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At least 253 records · Page 14Linked to original sources
PubMed2005

Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information.

MOTIVATION: There has been great expectation that the knowledge of an individual's genotype will provide a basis for assessing susceptibility to diseases and designing individualized therapy. Non-synonymous single nucleotide polymorphisms (nsSNPs) that lead to an amino acid change in the protein product are of particular interest because they account for nearly half of the known genetic variations related to human inherited diseases. To facilitate the identification of disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the phenotypic effects of nsSNPs. RESULTS: We prepared a training set based on the variant phenotypic annotation of the Swiss-Prot database and focused our analysis on nsSNPs having homologous 3D structures. Structural environment parameters derived from the 3D homologous structure as well as evolutionary information derived from the multiple sequence alignment were used as predictors. Two machine learning methods, support vector machine and random forest, were trained and evaluated. We compared the performance of our method with that of the SIFT algorithm, which is one of the best predictive methods to date. An unbiased evaluation study shows that for nsSNPs with sufficient evolutionary information (with not <10 homologous sequences), the performance of our method is comparable with the SIFT algorithm, while for nsSNPs with insufficient evolutionary information (<10 homologous sequences), our method outperforms the SIFT algorithm significantly. These findings indicate that incorporating structural information is critical to achieving good prediction accuracy when sufficient evolutionary information is not available. AVAILABILITY: The codes and curated dataset are available at http://compbio.utmem.edu/snp/dataset/

Algorithms↗
PubMed2025

Recurrent Evolutionary Innovations in Rodent and Primate Schlafen Genes.

SCHLAFEN proteins are a large family of RNase-related enzymes carrying essential immune and developmental functions. Despite these important roles, Schlafen genes display varying degrees of evolutionary conservation in mammals. While this appears to influence their molecular activities, a detailed understanding of these evolutionary innovations is still lacking. Here, we used in-depth phylogenomic approaches to characterize the evolutionary trajectories and selective forces shaping mammalian Schlafen genes. We traced lineage-specific Schlafen amplifications and found that recent duplicates evolved under distinct selective forces, supporting repeated subfunctionalization cycles. Codon-level natural selection analyses in primates and rodents identified recurrent positive selection over Schlafen protein domains engaged in viral interactions. Combining known crystal structures and predicted protein structures, we discovered a novel class of rapidly evolving residues enriched at the contact interface of SCHLAFEN protein dimers. Our results suggest that inter-SCHLAFEN compatibilities are under strong selective pressures and are likely to impact their molecular functions. We posit that cycles of genetic conflicts with pathogens and between paralogs drove Schlafens' recurrent evolutionary innovations in mammals.

Animals↗
PubMed2004

Evolutionary mapping of the SHV beta-lactamase and evidence for two separate IS26-dependent blaSHV mobilization events from the Klebsiella pneumoniae chromosome.

OBJECTIVES: To determine the most likely evolutionary pathway that has led to the development of extended-spectrum SHV derivatives, and to the mobilization of blaSHV. MATERIALS AND METHODS: Evolutionary mapping used a shortest-path analysis of aligned blaSHV variants, and other basic bioinformatic approaches, such as CLUSTAL W and Blast were employed. RESULTS: Two main branches of the blaSHV evolutionary tree were located; both are derived from variant blaSHV-1 alleles. Identical mutations, responsible for extended-spectrum SHV substrate profiles, have been selected independently in each branch. There is evidence for a pool of non-mobile blaSHV framework sequences. Analysis of the genome sequence of Klebsiella pneumoniae confirms the chromosomal origin of blaSHV, whose mobilization has occurred at least twice, once for each of the main evolutionary branches. Both these mobilization events have been catalysed by IS26. Evolution of blaSHV to give common extended-spectrum variants is most likely to have occurred following mobilization. CONCLUSIONS: These data shed new light on the evolution and mobilization of blaSHV, and these observations may be useful in predicting what might happen in future, both for blaSHV, and for other beta-lactamase genes.

Alleles↗
PubMed2025

Distinct Evolutionary Signatures of Human Parainfluenza Viruses 2 and 4 Reveal Host Antagonism Divergence and Phylogenetic Discordance.

Human parainfluenza virus 2 (HPIV-2) and human parainfluenza virus 4 (HPIV-4) are significant but underappreciated respiratory pathogens, particularly among high-risk populations including children, the elderly, and immunocompromised individuals. In this study, we sequenced 101 HPIV-2 and HPIV-4 genomes from respiratory samples collected in western Washington State and performed comprehensive evolutionary analyses using both new and publicly available sequences. Phylogenetic and phylodynamic analyses revealed that both HPIV-2 and HPIV-4 evolve at significantly faster rates compared to the mumps virus, a reference human orthorubulavirus. Notably, while HPIV-2 demonstrated the highest evolutionary rates in the surface glycoprotein HN, consistent with humoral immune-driven selection, the innate immune antagonist V/P gene evolved fastest in HPIV-4. We identified a hypervariable region within the HPIV-4V/P protein (residues 35 to 75), which structural modeling placed in a loop overlapping a known interferon antagonism domain in other paramyxovirus V proteins, though HPIV-4 is functionally incompetent in this activity. Expanded phylogenetic analysis across the Paramyxoviridae family uncovered a striking evolutionary discordance: while the HN glycoprotein and L polymerase of HPIV-4 and its 2 closest bat-derived viruses clustered within the Orthorubulavirus genus, their nucleoprotein (N), phosphoprotein (P), matrix (M), and fusion (F) proteins formed a distinct lineage outside the Rubulavirinae subfamily. Together, these findings highlight the distinct evolutionary trajectories of HPIV-2 and HPIV-4, raise hypotheses around complex Paramyxoviridae zoonotic events including recombination-like patterns, and demonstrate limitations of current L protein-based taxonomic classification schemes.

Humans↗
PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗
PubMed2005

Lineage-specific differences in evolutionary mode in a salamander courtship pheromone.

Functionally equivalent genes may evolve heterogeneously across closely related taxa as a consequence of lineage-specific selective pressures. Such disparate evolutionary modes are especially prevalent in genes that encode postcopulatory reproductive proteins, presumably as a result of sexual selection. We might therefore expect genes that mediate reproduction prior to insemination to evolve in a similar manner. Plethodontid receptivity factor (PRF), a proteinaceous salamander pheromone produced by the male, increases female receptivity during courtship interactions. To test for lineage-specific differences in PRF's evolution, we intensively sampled PRF genes across the eastern Plethodon phylogeny (27 spp.; 34 populations) to compare gene diversification, rates of evolution, modes of selection, and types of amino acid substitution. Our analyses indicate that PRF evolutionary dynamics vary considerably from lineage to lineage. Underlying this heterogeneity, however, are two well-defined transitions in evolutionary mode. The first mode is representative of a typical protein profile, wherein neutral divergence and purifying selection are the dominant features. The second mode is characterized by incessant, cyclical evolution driven by positive selection. In this mode, the positively selected sites are bound by a limited assortment of acceptable amino acids that appear to evolve independently of other sites, resulting in a tremendous number of unique PRF alleles. Several of these selected sites are implicated in receptor binding. These sites are apparently involved in a molecular tango in which the male signal and female receptors coevolve within a confined molecular space. PRF's lineage-specific evolutionary dynamics, in combination with evidence of a molecular tango, highlight the molecular action of sexual selection on a chemical signal that is used during courtship.

Amino Acid Sequence↗
PubMed2006

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.

Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.

Animals↗
PubMed2003

CnidBase: The Cnidarian Evolutionary Genomics Database.

CnidBase, the Cnidarian Evolutionary Genomics Database, is a tool for investigating the evolutionary, developmental and ecological factors that affect gene expression and gene function in cnidarians. In turn, CnidBase will help to illuminate the role of specific genes in shaping cnidarian biodiversity in the present day and in the distant past. CnidBase highlights evolutionary changes between species within the phylum Cnidaria and structures genomic and expression data to facilitate comparisons to non-cnidarian metazoans. CnidBase aims to further the progress that has already been made in the realm of cnidarian evolutionary genomics by creating a central community resource which will help drive future research and facilitate more accurate classification and comparison of new experimental data with existing data. CnidBase is available at http://cnidbase.bu.edu/.

Animals↗
PubMedDate not supplied

On the virtues and pitfalls of the molecular evolutionary clock.

"Informational" macromolecules--i.e., proteins and nucleic acids--have in their sequences a register of evolutionary history. Zuckerkandl and Pauling suggested in 1965 that these molecules might provide a "molecular clock" of evolution. The molecular clock would time evolutionary events and make it possible to reconstruct phylogenetic history--the branching relationships among lineages leading to modern species. Kimura's neutrality theory postulates that rates of molecular evolution are stochastically constant and, hence, that there is a molecular clock. A variety of tests have shown that molecular evolution does not behave like a stochastic clock. The variance in evolutionary rates is much too large and thus inconsistent with the neutrality theory. This, however, does not invalidate the clock, but rather leaves it without a theoretical foundation to anticipate its properties. Sequence comparisons show that molecular evolution is sufficiently regular to serve in many situations as a clock, but uncertainty concerning the properties of the clock (for example, about the circumstances that may yield large oscillations in substitution rates from time to time or from lineage to lineage) demands that it be used with caution. Few DNA or protein sequences are known from organisms that range from closely related, e.g., different mammals, to very remote, e.g., mammals and fungi. One example is cytochrome c, which has an acceptable clockwise behavior over the whole span, in spite of some irregularities. Another example is the copper-zinc superoxide dismutase (SOD), which behaves like a very erratic clock. The SOD average rate of amino acid substitution per 100 residues per 100 million years (MY) is 5.5 when fungi and animals are compared, 9.1 when comparisons are made between insects and mammals, and 27.8 when mammals are compared with each other. The question is which mode is more common over broad evolutionary spans: the regularity of cytochrome c or the capriciousness of SOD? Additional data sets will be required in order to obtain the answer and to develop expectations about the accuracy of the clock in particular instances. Until such data exist, conclusions solely based on the molecular clock are potentially fraught with error.

Amino Acid Sequence↗
PubMed2002

Evolution of eukaryotic translation elongation and termination factors: variations of evolutionary rate and genetic code deviations.

Translation is carried out by the ribosome and several associated protein factors through three consecutive steps: initiation, elongation, and termination. Termination remains the least understood of them, partly because of the nonuniversality of the factors involved. To get some insights on the evolution of eukaryotic translation termination, we have compared the phylogeny of the release factors eRF1 and eRF3 to that of the elongation factors EF-1alpha and EF-2, with special focus on ciliates. Our results show that these four translation proteins have experienced different modes of evolution. This is especially evident for the EF-1alpha, EF-2, and eRF1 ciliate sequences. Ciliates appear as monophyletic in the EF-2 phylogenetic tree but not in the EF-1alpha and eRF1 phylogenetic trees. This seems to be mainly because of phylogeny reconstruction artifacts (the long-branch attraction) produced by the acceleration of evolutionary rate of ciliate EF-1alpha and eRF1 sequences. Interaction with the highly divergent actin found in ciliates, or on the contrary, loss of interaction, could explain the acceleration of the evolutionary rate of the EF-1alpha sequences. In the case of ciliate eRF1 sequences, their unusually high evolutionary rate may be related to the deviations in the genetic code usage found in diverse ciliates. These deviations involve a relaxation (or even abolition) of the recognition of one or two stop codons by eRF1. To achieve this, structural changes in eRF1 are needed, and this may affect its evolutionary rate. Eukaryotic translation seems to have followed a mosaic evolution, with its different elements governed by different selective pressures. However, a correlation analysis shows that, beneath the disagreement shown by the different translation proteins, their concerted evolution can still be made apparent when they are compared with other proteins that are not involved in translation.

Animals↗
PubMed2002

Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium).

Levels and patterns of nucleotide diversity vary widely among lineages. Because allopolyploid species contain duplicated (homoeologous) genes, studies of nucleotide diversity at homoeologous loci may facilitate insight into the evolutionary dynamics of duplicated loci. In this study, we describe patterns of sequence diversity from an alcohol dehydrogenase homoeologous locus pair (AdhC) in allotetraploid cotton (Gossypium, Malvaceae). These data are compared with equivalent information from another homoeologous alcohol dehydrogenase gene pair (AdhA, Small, Ryburn, and Wendel 1999. Mol. Biol. Evol. 16:491-501) which has an overall slower evolutionary rate than AdhC. As expected from the predicted correlation between nucleotide diversity and evolutionary rate, nucleotide diversity was higher for AdhC than for AdhA. In addition, nucleotide diversity is higher in the D-subgenome of allotetraploid cotton for AdhC, confirming earlier observations for AdhA. These observations indicate that for these two pairs of Adh loci, the null hypothesis of equivalent evolutionary dynamics for duplicated genes in allotetraploid cotton is rejected.

Alcohol Dehydrogenase↗
PubMed2000

Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

Assessment of the evolutionary process is crucial for understanding the effect of protein structure and function on sequence evolution and for many other analyses in molecular evolution. Here, we used simulations to study how taxon sampling affects accuracy of parameter estimation and topological inference in the absence of branch length asymmetry. With maximum-likelihood analysis, we find that adding taxa dramatically improves both support for the evolutionary model and accurate assessment of its parameters when compared with increasing the sequence length. Using a method we call "doppelgänger trees," we distinguish the contributions of two sources of improved topological inference: greater knowledge about internal nodes and greater knowledge of site-specific rate parameters. Surprisingly, highly significant support for the correct general model does not lead directly to improved topological inference. Instead, substantial improvement occurs only with accurate assessment of the evolutionary process at individual sites. Although these results are based on a simplified model of the evolutionary process, they indicate that in general, assuming processes are not independent and identically distributed among sites, more extensive sampling of taxonomic biodiversity will greatly improve analytical results in many current sequence data sets with moderate sequence lengths.

Evolution, Molecular↗
PubMed1995

Evolutionary dynamics of enzymes.

This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute substrate specificity. We infer from this depiction of the three classes of enzymes, a general relation between the two functional properties, reaction rate and substrate specificity, namely, enzymes with diffusion-controlled rates have absolute substrate specificity. By appealing to energetic considerations, we furthermore show that enzymes with diffusion-controlled rates (types 2 and 3a) form a small subset of the class of all enzymes. This codification of present-day enzymes derived from an evolutionary model, essentially relates the structural properties of enzymes, as described by their thermodynamic parameters, to their functional properties, as represented by the reaction rate and substrate specificity.

Animals↗
PubMed2000

Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions.

If we are to plan conservation strategies that minimize the loss of evolutionary history through human-caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee & May (1997, Science 278, 692-694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction-management pay-off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human-caused extinctions may therefore be more severe, yet more manageable, than first suggested.

Biological Evolution↗
PubMed2001

Evolutionary disarmament in interspecific competition.

Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

Adaptation, Biological↗
PubMed2004

Fitness and evolutionary stability in game theoretic models of finite populations.

We investigate two methods of measuring fitness in evolutionary games played among members of a finite population. Classical notions of stability account for the action of selection only, and use immediate reproductive gains as a measure of fitness. This classical interpretation of fitness is what we call reproductive fitness (RF), and is found in the early studies of evolutionary stability in finite populations. More recent work has incorporated the influence of random genetic drift by applying fixation probability (FP) as a measure of fitness. When defined in this way, fitness represents a measure of ultimate evolutionary success. Our main result describes an equivalence between candidate evolutionarily stable strategies under both the RF and FP interpretations of fitness. We apply this result to matrix games in which the use of mixed strategies is permitted, and find here an equivalence between the RF and FP conditions for evolutionary stability.

Biological Evolution↗
PubMed2005

Directionality theory: a computational study of an entropic principle in evolutionary processes.

Analytical studies of evolutionary processes based on the demographic parameter entropy-a measure of the uncertainty in the age of the mother of a randomly chosen newborn-show that evolutionary changes in entropy are contingent on environmental constraints and can be characterized in terms of three tenets: (i) a unidirectional increase in entropy for populations subject to bounded growth constraints; (ii) a unidirectional decrease in entropy for large populations subject to unbounded growth constraints; (iii) random, non-directional change in entropy for small populations subject to unbounded growth constraints. This article aims to assess the robustness of these analytical tenets by computer simulation. The results of the computational study are shown to be consistent with the analytical predictions. Computational analysis, together with complementary empirical studies of evolutionary changes in entropy underscore the universality of the entropic principle as a model of the evolutionary process.

Biological Evolution↗
PubMed2006

Evolutionary games on cycles.

Traditional evolutionary game theory explores frequency-dependent selection in well-mixed populations without spatial or stochastic effects. But recently there has been much interest in studying the evolutionary game dynamics in spatial settings, on lattices and other graphs. Here, we present an analytic approach for the stochastic evolutionary game dynamics on the simplest possible graph, the cycle. For three different update rules, called 'birth-death' (BD), 'death-birth' (DB) and 'imitation' (IM), we derive exact conditions for natural selection to favour one strategy over another. As specific examples, we consider a coordination game and Prisoner's Dilemma. In the latter case, selection can favour cooperators over defectors for DB and IM updating. We also study the case where the replacement graph of evolutionary updating remains a cycle, but the interaction graph for playing the game is a complete graph. In this setting, all three update rules lead to identical conditions in the limit of weak selection, where we find the '1/3-law' of well-mixed populations.

Biological Evolution↗