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PubMed1998

Phylogenetic analysis of the Chlamydia trachomatis major outer membrane protein and examination of potential pathogenic determinants.

Phylogenetic analysis was utilized to investigate biological relationships (tissue tropism, disease presentation, and epidemiologic success), as evidenced by coevolution, among human strains of Chlamydia trachomatis. Nucleotide sequences of omp1, the gene encoding the major outer membrane protein (MOMP) of C. trachomatis, were determined for 40 strains representing 11 serovars. These data were combined with available omp1 sequences from GenBank for an analysis encompassing a total of 69 strains representing 17 serovars infecting humans. Phylogenetic analysis of the nucleotide and inferred amino acid sequences showed no evolutionary relationships among serovars that corresponded to biological or pathological phenotypes (tissue tropism, disease presentation, and epidemiologic success). In addition, no specific residues that may have evolved to play a role in determining biologically relevant characteristics of chlamydia, such as tissue specificity, disease presentation, and epidemiologic success, were apparent in the MOMP. These results suggest that variation in MOMP may have arisen from a need to be diverse in the presence of immune pressure rather than as a function of pathogenicity. Therefore, the role of MOMP in disease pathogenesis and infection may be passive, and it may not be the major ligand responsible for directing infection of various human cell types.

Bacterial Outer Membrane Proteins↗
PubMed2003

Gradual adaptation of HIV to human host populations: good or bad news?

The continuous evolution and adaptation of HIV to its host has produced extensive global viral diversity. Understanding the kinetics and directions of this continuing adaptation and its impact on viral fitness, immunogenicity and pathogenicity will be crucial to the successful design of effective HIV vaccines. Here we discuss some potential scenarios of viral and host coevolution.

Adaptation, Biological↗
PubMed1998

Molecular coevolution within a Drosophila clock gene.

The period (per) gene in Drosophila melanogaster provides an integral component of biological rhythmicity and encodes a protein that includes a repetitive threonine-glycine (Thr-Gly) tract. Similar repeats are found in the frq and wc2 clock genes of Neurospora crassa and in the mammalian per homologues, but their circadian functions are unknown. In Drosophilids, the length of the Thr-Gly repeat varies widely between species, and sequence comparisons have suggested that the repeat length coevolves with the immediately flanking amino acids. A functional test of the coevolution hypothesis was performed by generating several hybrid per transgenes between Drosophila pseudoobscura and D. melanogaster, whose repetitive regions differ in length by about 150 amino acids. The positions of the chimeric junctions were slightly altered in each transgene. Transformants carrying per constructs in which the repeat of one species was juxtaposed next to the flanking region of the other were almost arrhythmic or showed a striking temperature sensitivity of the circadian period. In contrast, transgenes in which the repeat and flanking regions were conspecific gave wild-type levels of circadian rescue. These results support the coevolutionary interpretation of the interspecific sequence changes in this region of the PER molecule and reveal a functional dimension to this process related to the clock's temperature compensation.

Amino Acid Sequence↗
PubMed2026

Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.

Mitochondrial function depends on tight coordination between mitochondrial and nuclear genomes, which requires long-term coevolution to maintain mitonuclear coadaptation. While mitonuclear incompatibility is typically studied in the context of hybridization, other evolutionary scenarios that may disrupt coadaptation between the two genomes remain less explored. Here, we propose that extreme ecological niche shifts may disrupt mitonuclear coadaptation, which we test in carnivorous Miletinae butterflies with an extreme dietary transition. By generating high-quality genome assemblies, we found that Miletinae exhibit extensive chromosomal rearrangements. Comparative phylogenomic analyses revealed a striking asymmetric mitonuclear evolutionary response: Miletinae exhibit elevated mitochondrial nucleotide substitution rates compared to phytophagous relatives, whereas nuclear rates remain stable. This shift reverses the typical lepidopteran pattern where nuclear rates exceed mitochondrial rates. Interestingly, this mitochondrial acceleration is driven primarily by relaxed purifying selection rather than positive selection. To sustain mitochondrial function, the nuclear genome of Miletinae underwent pervasive, multilayered compensatory evolution. We detected strong signatures of positive selection and accelerated evolution in nuclear genes directly interacting with mitochondrial components across oxidative phosphorylation (OXPHOS) complexes, the mitochondrial translation, and replication and transcription machinery. Furthermore, this nuclear compensatory response extends to systems governing mitochondrial homeostasis, including protein quality control and RNA degradation and stabilization. Our results support a model in which extreme ecological transitions can disrupt ancestral mitonuclear coadaptation and promote the emergence of a new coadapted state through systemic nuclear compensation. This study broadens the conceptual framework of mitonuclear coevolution and highlights its role in facilitating evolutionary persistence after major ecological shifts.

Animals↗
PubMed2005

Rapid creation of a novel protein function by in vitro coevolution.

We have developed a simple and efficient method for creation of novel protein functions in an existing protein scaffold. The in vitro coevolution method involves design of a hypothetical pathway for the target function followed by stepwise directed evolution of the corresponding protein along the pathway. As a test case, this strategy was used to engineer variants of human estrogen receptor alpha ligand-binding domain (hERalphaLBD) with novel corticosterone activity. Two steroids, testosterone and progesterone, that provide a progressive structural bridge between 17beta-estradiol and corticosterone, were chosen to assist the directed evolution of hERalphaLBD. A total of approximately 10(6) variants were screened in four rounds of random mutagenesis, resulting in two hERalphaLBD variants that respond to corticosterone. Creation of this new ligand activity required the presence of four simultaneous mutations. In addition, several required mutations were located outside the ligand binding pocket and yet exerted important action on ligand binding. Our results demonstrate the ability of in vitro coevolution to create novel protein function that is difficult or impossible to achieve by existing protein engineering approaches and also shed light on the natural evolution of nuclear hormone receptors. This in vitro coevolution approach should provide a powerful, broadly applicable tool for engineering biological molecules and systems with novel functions.

Corticosterone↗
PubMed2004

Cytonuclear coevolution: the genomics of cooperation.

Without mitochondria we would be in big trouble, and there would be a global biological energy crisis if it were not for chloroplasts. Fortunately, genomic evolution over the past two billion years has ensured that the functions of these key organelles are with us to stay. Whole-genome analyses have not only proven that mitochondria and chloroplasts are descended from formerly free-living bacteria, but have also shown that it is difficult to define eukaryotes without reference to the fusion and coevolution of host and endosymbiont genomes. Here, we review how the macro- and microevolutionary insights that follow from the genomics of cytonuclear interactions are uniting molecular evolution, structural proteomics, population genetics and problems in aging and disease. Our goals are to clarify the coevolutionary events that have governed nuclear and organelle evolution, and to encourage further critical analyses of these interactions as problems in the study of co-adapted gene complexes.

Journal Article↗
PubMed2004

Conservation and coevolution in the scale-free human gene coexpression network.

The role of natural selection in biology is well appreciated. Recently, however, a critical role for physical principles of network self-organization in biological systems has been revealed. Here, we employ a systems level view of genome-scale sequence and expression data to examine the interplay between these two sources of order, natural selection and physical self-organization, in the evolution of human gene regulation. The topology of a human gene coexpression network, derived from tissue-specific expression profiles, shows scale-free properties that imply evolutionary self-organization via preferential node attachment. Genes with numerous coexpressed partners (the hubs of the coexpression network) evolve more slowly on average than genes with fewer coexpressed partners, and genes that are coexpressed show similar rates of evolution. Thus, the strength of selective constraints on gene sequences is affected by the topology of the gene coexpression network. This connection is strong for the coding regions and 3' untranslated regions (UTRs), but the 5' UTRs appear to evolve under a different regime. Surprisingly, we found no connection between the rate of gene sequence divergence and the extent of gene expression profile divergence between human and mouse. This suggests that distinct modes of natural selection might govern sequence versus expression divergence, and we propose a model, based on rapid, adaptation-driven divergence and convergent evolution of gene expression patterns, for how natural selection could influence gene expression divergence.

3' Untranslated Regions↗
PubMed2002

Consequences of plant-herbivore coevolution on the dynamics and functioning of ecosystems.

The potential consequences of plant-herbivore coevolution for ecosystem functioning are investigated using a simple nutrient-limited ecosystem model in which plant and herbivore traits are subject to adaptive dynamics. Although the ecological model is very simple and always reaches a stable equilibrium in the absence of evolution, coevolution can generate a great diversity of dynamical behaviors. The evolutionary dynamics can lead to a stable equilibrium. If the evolution of plants is fast enough, certain values of the trade-off parameters lead to complex evolutionary cycles bounded by physiological constraints. The dynamical behavior of the model is very different when the dynamics of inorganic nutrient is ignored and plant competition is modeled by a logistic growth function. This emphasizes the importance of including explicit nutrient dynamics in studies of plant-herbivore coevolution.

Adaptation, Biological↗
PubMed1987

Gradients for the evolution of bimatrix games.

The evolutionary dynamics of bimatrix games is studied for rescaled partnership games and zero sum games. The former case leads to gradient systems. The selection equations for sexual and asexual reproduction of genotypes corresponding to mixed strategies are analysed. As examples, the origin of anisogamy and cyclic chases for predator-prey coevolution are studied.

Animals↗
PubMed2003

Host-parasite relationships among bolete infecting Hypomyces species.

Host specificity of the mycoparasite Hypomyces microspermus to the Xerocomus chrysenteron group has been observed, but primarily from European collections. Our objectives were to test host specificity among Hypomyces spp. associated with boletes in California oak-woodlands, investigate population biology of these parasites, and to initiate studies on host-parasite coevolution. Bolete samples were collected from four locations separated by up to 600 km. Hypomyces isolates were cultured and host tissue samples taken for molecular identification. Based on AFLP analysis, four distinct Hypomyces clades were found with little genotypic diversity within each group. ITS-rDNA regions of selected isolates from each group were sequenced and analyzed along with sequences from a previously published phylogeny. Isolates from two AFLP groups clustered with H. microspermus whereas isolates from the other two AFLP groups clustered with H. chrysospermus. ITS-RFLP followed by sequence analysis identified three bolete hosts: (1) X. dryophilus; (2) a Xerocomus species closely related to X. dryophilus with affinities to X. chrysenteron; and (3) a Xerocomus species related to the X. subtomentosus group, which is not closely related to X. dryophilus and X. chrysenteron. H. microspermus infected X. dryophilus and the species with affinities to X. chrysenteron, whereas H. chrysospermus infected the species with affinities to X. chrysenteron and the species related to the X. subtomentosus group. These results support previous observations that H. microspermus is host-specific to the X. chriysenteron group, and that H. chrysospermus is more of a generalist pathogen. We also conclude that host-parasite coevolution studies within this system will not be possible until a phylogeny of North American boletes is in place.

Basidiomycota↗
PubMed2002

Non-parallel coevolution of sender and receiver in the acoustic communication system of treefrogs.

Advertisement calls of closely related species often differ in quantitative features such as the repetition rate of signal units. These differences are important in species recognition. Current models of signal-receiver coevolution predict two possible patterns in the evolution of the mechanism used by receivers to recognize the call: (i) classical sexual selection models (Fisher process, good genes/indirect benefits, direct benefits models) predict that close relatives use qualitatively similar signal recognition mechanisms tuned to different values of a call parameter; and (ii) receiver bias models (hidden preference, pre-existing bias models) predict that if different signal recognition mechanisms are used by sibling species, evidence of an ancestral mechanism will persist in the derived species, and evidence of a pre-existing bias will be detectable in the ancestral species. We describe qualitatively different call recognition mechanisms in sibling species of treefrogs. Whereas Hyla chrysoscelis uses pulse rate to recognize male calls, Hyla versicolor uses absolute measurements of pulse duration and interval duration. We found no evidence of either hidden preferences or pre-existing biases. The results are compared with similar data from katydids (Tettigonia sp.). In both taxa, the data are not adequately explained by current models of signal-receiver coevolution.

Animals↗
PubMed1993

[Theoretical analysis of some features of compensatory substitution in stem regions of transport RNA].

Some families of isoacceptor tRNAs were studies using VOSTORG software package for phylogenetic analysis. While analysing the evolutionary trees in was shown that the fixation of double substitutions AU<-->GC in spiral double-stranded regions passes two stages with intermediate station, such as non-canonical base pairs. In all the families studied double substitutions can be explained not only by passages through slightly deleterious GU pairs. Comparative analysis of B2-like repeats shown the absence of compensatory substitutions in the parts which are homologous to RNA stem regions. The data obtained let us assume that compensatory substitutions in the RNA helical regions represent an expressive example of non-directed adaptive molecular coevolution.

Animals↗
PubMed2000

The origin of autumn colours by coevolution.

We lack an adaptive explanation for a striking phenomenon, that of bright colours displayed in autumn by the leaves of many deciduous trees. The usual explanation is that it is simply a non-adaptive secondary effect of leaf senescence. A game-theoretic model of biological signalling provides an adaptive hypothesis for autumn colours showing that they can be the result of a process of coevolution between insects and trees: if leaf colour acts as a warning indicator of the tree's vigour to autumn parasite insects, trees can gain advantage from the reduction of parasite load and insects can gain advantage from location of the most profitable hosts to lay their eggs. The results of the model are consistent with Zahavi's handicap principle. Possible explanations for the origin of the system and evidence from natural history are discussed.

Animals↗
PubMedDate not supplied

[Parameters adaptation in the populations models].

Ecology-evolutionary models of low dimensions were developed on the basis of competitive selection criteria. Dynamics of variables (number of individuals) and the search of evolutionary-stable values of parameters (biological characterictics of populations) were monitored in the suggested models. If the environmental temperature is changing periodically, the average (a) and width (d) of temperature tolerance range appears to be the important parameters. By model experiments it was established that stable values of temperature (a), favorable for development of highly specialized algae (d is low) were close to minimum and maximum of temperature curve. And for the low specialized algae (d is high) this values were close to the average temperature of environment. In a similar manner, a set of evolutionally stable parameters (a, d) was established for either of the two interacted populations (competitors and "predator-prey"). The hypotheses concerning it's geometric structure and the process of coevolution is formulated.

Adaptation, Physiological↗