species. The degradation of purines to urate is common to all animal species, but the degradation of urate is much less complete in higher animals. The comparison of subcellular distribution, intraperoxisomal localization forms, molecular structures, and some other properties of urate-degrading enzymes (urate oxidase, allantoinase, and allantoicase) among animals is described. Liver urate oxidase (uricase) is located in the peroxisomes in all animals with urate oxidase. On the basis of the comparison of intraperoxisomal localization forms, mol wt, and solubility of liver urate oxidase among animals, it is suggested that amphibian urate oxidase is a transition form in the evolution of aquatic animals to land animals. Allantoinase and allantoicase are different proteins in fish liver, but the two enzymes form a complex in amphibian liver. The subcellular localization of allantoinase and allantoicase varies among fishes. Hepatic allantoinase is located both in the peroxisomes and in the cytosol in saltwater fishes, and only in the cytosol in freshwater fishes. Hepatic allantoicase is located on the outer surface of the peroxisomal membrane in the mackerel group and in the peroxisomal matrix in the sardine group. Amphibian hepatic allantoinase-allantoicase complex is probably located in the mitochondria. On the basis of previous data, changes of allantoinase and allantoicase in molecular structure and intracellular localization during animal evolution may be as follows: Fish liver allantoinase is a single peptide with a mol wt of 54,000, and is located both in the peroxisomes and in the cytosol, or only in the cytosol. Fish liver allantoicase consists of two identical subunits with a mol wt of 48,000, and is located in the peroxisomal matrix or on the outer surface of the peroxisomal membrane. The evolution of fishes to amphibia resulted in the dissociation of allantoicase into subunits, and in the association of allantoinase with the subunit of allantoicase. This amphibian enzyme was lost by further evolution.

Amidohydrolases↗

PubMed2001

Evolution in silico and in vitro: the RNA model.

Theoretical concepts and experiments dealing with the evolution of molecules in vitro reached a state that allows for direct applications to the design of biomolecules with predefined properties. RNA evolution in vitro represents a basis for the development of a new and comprehensive model of evolution, focusing on the phenotype and its fitness relevant properties. Relations between genotypes and phenotypes are described by mappings from genotype space onto a space of phenotypes, which are many-to-one and thus give ample room for neutrality as expressed by the existence of extended neutral networks in genotype space. The RNA model reduces genotype-phenotype relations to mappings from sequences into secondary structures of minimal free energies and allows for derivation of otherwise inaccessible quantitative results. Continuity and discontinuity in evolution are defined through a new notion of accessibility in phenotype space that provides a basis for straight forward interpretation of computer simulations on RNA optimization; furthermore, it reveals the constructive role of random genomic drift in the search for phenotypes of higher fitness. The effects of population size on the course of evolutionary optimization can be predicted quantitatively by means of a simple stochastic model based on a birth-anddeath process with immigration.

Base Sequence↗

PubMed2005

Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii.

Genome dynamics that allow pathogens to escape host immune responses are fundamental to our understanding of host-pathogen interactions. Here we present the first population-based study of the process of concerted evolution in the repetitive domain of a protein-coding gene. This gene, SOWgp, encodes the immunodominant protein in the parasitic phase of the human pathogenic fungi Coccidioides immitis and C. posadasii. We sequenced the entire gene from strains representing the geographic ranges of the two Coccidioides species. By using phylogenetic and genetic distance analyses we discovered that the repetitive part of SOWgp evolves by concerted evolution, predominantly by the mechanism of unequal crossing over. We implemented a mathematical model originally developed for multigene families to estimate the rate of homogenization and recombination of the repetitive array, and the results indicate that the pattern of concerted evolution is a result of homogenization of repeat units proceeding at a rate close to the nucleotide point mutation rate. The release of the SOWgp molecules by the pathogen during proliferation may mislead the host: we speculate that the pathogen benefits from concerted evolution of repeated domains in SOWgp by an enhanced ability to misdirect the host's immune system.

Antigens, Fungal↗

PubMed2006

Concerted evolution of two novel protein families in Caenorhabditis species.

Among a large number of homologous gene clusters in C. elegans, two gene families that appear to undergo concerted evolution were studied in detail. Both gene families are nematode specific and encode small secreted proteins of unknown function. For both families in three Caenorhabditis species, concerted groups of genes are characterized by close genomic proximity and by genes in inverted orientation. The rate of protein evolution in one of the two families could be calibrated by comparison with a closely related nonconcerted singleton gene with one-to-one orthologs in all three species. This comparison suggests that protein evolution in concerted gene clusters is two- to sevenfold accelerated. A broader survey of clustered gene families, focused on adjacent inverted gene pairs, identified an additional seven families in which concerted evolution probably occurs. All nine identified families encode relatively small proteins, eight of them encode putative secreted proteins, and most of these have very unusual amino acid composition or sequence. I speculate that these genes encode rapidly evolving antimicrobial peptides.

Amino Acid Sequence↗

PubMed2006

No accelerated rate of protein evolution in male-biased Drosophila pseudoobscura genes.

Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura.

Amino Acid Substitution↗

PubMed2003

Evolution of prey behavior in response to changes in predation regime: damselflies in fish and dragonfly lakes.

In a large behavioral experiment we reconstructed the evolution of behavioral responses to predators to explore how interactions with predators have shaped the evolution of their prey's behavior. All Enallagma damselfly species reduced both movement and feeding in the presence of coexisting predators. Some Enallagma species inhabit water bodies with both fish and dragonflies, and these species responded to the presence of both predators, whereas other Enallagma species inhabit water bodies that have only large dragonflies as predators, and these species only responded to the presence of dragonflies. Lineages that shifted to live with large dragonflies showed no evolution in behaviors expressed in the presence of dragonflies, but they evolved greater movement in the absence of predators and greater movement and feeding in the presence of fish. These results suggest that Enallagma species have evolutionarily lost the ability to recognize fish as a predator. Because species coexisting with only dragonfly predators have also evolved the ability to escape attacking dragonfly predators by swimming, the decreased predation risk associated with foraging appears to have shifted the balance of the foraging/predation risk trade-off to allow increased activity in the absence of mortality threats to evolve in these lineages. Our results suggest that evolution in response to changes in predation regime may have greater consequences for characters expressed in the absence of mortality threats because of how the balance between the conflicting demands of growth and predation risk are altered.

Animals↗

PubMed2002

The role of reelin in the development and evolution of the cerebral cortex.

Reelin is an extracellular matrix protein that is defective in reeler mutant mice and plays a key role in the organization of architectonic patterns, particularly in the cerebral cortex. In mammals, a "reelin signal" is activated when reelin, secreted by Cajal-Retzius neurons, binds to receptors of the lipoprotein receptor family on the surface of cortical plate cells, and triggers Dab1 phosphorylation. As reelin is a key component of cortical development in mammals, comparative embryological studies of reelin expression were carried out during cortical development in non-mammalian amniotes (turtles, squamates, birds and crocodiles) in order to assess the putative role of reelin during cortical evolution. The data show that reelin is present in the cortical marginal zone in all amniotes, and suggest that reelin has been implicated in the evolution of the radial organization of the cortical plate in the synapsid lineage leading from stem amniotes to mammals, as well as in the lineage leading to squamates, thus providing an example of homoplastic evolution (evolutionary convergence). The mechanisms by which reelin instructs radial cortical organization in these two lineages seem different: in the synapsid lineage, a drastic amplification of reelin production occurred in Cajal-Retzius cells, whereas in squamates, in addition to reelin-secreting cells in the marginal zone, a second layer of reelin-producing cells developed in the subcortex. Altogether, our results suggest that the reelin-signaling pathway has played a significant role in shaping the evolution of cortical development.

Animals↗

PubMed2006

The diversity challenge in directed protein evolution.

Over the past decade, we have witnessed a bloom in the field of evolutive protein engineering which is fueled by advances in molecular biology techniques and high-throughput screening technology. Directed protein evolution is a powerful algorithm using iterative cycles of random mutagenesis and screening for tailoring protein properties to our needs in industrial applications and for elucidating proteins' structure function relationships. This review summarizes, categorizes and discusses advantages and disadvantages of random mutagenesis methods used for generating genetic diversity. These random mutagenesis methods have been classified into four main categories depending on the method employed for nucleotide substitutions: enzyme based methods (Category I), synthetic chemistry based methods (Category II), whole cell methods (Category III) and combined methods (Category I-II, I-III and II-III). The basic principle of each method is discussed and varied mutagenic conditions are summarized in Tables and compared (benchmarked) to each other in terms of: mutational bias, controllable mutation frequency, ability to generate consecutive nucleotide substitutions and subset diversity, dependency on gene length, technical simplicity/robustness and cost-effectiveness. The latter comparison shows how highly-biased and limited current diversity creating methods are. Based on these limitations, strategies for generating diverse mutant libraries are proposed and discussed (RaMuS-Flowchart; KISS principle). We hope that this review provides, especially for researchers just entering the field of directed evolution, a guide for developing successful directed evolution strategies by selecting complementary methods for generating diverse mutant libraries.

Base Composition↗

PubMed2004

Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex.

The presence of a distinct nucleus, the compartment for confining the genome, transcription and RNA maturation, is a central (and eponymous) feature that distinguishes eukaryotes from prokaryotes. Structural integrity of the nucleus is maintained by the nuclear envelope (NE). A crucial element of this structure is the nuclear pore complex (NPC), a macromolecular machine with over 90 protein components, which mediates nucleo-cytoplasmic communication. We investigated the provenance of the conserved domains found in these perinuclear proteins and reconstructed a parsimonious scenario for NE and NPC evolution by means of comparative-genomic analysis of their components from the available sequences of 28 sequenced eukaryotic genomes. We show that the NE and NPC proteins were tinkered together from diverse domains, which evolved from prokaryotic precursors at different points in eukaryotic evolution, divergence from pre-existing eukaryotic paralogs performing other functions, and de novo. It is shown that several central components of the NPC, in particular, the RanGDP import factor NTF2, the HEH domain of Src1p-Man1, and, probably, also the key domains of karyopherins and nucleoporins, the HEAT/ARM and WD40 repeats, have a bacterial, most likely, endosymbiotic origin. The specialized immunoglobulin (Ig) domain in the globular tail of the animal lamins, and the Ig domains in the nuclear membrane protein GP210 are shown to be related to distinct prokaryotic families of Ig domains. This suggests that independent, late horizontal gene transfer events from bacterial sources might have contributed to the evolution of perinuclear proteins in some of the major eukaryotic lineages. Snurportin 1, one of the highly conserved karyopherins, contains a cap-binding domain which is shown to be an inactive paralog of the guanylyl transferase domain of the mRNA-capping enzyme, exemplifying recruitment of paralogs of pre-exsiting proteins for perinuclear functions. It is shown that several NPC proteins containing super-structure- forming alpha-helical and beta-propeller modules are most closely related to corresponding proteins in the cytoplasmic vesicle biogenesis and coating complexes. From these observations, we infer an autogenous scenario of nuclear evolution in which the nucleus emerged in the primitive eukaryotic ancestor (the "prekaryote") as part of cell compartmentalization triggered by archaeo-bacterial symbiosis. A pivotal event in this process was the radiation of Ras-superfamily GTPases yielding Ran, the key regulator of nuclear transport. A primitive NPC with approximately 20 proteins and a Src1p-Man1-like membrane protein with a DNA-tethering HEH domain are inferred to have been integral perinuclear components in the las common ancestor of modern eukaryotes.

Amino Acid Sequence↗

PubMed1998

[Reconstruction of possible paths of the origin and morphological evolution of bacteriophages].

The problem of the origin and evolution of viruses and, in particular, the origin and evolution of bacteriophages is of considerable interest. However, so far, this problem has not been solved with quantitative methods of molecular systematics. In the present study, an attempt to reconstruct the possible paths of appearance and evolution of bacteriophages based on their structural features and morphogenesis, as well as general characteristics of their life cycles and genome organization, was carried out. A scheme describing phylogeny of the main bacteriophage groups and evolution of their life cycles is suggested. Existence of two independently evaluating types of morphogenesis ("budding outward" and "budding inward") is postulated.

Bacteriophages↗

PubMed1999

Infection chains and evolution rates of hepatitis B virus in cardiac transplant recipients infected nosocomially.

Following an outbreak of hepatitis B virus (HBV) infection amongst immunosuppressed transplant recipients, the complete sequences of the HBV-DNA isolated from nine of the affected patients were determined. The DNA sequences were found to differ from each other by a maximum of three nucleotides and belonged to the same serotype (ayw3). By contrast, the sequences differed by 18 nucleotides from the most similar HBV-DNA sequence published, indicating a common source of infection. The infection chains that have been constructed according to the base differences between the DNAs agreed well with those previously established on the basis of epidemiological data [Drescher et al. (1994) Journal of Hospital Infection 26:81-92]. At least two HBV populations, differing by one or two nucleotides, were detected in four patients, and coexisted for differing periods of time. Mutations of the core and X-peptide were not found. The data were used to calculate evolution rates of HBV DNA, both for HBV persisting within a patient and for infection chains. The rates obtained were of the same order as described previously for immunocompetent patients, indicating that the immunosuppressive medication did not influence the evolution rate. However, the evolution rate was found to decrease with increasing evolution time.

Cross Infection↗

PubMed2001

Inference and prediction of courses of the diseases caused by pathologic viruses by estimating molecular evolution of within-host virus.

A new approach for inferring the evolutionary process of within-host virus is presented in this study. This approach includes a sequential-linking algorithm developed by us that can deal with the sequential viral samples that are obtained at different time points from the same host, and reconstruct a longitudinal phylogenetic tree in which the evolutionary relations between viral variants can be shown. A codon-based model, which uses a Markov process to describe substitutions between codons, is also employed in this approach to calculate synonymous and non-synonymous substitution rates and to distinguish positive selection and neutral evolution. The approach is applied to a data set of the V3 region of the HIV-1 envelope genes sequenced in different years after infection of a single patient. The results suggest that this approach may provide a more realistic description of viral evolution than the traditional evolution models because it accounts for both neutral and adaptive evolution. Most important of all, since this approach make it possible to follow up the evolutionary process of within-host virus by analyzing the sequential viral samples, it could be used in inference and prediction of the course of the diseases caused by pathologic viruses and evaluation of the treatment.

Algorithms↗

PubMedDate not supplied

[The evolution of the structure of the neocortex in mammals: a new theory of cytoarchitecture].

INTRODUCTION: The evolution of the structural organization of the mammalian neocortex can only be appreciated studying its ontogenetic development. DEVELOPMENT: We studied its evolution in embryos of different mammals (hamster, mouse, rat, cat and man) using the Golgi method. Development of the neocortex starts with the establishment of a primordial plexiform layer (PPL) in the telencephalus. This PPL represents a primitive cortical organization which is shared by amphibians, reptiles and mammals. From the PPL derived: the layer 1 with its elements including: the Cajal Retzius cells (CR) and primitive afferent fibres of a possibly origin in mesencephalic nuclei and the elements the interstitial cells and afferent fibres of the subplaca. The formation of the PPL is a prerequisite for the subsequent formation of the cortical plate (CP) from which the remaining layers of the neocortex derived. The ascending neuronal migration, the morphology of pyramidal neurons and the inside outside arrangement of neurons within the CP are evolutionary processes controlled by the CR cells. These neurons secrete a glycoprotein reelin which attracts the migrating neurons toward the first layer. All migrating neuroblasts, guided by the radial glia, must reach layer 1, establish contacts with the CR cells, develop an apical dendrite and become pyramidal cells. Without losing either their original contact with layer 1 or their cortical level, each neuron has to elongate its apical dendrite to accommodate the arrival of subsequent neurons, such that all develop a common initial pyramidal morphology. Older neurons have longer apical dendrites and deeper cortical level than the newer ones. The subsequent morphological and functional maturation of the CP neurons also follows an ascending progression and is under thalamic control. Two basic types of neurons develop in the neocortex following its ascending stratification. Some neurons maintain their original contact with the first layer to become the pyramidal cells. Others lose their original contact with layer 1 and become stellate interneurons. These neurons are free to develop specific size, spatial morphology and synaptic endings. The CP is a mammalian innovation and represents a biologically open and stratified nucleus which adds, during mammalian evolution, new pyramidal cell strata to those already present. CONCLUSIONS: Based on the above observations, we propose a new cytoarchitectural theory and nomenclature for the structural evolution of the mammalian neocortex. The theory emphasizes the ascending structural and functional stratification of the mammalian neocortex and the increase in the number of pyramidal cell strata reflecting the motor needs of each species.

Animals↗

PubMed2001

The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution.

Under what conditions might organisms be capable of rapid adaptive evolution? We reviewed published studies documenting contemporary adaptations in natural populations and looked for general patterns in the population ecological causes. We found that studies of contemporary adaptation fall into two general settings: (1) colonization of new environments that established newly adapted populations, and (2) local adaptations within the context of a heterogeneous environments and metapopulation structure. Local ecological processes associated with colonizations and introductions included exposure to: (1) a novel host or food resource; (2) a new biophysical environment; (3) a new predator community; and (4) a new coexisting competitor. The new environments that were colonized often had depauperate communities, sometimes because of anthropogenic disturbance. Local adaptation in heterogeneous environments was also often associated with recent anthropogenic changes, such as insecticide and herbicide resistance, or industrial melanism. A common feature of many examples is the combination of directional selection with at least a short-term opportunity for population growth. We suggest that such opportunities for population growth may be a key factor that promotes rapid evolution, since directional selection might otherwise be expected to cause population decline and create the potential for local extinction, which is an ever-present alternative to local adaptation. We also address the large discrepancy between the rate of evolution observed in contemporary studies and the apparent rate of evolution seen in the fossil record.

Adaptation, Biological↗

PubMed2003

Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates.

The major transitions in human evolution from prokaryotes to eukaryotes, from protozoans to metazoans, from the first animals to bilaterians and finally from a primitive chordate to vertebrates were all accompanied by increases in genome complexity. Rare fusion of divergent genomes rather than continuous single gene duplications could explain these jumps in evolution. The origin of eukaryotes was proposed to be due to a symbiosis of Archaea and Bacteria. Symbiosis is clearly seen as the source for mitochondria. A fundamental difference of higher eukaryotes is the cycle from haploidy to diploidy, a well-regulated genome duplication. Of course, self-fertilization exists, but the potential of sex increases with the difference of the haploid stages, such as the sperm and the egg. What should be the advantage of having two identical copies of a gene? Still, genes duplicate all the time and even genomes duplicate rather often. In plants, polyploidy is well recognized, but seems to be abundant in fungi and even in animals, too. However, hybridization, rather than autopolyploidy, seems to be the potential mechanism for creating something new. The problem with chimaeric, symbiotic or reticulate evolution events is that they blur phylogenetic lineages. Unrecognized paralogous genes or random loss of one of the paralogs in different lineages can lead to false conclusions. Horizontal genome transfer, genome fusion or hybridization might be only truly innovative combined with rare geological transitions such as change to an oxygen atmosphere, snowball Earth events or the Cambrian explosion, but correlates well with the major transitions in evolution.

Animals↗

PubMed2003

Modular assembly of genes and the evolution of new functions.

Modular assembly of novel genes from existing genes has long been thought to be an important source of evolutionary novelty. Thanks to major advances in genomic studies it has now become clear that this mechanism contributed significantly to the evolution of novel biological functions in different evolutionary lineages. Analyses of completely sequenced bacterial, archaeal and eukaryotic genomes has revealed that modular assembly of novel constituents of various eukaryotic intracellular signalling pathways played a major role in the evolution of eukaryotes. Comparison of the genomes of single-celled eukaryotes, multicellular plants and animals has also shown that the evolution of multicellularity was accompanied by the assembly of numerous novel extracellular matrix proteins and extracellular signalling proteins that are absolutely essential for multicellularity. There is now strong evidence that exon-shuffling played a general role in the assembly of the modular proteins involved in extracellular communications of metazoa. Although some of these proteins seem to be shared by all major groups of metazoa, others are restricted to certain evolutionary lineages. The genomic features of the chordates appear to have favoured intronic recombination as evidenced by the fact that exon-shuffling continued to be a major source of evolutionary novelty during vertebrate evolution.

Evolution, Molecular↗