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Results for “evolutionary innovation”

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At least 217 records · Page 12Linked to original sources
PubMed1999

Orthologs, paralogs and genome comparisons.

During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.

Animals↗
PubMed2025

Systems biology successes and areas for opportunity in prostate cancer.

Systems biology approaches have been applied to prostate cancer to model how individual cellular and molecular components interact to influence cancer development, progression, and treatment responses. The integration of multi-omic experimental data with computational models has provided insights into the molecular characteristics of prostate cancer and emerging treatment strategies that have the potential to improve patient outcomes. Here, we highlight recent advancements that have emerged from systems modeling in prostate cancer. These include descriptions of the molecular landscape of prostate cancer and how genomic alterations inform computational models of disease progression, how evolutionary processes give rise to mechanisms of therapeutic resistance, and the development of innovative treatment strategies such as adaptive therapy. We also highlight current challenges in prostate cancer that can be addressed through systems biology approaches. These include tumor heterogeneity, poor immunotherapy response, a paucity of experimental model systems, and the ongoing translation of computational models for clinical decision making. Leveraging systems biology approaches has the potential to lead to a better understanding of the disease and better patient outcomes in the treatment of prostate cancer.

Humans↗
PubMed2026

Balancing under constraint: Structural insights into norovirus evolution and antigenic innovation.

Norovirus is the leading cause of acute viral gastroenteritis worldwide. While genomic studies have revealed its diversity and evolutionary patterns, the structural mechanisms driving viral adaptation remain poorly understood. Here, we establish a comprehensive structural database of norovirus VP1 P-domains across nine genogroups (GI-GIX) through large-scale AlphaFold2 predictions. By integrating phylogenetic analysis of VP1 sequences and structures, we demonstrate that sequence and structural evolution show overall concordance under purifying selection, yet significant local discrepancies reveal distinct patterns of convergent evolution shaped by structural constraints and functional divergence. Focusing on the predominant GII.4 genotype, we found that compared to near-full-genome and nucleotide trees, only the VP1 amino acid tree reliably clustered GII.4 variants in chronological order as monophyletic groups. We further identify a hierarchical evolutionary strategy: positive selection may drive structural hypervariability in major antigenic epitopes D and C for immune escape, with epitope D exhibiting pronounced structural flexibility that complicates its structural characterization, whereas coevolutionary analysis uncovers a broad network of compensatory interactions spanning multiple epitopes, with striking enrichment in epitope A. These epitopes exhibited a pattern of "sequence plasticity with structural conservation", maintained by coevolutionary constraints that preserve conformational integrity. Together, these findings suggest that norovirus vaccine strategies targeting the structurally conserved conformations of epitopes A and G could overcome the limitations of traditional strain-specific approaches, offering a pathway toward broad protection against evolving viral diversity.

Norovirus↗
PubMed2026

The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

Animals↗
PubMed2005

Molecular evidence from ascidians for the evolutionary origin of vertebrate cranial sensory placodes.

Cranial sensory placodes are specialised areas of the head ectoderm of vertebrate embryos that contribute to the formation of the cranial sense organs and associated ganglia. Placodes are often considered a vertebrate innovation, and their evolution has been hypothesised as one key adaptation underlying the evolution of active predation by primitive vertebrates. Here, we review recent molecular evidence pertinent to understanding the evolutionary origin of placodes. The development of vertebrate placodes is regulated by numerous genes, including members of the Pax, Six, Eya, Fox, Phox, Neurogenin and Pou gene families. In the sea squirt Ciona intestinalis (a basal chordate and close relative of the vertebrates), orthologues of these genes are deployed in the development of the oral and atrial siphons, structures used for filter feeding by the sessile adult. Our interpretation of these findings is that vertebrate placodes and sea squirt siphon primordia have evolved from the same patches of specialised ectoderm present in the common ancestor of the chordates.

Animals↗
PubMed2002

Codon and rate variation models in molecular phylogeny.

This article generalizes previous models for codon substitution and rate variation in molecular phylogeny. Particular attention is paid to (1) reversibility, (2) acceptance and rejection of proposed codon changes, (3) varying rates of evolution among codon sites, and (4) the interaction of these sites in determining evolutionary rates. To accommodate spatial variation in rates, Markov random fields rather than Markov chains are introduced. Because these innovations complicate maximum likelihood estimation in phylogeny reconstruction, it is necessary to formulate new algorithms for the evaluation of the likelihood and its derivatives with respect to the underlying kinetic, acceptance, and spatial parameters. To derive the most from maximum likelihood analysis of sequence data, it is useful to compute posterior probabilities assigning residues to internal nodes and evolutionary rate classes to codon sites. It is also helpful to search through tree space in a way that respects accepted phylogenetic relationships. Our phylogeny program LINNAEUS implements algorithms realizing these goals. Readers may consult our companion article in this issue for several examples.

Algorithms↗
PubMed2006

A paradigm for viewing biologic systems as scale-free networks based on energy efficiency: implications for present therapies and the future of evolution.

A network constitutes an abstract description of the relationships among entities, respectively termed links and nodes. If a power law describes the probability distribution of the number of links per node, the network is said to be scale-free. Scale-free networks feature link clustering around certain hubs based on preferential attachments that emerge due either to merit or legacy. Biologic systems ranging from sub-atomic to ecosystems represent scale-free networks in which energy efficiency forms the basis of preferential attachments. This paradigm engenders a novel scale-free network theory of evolution based on energy efficiency. As environmental flux induces fitness dislocations and compels a new meritocracy, new merit-based hubs emerge, previously merit-based hubs become legacy hubs, and network recalibration occurs to achieve system optimization. To date, Darwinian evolution, characterized by innovation sampling, variation, and selection through filtered termination, has enabled biologic progress through optimization of energy efficiency. However, as humans remodel their environment, increasing the level of unanticipated fitness dislocations and inducing evolutionary stress, the tendency of networks to exhibit inertia and retain legacy hubs engender maladaptations. Many modern diseases may fundamentally derive from these evolutionary displacements. Death itself may constitute a programmed adaptation, terminating individuals who represent legacy hubs and recalibrating the network. As memes replace genes as the basis of innovation, death itself has become a legacy hub. Post-Darwinian evolution may favor indefinite persistence to optimize energy efficiency. We describe strategies to reprogram or decommission legacy hubs that participate in human disease and death.

Animals↗
PubMed2006

The role of mitochondrial respiration in physiological and evolutionary adaptation.

Aerobic mitochondria serve as the power sources of eukaryotes by producing ATP through oxidative phosphorylation (OXPHOS). The enzymes involved in OXPHOS are multisubunit complexes encoded by both nuclear and mitochondrial DNA. Thus, regulation of respiration is necessarily a highly coordinated process that must organize production, assembly and function of mitochondria to meet an organism's energetic needs. Here I review the role of OXPHOS in metabolic adaptation and diversification of higher animals. On a physiological timescale, endocrine-initiated signaling pathways allow organisms to modulate respiratory enzyme concentration and function under changing environmental conditions. On an evolutionary timescale, mitochondrial enzymes are targets of natural selection, balancing cytonuclear coevolutionary constraints against physiological innovation. By synthesizing our knowledge of biochemistry, physiology and evolution of respiratory regulation, I propose that we can now explore questions at the interface of these fields, from molecular translation of environmental cues to selection on mitochondrial haplotype variation.

Adaptation, Physiological↗
PubMed2026

The novel transcriptional activator Bhr1 combining NTPase and Zn(II)2Cys6 DNA-binding domains controls (hemi-)cellulase response to mannose-rich substrates in the white-rot fungus Dichomitus squalens.

The regulatory landscape responsible for lignocellulose degradation in white-rot basidiomycete fungi remains largely unexplored. In this study, we characterize a novel transcriptional activator, Bhr1, in the white-rot fungus Dichomitus squalens. Bhr1 exhibits an unusual domain architecture that combines a septin-like P-loop NTPase fold with Zn(II)2Cys6 DNA-binding domains and plays a critical role in activating (hemi-)cellulase enzyme production when D. squalens is exposed to mannose-rich substrates. Using CRISPR/Cas9-mediated gene editing, we generated a bhr1 disruption mutant that displayed distinct phenotypes and enzyme activity profiles on mannose and guar gum compared to the wild type. RNA sequencing data indicate that Bhr1 induces specific (hemi-)cellulase-encoding genes without altering the expression of genes encoding sugar transporters or sugar metabolic enzymes. Phylogenetic analyses show that Bhr1 is basidiomycete specific and largely restricted to saprotrophic and plant-associated Agaricomycetes fungi. Based on the domain architecture of Bhr1 and the effects of its disruption in D. squalens, our findings reveal a lineage-specific regulatory innovation in basidiomycetes that is distinct from those described in ascomycetes. Elucidating the function and evolutionary conservation of Bhr1 advances our understanding of lignocellulose degradation at the molecular level in basidiomycete fungi and may inform studies of their ecological adaptation and the development of biotechnological applications.IMPORTANCEUnderstanding the transcriptional regulatory mechanisms in white-rot fungi, such as Dichomitus squalens, is crucial for advancing our knowledge of lignocellulose degradation. This study identifies D. squalens Bhr1 as a key regulator of (hemi-)cellulase production on mannose-rich substrates and further distinguishes basidiomycete transcription factors involved in plant biomass degradation from their ascomycete counterparts. Our findings highlight the significance of lineage-specific regulators in facilitating adaptive enzyme production for efficient biomass utilization, which is critical to carbon cycling in terrestrial ecosystems. This work establishes a foundation for exploring novel regulatory strategies among wood-degrading fungi, potentially enabling targeted strain engineering in biotechnological applications.

Mannose↗
PubMed2006

Evolution of class III homeodomain-leucine zipper genes in streptophytes.

Land plants underwent tremendous evolutionary change following the divergence of the ancestral lineage from algal relatives. Several important developmental innovations appeared as the embryophyte clade diversified, leading to the appearance of new organs and tissue types. To understand how these changes came about, we need to identify the fundamental genetic developmental programs that are responsible for growth, patterning, and differentiation and describe how these programs were modified and elaborated through time to produce novel morphologies. Class III homeodomain-leucine zipper (class III HD-Zip) genes, identified in the model plant Arabidopsis thaliana, provide good candidates for basic land plant patterning genes. We show that these genes may have evolved in a common ancestor of land plants and their algal sister group and that the gene family has diversified as land plant lineages have diversified. Phylogenetic analysis, expression data from nonflowering lineages, and evidence from Arabidopsis and other flowering plants indicate that class III HD-Zip genes acquired new functions in sporophyte apical growth, vascular patterning and differentiation, and leaf development. Modification of expression patterns that accompanied diversification of class III HD-Zip genes likely played an important role in the evolution of land plant form.

Base Sequence↗
PubMed2002

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems.

Animals↗
PubMed2026

Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard.

Viviparity (live-bearing) is a major evolutionary transition repeatedly linked with ecological and evolutionary diversification throughout vertebrates. Live-bearing reproduction entails a novel suite of phenotypes and life history traits, but the genetic processes by which such a reproductive innovation evolves are unknown. Remarkable among amniotes, the common lizard (Zootoca vivipara) has extant oviparous (egg-laying) and viviparous lineages and a to-date unresolved history of parity mode emergence. This species represents an ideal model to reconstruct the evolutionary and genetic mechanisms of how viviparity arises. By analyzing whole genomes of individuals from across the species' distribution, we robustly show that viviparity evolved once. However, gene flow from oviparous to viviparous populations is found to be long-term and extensive, causing pronounced gene tree discordance. We inferred signals of selection for viviparity in many independent regions across the genome, and these were recruited over considerable time. Genomic barriers to gene flow between oviparity and viviparity were found genome wide. These are enriched for regions under selection for parity mode and for genes known to be involved in pregnancy and parturition in squamates and mammals. Further implicating their functional role in viviparity, we show that genes in genomic regions under selection and resisting gene flow are more highly expressed in the uterus of viviparous lizards during pregnancy. Our study demonstrates that viviparity in an amniote evolved by selection in the face of gene flow and primarily by the genome-wide accumulation of functional regulatory variants. These results reveal how complex adaptive innovations can arise and be maintained.

Animals↗
PubMedDate not supplied

Determining the role that ecological and developmental constraints play in controlling disparity: examples from the crinoid and blastozoan fossil record.

It is widely believed that morphological constraints are responsible for the observed pattern of decreasing major morphological innovation in both the Metazoa and Metaphytes over geological time. This is readily seen as the decreasing trend of origination of higher taxa: phyla, classes, and orders. Currently, there are two competing evolutionary hypotheses that have been proposed to explain this phenomenon: (1) the empty ecospace hypothesis and (2) the developmental constraint hypothesis. To distinguish between hypotheses 1 and 2, the change of morphological innovation before and after several mass extinction events was measured in the Crinoidea and Blastozoa. Mass extinction intervals provided a means in which to remove ecospace limiting constraints and allow the developmental constraint hypothesis to be thoroughly tested. Within the Crinoidea, disparity was measured before and after three mass extinctions. Within the Blastozoa, disparity was measured before and after two mass extinctions. For each taxon, three suites of characters were analyzed: ecological, nonecological, or "developmental" and a combination of the two previous suites plus 50 additional characters. Four different measures of disparity were used to analyze each character suite. In the majority of the cases investigated, disparity rebounds to comparable levels or in some cases higher levels in both the Crinoidea and Blastozoa. The results indicate that developmental constraints are not responsible for the decrease in disparity throughout the geologic range of the taxa. The more likely scenario is that increasingly structured ecological guilds have made it much more difficult to allow large increases in disparity.

Animals↗
PubMed2001

Are we alone? Lessons from the evolution of life on earth.

The understanding of life on Earth that we have obtained from the science of evolutionary biology offers clues to the qustion of what life might be like if found elsewhere. After presenting the basics of the evolutionary process, I discuss the factors that determine the outcome of evolution, the role of key innovations and extinction in evolution, and whether the evolution of human life is inevitable.

Adaptation, Physiological↗
PubMed1990

Imperatives for the future of critical care nursing.

In the past, nursing has tended to rely on others to predict the professional future and to suggest specific actions and strategies to make that future a reality. Each of us entered nursing practice with a vision of what the profession of nursing is. Although we may have become distracted in the interim, each of us continues to have a desired vision of the future. Critical care nursing practice can either serve as the basis for innovative leadership in the continuing evolution of autonomous nursing practice or it can continue on an evolutionary track of critical care medical practice implemented by nurses. If your vision of the future is one in which critical care nurses engage in more than the implementation of pharmaceutical and medical treatment regimens, then your vision is worth making a reality. If you believe that critical care nurses make unique and valuable patient care contributions--greater than simply retooling with every technologic advance--you need to help other nurses begin to consider your perspective. Contrary to what many people believe, the future does not just happen. Someone, whether it be a nurse, a physician, or another professional, determines by action or failure to act what the future will hold. Each nurse needs to accept responsibility for the current state of nursing. We each own a piece of nursing's future practice. I want to be sure that my piece of the future matches my vision for critical care nursing. I challenge each of you to acknowledge your vision and to begin to take action to place that vision into critical care nursing's future.

Critical Care↗
PubMed1997

On the use of neural network techniques to analyse sleep EEG data. First communication: application of evolutionary and genetic algorithms to reduce the feature space and to develop classification rules.

To automate sleep stage scoring, the system sleep analysis system to challenge innovative artificial networks (SASCIA) has been developed and implemented. The aims of our investigation were twofold: In addition to automatic sleep stage scoring the hypothesis was tested that the information of only 1 EEG channel (C4-A2) should be sufficient to automatically generate sleep profiles which are comparable with profiles made by sleep experts on the basis of at least 3-channel EEG (C4-A2), EOG and EMG, as EOG and EMG are seen as epiphenomena during sleep and the full information about the sleep stage should--according to our hypothesis--be available in the EEG. The main components of the SASCIA sleep analysis system are designed to meet the requirements of flexible adaptation to the interindividual differences of the sleep EEG. The core of the SASCIA sleep analysis system consists of neural networks. Supervised learning was implemented and the experts' scorings were included into the learning set and test set. The feature selections out of a large number (118) are performed by genetic algorithms and the topologies of the networks are optimized by evolutionary algorithms. Different mathematical procedures were used to evaluate and optimize the efficiency of the system. The profiles generated by SASCIA are in reasonable agreement with the sleep stages scored by experts according to RKR. The development of the system is communicated in three parts: the first communication deals with the application of the neural network techniques using evolutionary and genetic algorithms and with the selection of feature space. The second communication shows the training of these evolutionary optimized network techniques with multiple subjects and the application of context rules, while the third communication shows an improvement in the robustness by the simultaneous application of 9 different networks obtained from 9 subject types which were used in combination with context rules.

Algorithms↗
PubMed1996

[The nature of personality: a co-evolutionary perspective].

Personality psychologists' attempts to explain human diversity have traditionally focused upon processes of person-situation interaction, and genotype-environment interaction. The great variability of genotypes and environments within cultures has remained unexplained in these efforts. Which processes may be responsible for the genetic and environmental variability within cultures? Answers to this question are sought in processes of genetic-cultural coevolution: mutation and sexual recombination of genes, innovation and synthesis of memes (units of cultural transmission), genotype-->environment and meme-->environment effects, and frequency-dependent natural and cultural selection. This twofold evolutionary explanation of personality differences within cultures suggests that a solid foundation of personality psychology requires bridging biology and cultural science.

Biological Evolution↗
PubMed1994

Gene duplications and the origins of vertebrate development.

All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates. Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

Amino Acid Sequence↗