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PubMed2004

Application of proteomics in phylogenetic and evolutionary studies.

There are few papers that deal specifically with evolutionary studies and proteomics. However, applying proteomics to these studies promises to open new perspectives apropos the construction of phylogenetic trees and the detection of evolutionary changes. Principles and methods of phylogenetic systematics could be used to compare and evaluate proteomes. This would permit the detection and characterization of specific proteins that have evolutionary value in defining monophyly, paraphyly, and polyphyly.

Algorithms↗
PubMed2004

Evolutionary trace analysis of scorpion toxins specific for K-channels.

Scorpion alpha-K(+) channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin's molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called alpha-KTx 6.6-6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin-coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of alpha-KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel-binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut-off value, which may be involved in the binding of ERG (ether-a-go-go-related gene) channel-specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel-binding sites of the toxins. Because, the side-chain variation in the trace positions is strongly linked with the functional alteration and channel-binding surface transfer of alpha-KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity.

Animals↗
PubMed2005

A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators.

We developed a pharmacophore-based evolutionary approach for virtual screening. This tool, termed the Generic Evolutionary Method for molecular DOCKing (GEMDOCK), combines an evolutionary approach with a new pharmacophore-based scoring function. The former integrates discrete and continuous global search strategies with local search strategies to expedite convergence. The latter, integrating an empirical-based energy function and pharmacological preferences (binding-site pharmacological interactions and ligand preferences), simultaneously serves as the scoring function for both molecular docking and postdocking analyses to improve screening accuracy. We apply pharmacological interaction preferences to select the ligands that form pharmacological interactions with target proteins, and use the ligand preferences to eliminate the ligands that violate the electrostatic or hydrophilic constraints. We assessed the accuracy of our approach using human estrogen receptor (ER) and a ligand database from the comparative studies of Bissantz et al. (J Med Chem 2000;43:4759-4767). Using GEMDOCK, the average goodness-of-hit (GH) score was 0.83 and the average false-positive rate was 0.13% for ER antagonists, and the average GH score was 0.48 and the average false-positive rate was 0.75% for ER agonists. The performance of GEMDOCK was superior to competing methods such as GOLD and DOCK. We found that our pharmacophore-based scoring function indeed was able to reduce the number of false positives; moreover, the resulting pharmacological interactions at the binding site, as well as ligand preferences, were important to the screening accuracy of our experiments. These results suggest that GEMDOCK constitutes a robust tool for virtual database screening.

Binding Sites↗
PubMed2005

Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression.

A multiple linear regression method was applied to predict real values of solvent accessibility from the sequence and evolutionary information. This method allowed us to obtain coefficients of regression and correlation between the occurrence of an amino-acid residue at a specific target and its sequence neighbor positions on the one hand, and the solvent accessibility of that residue on the other. Our linear regression model based on sequence information and evolutionary models was found to predict residue accessibility with 18.9% and 16.2% mean absolute error respectively, which is better than or comparable to the best available methods. A correlation matrix for several neighbor positions to examine the role of evolutionary information at these positions has been developed and analyzed. As expected, the effective frequency of hydrophobic residues at target positions shows a strong negative correlation with solvent accessibility, whereas the reverse is true for charged and polar residues. The correlation of solvent accessibility with effective frequencies at neighboring positions falls abruptly with distance from target residues. Longer protein chains have been found to be more accurately predicted than their smaller counterparts.

Amino Acids↗
PubMed2005

Evolutionary plasticity of protein families: coupling between sequence and structure variation.

In this work we examine how protein structural changes are coupled with sequence variation in the course of evolution of a family of homologs. The sequence-structure correlation analysis performed on 81 homologous protein families shows that the majority of them exhibit statistically significant linear correlation between the measures of sequence and structural similarity. We observed, however, that there are cases where structural variability cannot be mainly explained by sequence variation, such as protein families with a number of disulfide bonds. To understand whether structures from different families and/or folds evolve in the same manner, we compared the degrees of structural change per unit of sequence change ("the evolutionary plasticity of structure") between those families with a significant linear correlation. Using rigorous statistical procedures we find that, with a few exceptions, evolutionary plasticity does not show a statistically significant difference between protein families. Similar sequence-structure analysis performed for protein loop regions shows that evolutionary plasticity of loop regions is greater than for the protein core.

Amino Acids↗
PubMed2006

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

Proteins that interact with DNA are involved in a number of fundamental biological activities such as DNA replication, transcription, and repair. A reliable identification of DNA-binding sites in DNA-binding proteins is important for functional annotation, site-directed mutagenesis, and modeling protein-DNA interactions. We apply Support Vector Machine (SVM), a supervised pattern recognition method, to predict DNA-binding sites in DNA-binding proteins using the following features: amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. We use a rigorous statistical approach to study the performance of predictors that utilize different combinations of features and how this performance is affected by structural and sequence properties of proteins. Our results indicate that an SVM predictor based on a properly scaled profile of evolutionary conservation in the form of a position specific scoring matrix (PSSM) significantly outperforms a PSSM-based neural network predictor. The highest accuracy is achieved by SVM predictor that combines the profile of evolutionary conservation with low-resolution structural information. Our results also show that knowledge-based predictors of DNA-binding sites perform significantly better on proteins from mainly-alpha structural class and that the performance of these predictors is significantly correlated with certain structural and sequence properties of proteins. These observations suggest that it may be possible to assign a reliability index to the overall accuracy of the prediction of DNA-binding sites in any given protein using its sequence and structural properties. A web-server implementation of the predictors is freely available online at http://lcg.rit.albany.edu/dp-bind/.

Amino Acid Sequence↗
PubMed2000

Evolutionary ecology of human life history.

The human life history is characterized by several unusual features, including large babies, late puberty and menopause, and the fact that there is a strong cultural influence on reproductive decisions throughout life. In this review I examine human life history from an evolutionary ecological perspective. I first review the evidence for life history trade-offs between fertility and mortality in humans. Patterns of growth, fertility and mortality across the life span are then discussed and illustrated with data from a traditional Gambian population. After outlining the stages of the human life course, I discuss two phenomena of particular interest in evolutionary anthropology, both of which are apparently unique to humans and neither yet fully understood. First, I discuss the evolution of menopause, the curtailing of female reproduction long before death. The evidence that this evolved because investment in existing children's future reproductive success is more important than continuing child bearing into old age is reviewed, along with data relating to the biological constraints that may be operating. Second, I discuss the demographic transition. Declining fertility at a time of increasingly abundant resources represents a serious challenge to an evolutionary view of human life history and behaviour, and is thus examined in detail. Parental investment in children in competition with each other may be key to understanding both of these unusual human phenomena. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed2001

Necessary and sufficient conditions for evolutionary suicide.

Evolutionary suicide is an evolutionary process where a viable population adapts in such a way that it can no longer persist. It has already been found that a discontinuous transition to extinction is a necessary condition for suicide. Here we present necessary and sufficient conditions, concerning the bifurcation point, for suicide to occur. Evolutionary suicide has been found in structured metapopulation models. Here we show that suicide can occur also in unstructured population models. Moreover, a structured model does not guarantee the possibility of suicide: we show that suicide cannot occur in age-structured population models of the Gurtin-MacCamy type. The point is that the mutant's fitness must explicitly depend not only on the environmental interaction variable, but also on the resident strategy.

Adaptation, Biological↗
PubMed2002

Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28.

A large portion of human Xq28 has been completely characterized but the interval between G6PD and Xqter has remained poorly understood. Because of a lack of stable, high-density clone coverage in this region, we constructed a 1.6-Mb bacterial and P1 artificial chromosome (BAC and PAC, respectively) contig to expedite mapping, structural and evolutionary analysis, and sequencing. The contig helped to reposition previously mismapped genes and to characterize the XAP135 pseudogene near the int22h-2 repeat. BAC clones containing the distal int22h repeats also demonstrated spontaneous rearrangements and sparse coverage, which suggested that they were unstable. Because the int22h repeats are involved in genetic diseases, we examined them in great apes to see if they have always been unstable. Differences in copy number among the apes, due to duplications and deletions, indicated that they have been unstable throughout their evolution. Taking another approach toward understanding the genomic nature of distal Xq28, we examined the homologous mouse region and found an evolutionary junction near the distal int22h loci that separated the human distal Xq28 region into two segments on the mouse X chromosome. Finally, haplotype analysis showed that a segment within Xq28 has resisted excessive interchromosomal exchange through great ape evolution, potentially accounting for the linkage disequilibrium recently reported in this region. Collectively, these data highlight some interesting features of the genomic sequence in Xq28 and will be useful for positional cloning efforts, mouse mutagenesis studies, and further evolutionary analyses.

Animals↗
PubMed1996

Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.

Previously proposed methods for protein secondary structure prediction from multiple sequence alignments do not efficiently extract the evolutionary information that these alignments contain. The predictions of these methods are less accurate than they could be, because of their failure to consider explicitly the phylogenetic tree that relates aligned protein sequences. As an alternative, we present a hidden Markov model approach to secondary structure prediction that more fully uses the evolutionary information contained in protein sequence alignments. A representative example is presented, and three experiments are performed that illustrate how the appropriate representation of evolutionary relatedness can improve inferences. We explain why similar improvement can be expected in other secondary structure prediction methods and indeed any comparative sequence analysis method.

Amino Acid Sequence↗
PubMed1993

Multiple coding and the evolutionary properties of RNA secondary structure.

This article evaluates evolutionary properties of the transition from RNA primary sequence to RNA secondary structure. It focuses on the restrictions that the conservation of a protein code in an RNA sequence puts on its potential to evolve towards a specific secondary structure. Restricting the mutations to those that do not affect the coding for a protein restricts both the accessibility and the connectivity of the sequence space. The accessibility is restricted because only certain point mutations are allowed. The connectivity is restricted because no insertions and deletions are allowed. Simulating an evolutionary search process for a specific secondary structure shows that (i) the reduction of allowable point mutations allows for adaptation to some large-scale topology, but strongly reduces the possibility of small-scale adaptations, (ii) the abolition of insertions and deletions has very little effect on the results of the search process. During the evolutionary search process for a secondary structure with a specific topology and a high frequency of base-pairing the quasispecies moves into a subspace in which the similarity between secondary structures of neighboring sequences is relatively high. Increased similarity between second structures of neighboring sequences is also found in the Rev responsive element (RRE) in the lentiviruses Caprine arthritis-encephalitis virus and Visna virus. In these viruses a biased nucleotide frequency in the RRE region suggests that selection for the RRE RNA secondary structure affects the amino acid sequence of the env gene. Our results show a variation in the ruggedness of fitness landscapes which are based on a high degree of epistatic interactions. Fitness landscapes play an essential role, not only in biotic evolution, but also in all kinds of optimization processes (Hill Climbing, Simulated Annealing, Genetic Algorithms, etc). Variation in their ruggedness should therefore be taken into account in the analysis of these processes.

Amino Acid Sequence↗
PubMed1994

Codon usage and evolutionary rates of proteins.

The 61 codons and the three terminators were counted in the coding sequences of 31 families of proteins of higher vertebrates. The protein families were ordered according to their evolutionary rate. In each family, the ratio between the Observed and Expected frequency of each codon was obtained (O/E ratio). A strong and significant positive correlation was observed between the O/E ratio of the eight codons AAC, TAT, ATA, GAA, ACA, AAT, ATG and CGA and the evolutionary rate of the protein. A negative and significant correlation was observed for codons AAG and GAG. It was advanced that the functional constraints of proteins can influence the usage of codons, particularly for those trimers which are components of signal sequences. It was also observed that the O/E ratios of the terminators are negatively correlated with the evolutionary rate of the protein they terminate, and the correlation is significant for TAA and TGA, which in vertebrates might be older than TAG.

Animals↗
PubMed1995

Evolutionary predictions from invariant physical measures of dynamic processes.

The invariant physical measure of a dynamic process comprises the information necessary to compute statistical quantities of the system. It allows us to replace time averages over the system's trajectory by integrals over state-space. In particular, it allows us to compute the long-term growth rate of a fluctuating population and hence to make evolutionary predictions. This is explained here using a one-dimensional difference equation. The invariant physical measure reflects three types of selection in this model: K-selection when the resident has a stable equilibrium; r-selection when the resident exhibits complex dynamics; and c-selection, i.e. selection for lower complexity when the resident undergoes large fluctuations. For all three evolutionary scenarios the interaction of the physical measure with the higher moments of the distribution of offspring numbers is crucial. It is also shown how stochastic noise can affect the invariant physical measure and the evolutionary predictions made from it.

Animals↗
PubMed1995

Evolutionary cycling in predator-prey interactions: population dynamics and the red queen.

This paper describes the coevolution of phenotypes in a community comprising a population of predators and of prey. It is shown that evolutionary cycling is a likely outcome of the process. The dynamical systems on which this description is based are constructed from microscopic stochastic birth and death events, together with a process of random mutation. Births and deaths are caused in part by phenotype-dependent interactions between predator and prey individuals and therefore generate natural selection. Three outcomes of evolution are demonstrated. A community may evolve to a state at which the predator becomes extinct, or to one at which the species coexist with constant phenotypic values, or the species may coexist with cyclic changes in phenotypic values. The last outcome corresponds to a Red Queen dynamic, in which the selection pressures arising from the predator-prey interaction cause the species to evolve without ever reaching an equilibrium phenotypic state. The Red Queen dynamic requires an intermediate harvesting efficiency of the prey by the predator and sufficiently high evolutionary rate constant of the prey, and is robust when the model is made stochastic and phenotypically polymorphic. A cyclic outcome lies outside the contemporary focus on evolutionary equilibria, and argues for an extension to a dynamical framework for describing the asymptotic states of evolution.

Animals↗
PubMed1997

The evolutionary dynamics of selfish replicators: a two-level selection model.

The aim of the present paper is to study the evolutionary dynamics of selfish replicators in a constant genetic background. Selfish replicators are viewed as alleles at a single locus, having a pleiotropic effect. Infinitely many alleles are possible; they act on individual fitness and have various levels of ability to distort segregation. This results in a two-level process of selection, including inter-individual selection (effect on individual fitness) and intra-individual selection (ability to distort segregation). The model takes other parameters into account, such as dominance, inbreeding and inbreeding depression. The system can have two different behaviours. (1) In some cases, evolutionary cycles are possible. The cycles correspond to an alternation of phases with predominant inter-individual selection, corresponding to major-effect mutations, and phases with predominant intra-individual selection, corresponding to small-effect mutations. (2) For other values of the parameters, a synthetic fitness can be defined: this absolute allelic fitness is estimated as a function of one's fitness due to both inter-individual and intra-individual selection. During the course of evolution, the synthetic fitness increases. The optimisation of a synthetic fitness is the most general process. The optimised value is essentially homologous to the value optimised for resource allocation to male and female function in hermaphrodites (female function being homologous to the effect on individual fitness, and male function being homologous to distortion ability). The relative importance of both behaviours is discussed. It is argued that repeated sequences causing some human degenerative hereditary diseases may follow a two-step evolutionary process: a progressive increase in number of sequences accompanied by a decrease of the individual fitness would be followed by massive elimination of such sequences. But in general the optimisation of the synthetic fitness seems to be more likely.

Animals↗
PubMed2002

Thermodynamics and kinetics of protein folding: an evolutionary perspective.

This article appeals to an evolutionary model which postulates that primordial proteins were described by small polypeptide chains which (i) lack disulfide bridges, and (ii) display slow folding rates with multi-state kinetics, to determine relations between structural properties of proteins and their folding kinetics. We parameterize the energy landscape of proteins in terms of thermodynamic activation variables. The model studies evolutionary changes in these thermodynamic parameters, and we invoke relations between these activation variables and structural properties of the protein to predict the following correspondence between protein structure and folding kinetics. 1. Proteins with inter- and intra-chain disulfide bridges: large variability in both folding rates and stability of intermediates, multi-state kinetics. 2. Proteins which lack inter and intra-chain disulfide bridges. 2.1 Single-domain chains: fast folding rates; unstable intermediates; two-state kinetics. 2.2 Multi-domain monomers: intermediate rates; metastable intermediates; multi-state kinetics. 2.3 Multi-domain oligomers: slow rates; metastable intermediates; multi-state kinetics. The evolutionary model thus provides a kinetic characterization of one important subfamily of proteins which we describe by the following properties: Folding dynamics of single-domain proteins which lack disulfide bridges are described by two-state kinetics. Folding rate of this class of proteins is positively correlated with the thermodynamic stability of the folded state.

Disulfides↗
PubMed1995

Ancestry of an isolated subspecies of salamander, Ambystoma tigrinum stebbinsi Lowe: the evolutionary significance of hybridization.

Most phylogenetic systematists assume speciation results in dichotomously branching phylogenies. Hybridization that gives rise to a new lineage can produce character homoplasty that might obscure a species' true history. We report the results of a restriction-enzyme analysis of mitochondrial DNA (mtDNA) variation in three tiger salamander subspecies (Ambystoma trigrinum mavortium, Ambystoma tigrinum nebulosum, and Ambystoma trigrinum stebbinsi) and compare the results to studies of morphological and allozymic variation in these taxa. Allozymically, A. t. mavortium and A. t. nebulosum share most of their genomes (although each has several unique alleles), yet color pattern and mtDNA haplotypes are distinct. Color pattern and allozyme data suggest that A. t. stebbinsi shares a common ancestor with A. t. mavortium, while the A. t. stebbinsi mtDNA haplotype is derived from an A. t. nebulosum haplotype. Thus, our data suggest that A. t. stebbinsi originated through hybridization between A. t. mavortium and A. t. nebulosum. That hybridization can produce recognizably distinct evolutionary entities has long been recognized for plants, but the evolutionary significance of hybridization in animals should be examined more closely. Conservation agencies must recognize that hybrids and hybrid taxa are not necessarily evolutionary "mistakes," and they might have significant importance in the production of natural biodiversity.

Animals↗
PubMed1997

Evolutionary dynamics of cucumber mosaic virus satellite RNA during natural epidemics in Italy.

The evolutionary dynamics of 22 variants of cucumber mosaic virus satellite RNA (CMV satRNA) isolated in Italy during virus epidemics from 1988 to 1993 were investigated on the basis of their primary structure and biological properties. Most of the variants were amplified from total nucleic acid preparations extracted from field-infected plants, thus representing wild isolates of CMV satRNA. Eleven variants were associated with subgroup II CMV strains, 10 with subgroup I and 1 with a mixed infection by both strains. When inoculated onto tomato seedlings, the variants induced the phenotype (necrogenic or ameliorative) predicted by their nucleotide sequence. Phylogenetic relationships between the satRNA variants were determined using the stationary Markov model, a stochastic model for evolution. For each satRNA, the Markov analysis gave a good correlation between position in the phylogenetic tree and biological properties. The variants with ameliorative and necrogenic phenotypes in tomato followed two different evolutionary dynamics in nature. Tfn-satRNA, a 390-nt-long molecule, followed a third type of evolutionary dynamic far apart from that of the shorter satRNA molecules (i.e., those in the 334- to 340-nt-length class). Average values of the mean constant rate of nucleotide substitutions/site (Ksubs/site) indicated that in nature the variants tend to keep their heterogeneity unchanged from one epidemic episode to the other, even if the outbreaks occur in places very far from each other. This seems to be in agreement with the proposed maintenance of a functional molecular structure as a constraint to CMV satRNA evolution.

Computer Simulation↗