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PubMed1990

Evolutionary relationships among California serogroup viruses (Bunyaviridae) and Aedes mosquitoes (Diptera: Culicidae)

More than 100 published and four unpublished papers recording virus isolations of California (CAL) serogroup viruses from mosquitoes and other arthropods were analyzed, followed by a comparison of a contemporary classification of mosquitoes of the genus Aedes with a contemporary classification of CAL serogroup viruses. Using criteria of five or more total isolations of a given virus from a given species of mosquito, and a minimum infection rate of 1:10,000 or greater (more frequent), Aedes, and to a lesser extent Culiseta, species were found to be the arthropods most frequently involved as vectors. Such a comparison could not explain all virus-vector associations on the basis of coevolution of viruses in Aedes mosquito species, probably because of the crossing over of viruses to other mosquito species through horizontal transmission and because of deficiencies in currently available classifications. Coevolution of host-parasite systems is discussed, as are the inadequacies of contemporary taxonomic treatments of viruses and Aedes mosquitoes. The paper ends with hypothetical reconstructions of virus-mosquito relationships over time and possible routes of dispersal of California serogroup viruses to their present geographical distributions.

Aedes↗
PubMed2006

Emergent criticality from coevolution in random Boolean networks.

The coevolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of a gene regulatory network. We find that a critical state emerges spontaneously resulting from the interplay between topology and dynamics during the evolution. The final evolved state is shown to be independent of initial conditions. The network appears to be driven to a random Boolean network with uniform in-degree of 2 in the large-network limit. However, for biologically realized network sizes, significant finite-size effects are observed including a broad in-degree distribution and an average in-degree connections between 2 and 3. These results may be important for explaining the properties of gene regulatory networks.

Cell Physiological Phenomena↗
PubMed1990

Sexual reproduction as an adaptation to resist parasites (a review).

Darwinian theory has yet to explain adequately the fact of sex. If males provide little or no aid to offspring, a high (up to 2-fold) extra average fitness has to emerge as a property of a sexual parentage if sex is to be stable. The advantage must presumably come from recombination but has been hard to identify. It may well lie in the necessity to recombine defenses to defeat numerous parasites. A model demonstrating this works best for contesting hosts whose defense polymorphisms are constrained to low mutation rates. A review of the literature shows that the predictions of parasite coevolution fit well with the known ecology of sex. Moreover, parasite coevolution is superior to previous models of the evolution of sex by supporting the stability of sex under the following challenging conditions: very low fecundity, realistic patterns of genotype fitness and changing environment, and frequent mutation to parthenogenesis, even while sex pays the full 2-fold cost.

Adaptation, Biological↗
PubMed2003

Ejaculate-female coevolution in Drosophila mojavensis.

Interspecific studies indicate that sperm morphology and other ejaculatory traits diverge more rapidly than other types of character in Drosophila and other taxa. This pattern has largely been attributed to postcopulatory sexual selection involving interaction between the sexes. Such divergence has been suggested to lead rapidly to reproductive isolation among populations and thus to be an 'engine of speciation.' Here, we test two critical predictions of this hypothesis: (i) there is significant variation in reproductive traits among incipient species; and (ii) divergence in interacting sex-specific traits exhibits a coevolutionary pattern among populations within a species, by examining geographical variation in Drosophila mojavensis, a species in the early stages of speciation. Significant among-population variation was identified in sperm length and female sperm-storage organ length, and a strong pattern of correlated evolution between these interacting traits was observed. In addition, crosses among populations revealed coevolution of male and female contributions to egg size. Support for these two important predictions confirms that coevolving internal characters that mediate successful reproduction may play an important part in speciation. The next step is to determine exactly what that role is.

Analysis of Variance↗
PubMed2002

Evolutionary rate in the protein interaction network.

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution. Proteins with more interactors evolve more slowly not because they are more important to the organism, but because a greater proportion of the protein is directly involved in its function. At sites important for interaction between proteins, evolutionary changes may occur largely by coevolution, in which substitutions in one protein result in selection pressure for reciprocal changes in interacting partners. We confirm one predicted outcome of this process-namely, that interacting proteins evolve at similar rates.

Amino Acid Substitution↗
PubMed2006

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

BACKGROUND: The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. RESULTS: We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. CONCLUSION: Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.

Animals↗
PubMed2005

The coevolutionary dynamics of antagonistic interactions mediated by quantitative traits with evolving variances.

Quantitative traits frequently mediate coevolutionary interactions between predator and prey or parasite and host. Previous efforts to understand and predict the coevolutionary dynamics of these interactions have generally assumed that standing genetic variation is fixed or absent altogether. We develop a genetically explicit model of coevolution that bridges the gap between these approaches by allowing genetic variation itself to evolve. Analysis of this model shows that the evolution of genetic variance has important consequences for the dynamics and outcome of coevolution. Of particular importance is our demonstration that coevolutionary cycles can emerge in the absence of stabilizing selection, an outcome not possible in previous models of coevolution mediated by quantitative traits. Whether coevolutionary cycles evolve depends upon the strength of selection, the number of loci, and the rate of mutation in each of the interacting species. Our results also generate novel predictions for the expected sign and magnitude of linkage disequilibria in each species.

Biological Evolution↗
PubMed1987

[Adaptive significance of the limited gene expression of the immune system].

Evolutionary development of immunity multigene systems seems to involve host-parasite molecular coevolution, as evidenced by comparison of metasoans and unicellular organisms in fixation rates of neutral and adaptive point mutations per one pair of corresponding genes. The estimations we attempted revealed that organisms with maximal restriction of Ig-like gene repertoire expression by an individual immune cell are more adaptive in formation of competent antigen-induced immune response, provided that the magnitude of potential repertoire of functional Ig-like receptors exceeds lymphoid cell population size. In contrast, when phage and bacteria populations are in coevolution, there is no need to limit the repertoire of expressive genes encoding bacteria surface receptor proteins which are recognized by a phage adsorption system. Other hypotheses of evolutionary premises and stimulus of immune genes expression limitation (allelic, isotypic etc.) are critically discussed.

Adaptation, Physiological↗
PubMed2004

Local co-adaptation leading to a geographical mosaic of coevolution in a social parasite system.

The geographical mosaic theory of coevolution predicts differences in the advance or trajectory of the coevolutionary process between local communities due to their composition and the strength of ecological selection pressures through competition and resource availability. In this study, we investigate local co-adaptation in different populations of a social parasite. We conducted cross-fostering experiments to test for interpopulational differences in raiding efficiency between various populations of a slave-making ant and the defence abilities of local hosts. Here, we demonstrate that the success of raids strongly depends on the combination of populations of the parasite Harpagoxenus sublaevis and its host Leptothorax acervorum, indicating very localized coevolution. We found no absolute differences between slave-maker populations; the outcome of an encounter depended more on whether the two opponents occur in sympatry or allopatry. Furthermore, this study supports the results of our earlier work, that the unparasitized English L. acervorum population is most aggressive against the parasite.

Adaptation, Biological↗
PubMed1994

Size effects in Kauffman type evolution for rugged fitness landscapes.

Millions of sites are simulated in an NK fitness model of evolution and coevolution. We find a logarithmic size dependence of the number of hill-climbing iterations needed to reach a local fitness optimum (Nash equilibrium). We also check for chaotic behavior and determine the size of the damage clouds or avalanches. Random noise (simulated annealing) is shown to increase appreciably the fitness.

Algorithms↗
PubMed1990

Evolution of the P450 gene superfamily: animal-plant 'warfare', molecular drive and human genetic differences in drug oxidation.

Drug-metabolizing enzymes, such as those encoded by the cytochrome P450 genes, are noted for their high degree of interspecies and intraspecies variability. We believe that much of this diversity is the result of continuous molecularly driven coevolution of plants producing phytoalexins and animals responding with new enzymes to detoxify these chemicals. One consequence of human P450 gene evolution is polymorphism in drug metabolism, leading to marked differences in the response of individuals to the toxic and carcinogenic effects of drugs and other environmental chemicals.

Animals↗
PubMed2003

Ancient tripartite coevolution in the attine ant-microbe symbiosis.

The symbiosis between fungus-growing ants and the fungi they cultivate for food has been shaped by 50 million years of coevolution. Phylogenetic analyses indicate that this long coevolutionary history includes a third symbiont lineage: specialized microfungal parasites of the ants' fungus gardens. At ancient levels, the phylogenies of the three symbionts are perfectly congruent, revealing that the ant-microbe symbiosis is the product of tripartite coevolution between the farming ants, their cultivars, and the garden parasites. At recent phylogenetic levels, coevolution has been punctuated by occasional host-switching by the parasite, thus intensifying continuous coadaptation between symbionts in a tripartite arms race.

Agaricales↗
PubMed1992

Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses.

Papillomaviruses are attractive models for studying the molecular evolution of DNA viruses because of the large number of isolates that exhibit genomic diversity and host species and tissue specificity. To examine their relationship, we selected two amino acid sequences, one of 52 residues within the early gene E1 and the other of 44 residues within the late gene L1, which allowed insertion- and deletion-free alignment of all accessible papillomavirus sequences. We constructed phylogenetic trees from the amino acid and corresponding nucleotide sequences from 28 published and 20 newly determined animal and human papillomavirus (HPV) genomic sequences by using distance matrix, maximum-likelihood, and parsimony methods. The trees agreed in all important topological aspects. One major branch with two clearly separated clusters contained 11 HPV types associated with epidermodysplasia verruciformis. A second major branch had all the papillomaviruses involved in genital neoplasia and, in distant relationship, the cutaneous papillomaviruses HPV type 2a (HPV-2a), HPV-3, and HPV-10 as well as the "butcher's" papillomavirus HPV-7 and two simian papillomaviruses. Four artiodactyl (even-toed hoofed mammal) papillomaviruses, the cottontail rabbit papillomavirus, and avian (chaffinch) papillomavirus type 1 formed a third major branch. Last, four papillomaviruses exhibited little affinity to any of these three branches; these were the cutaneous types HPV-1a, HPV-4, and HPV-41 and B-group bovine papillomavirus type 4. The phylogeny suggests that some branches of papillomavirus evolution are restricted to particular target tissues and that a general process of long-term papillomavirus-host coevolution has occurred. This latter hypothesis is still conjectural because of bias in the current data base for human types and the paucity of animal papillomavirus sequences. The comparison of evolutionary distances for the most closely related types with those of 28 subtypes and variants of HPV-2, HPV-5, HPV-6, HPV-16, and HPV-18 supports the type as a natural taxonomic unit, with subtypes and variants being expressions of minor intratype genomic diversity similar to that found in the natural populations of all biological species. An exception to this seems to be HPV-2c, which has an evolutionary distance from HPV-2a of the intertype magnitude and may eventually have to be regarded as a distinct type. We describe an experimental approach that estimates the taxonomic and phylogenetic positions of newly identified papillomaviruses without viral isolation and complete genomic sequencing.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2006

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

Human hematopoiesis was evaluated using the techniques of controlled stem cell differentiation, two-dimensional gel electrophoresis-based proteomics, and functional genomics. We provide the first report that glia maturation factor gamma (GMFG) is a cytokine-responsive protein in erythropoietin-induced and granulocyte-colony stimulating factor-induced hematopoietic lineage development. Results from global functional genomics analysis indicate that GMFG possesses several other features: hematopoietic tissue-specific gene expression, a promoter concentrated with high-score hematopoiesis-specific transcription factors, and possible molecular coevolution with a rudimentary blood/immune system. On the basis of our findings, we hypothesize that GMFG is a hematopoietic-specific protein that may mediate the pluripotentiality and lineage commitment of human hematopoietic stem cells.

Amino Acid Sequence↗
PubMed2000

The spatial spread of altruism versus the evolutionary response of egoists.

Several recent models have shown that altruism can spread in viscous populations, i.e. in spatially structured populations within which individuals interact only with their immediate neighbours and disperse only over short distances. I first confirm this result with an individual-based model of a viscous population, where an individual can vary its level of investment into a behaviour that is beneficial to its neighbours but costly to itself. Two distinct classes of individuals emerge: egoists with no or very little investment into altruism, and altruists with a high level of investment; intermediate levels of altruism are not maintained. I then extend the model to investigate the consequences of letting interaction and dispersal distances evolve along with altruism. Altruists maintain short distances, while the egoists respond to the spread of altruism by increasing their interaction and dispersal distances. This allows the egoistic individuals to be maintained in the population at a high frequency. Furthermore, the coevolution of investment into altruism and interaction distance can lead to a stable spatial pattern, where stripes of altruists (with local interactions) alternate with stripes of egoists (with far-reaching interactions). Perhaps most importantly, this approach shows that the ease with which altruism spreads in viscous populations is maintained despite countermeasures evolved by egoists.

Altruism↗
PubMedDate not supplied

[Ecological strategy of bacteria: specific nature of the problem].

An attempt is made to sum up the results of the many years of using the conception of ecological strategy in bacterial ecology. Taking into account the specificities of microorganisms and their natural selection and the coevolution of microorganisms within evolving microbial communities, an inference is derived that the ecological strategy of most bacteria is the sum of a number of particular canonical strategies, some of which are common to higher organisms. It is proposed to term these particular strategies ecological tactics. The author considers this review as a basis for discussion.

Adaptation, Biological↗
PubMed1994

Darwinian evolution patterns in food products and beverages.

Although the development and survival of food products are regulated by mechanisms that bear little resemblance to those operating in the living world, their general evolutionary patterns share certain common features. These include punctuated equilibria, convergent evolution, the coevolution, the equivalence of symbiosis, and, rarely, even parasitism. The evolution of food products, like that of living organisms and other systems, is a nonlinear process. Consequently, its path can be affected not only by major events that drastically alter the environment but also by very minor events that may be unnoticeable at the time of their occurrence.

Animals↗
PubMed2006

Phylogenetic methodology for detecting protein interactions.

Detecting protein-protein interactions and assigning proteins to functional complexes are key challenges of modern biology. The rise of genomics has lead to evidence that correlated patterns of presence/absence and/or fusing of proteins in any organism suggest these proteins interact. Unfortunately, methods based on such data work best with divergent genomes, whereas major sequencing efforts in vertebrates, for example, are yielding alignments of the same set of proteins sampled from the same set of taxa (species). Using vertebrate mitochondrial genomes to illustrate a novel method, we associate proteins based on vectors of their evolutionary tree edge (branch or internode) lengths. This approach is based on the expectation that molecular coevolution is greatest between proteins that interact in some way. Mitochondrial DNA-encoded proteins are associated into groups largely consistent with the complexes they come from. This association is apparently not due to the tree structure or mutation processes, leaving coevolution as the best explanation. We show that it is important that the tree used to derive the edge-length vector is estimated accurately in terms of both topology and edge lengths. Although more complex substitution models reduce systematic error, they also inflate stochastic error. This makes the use of less complex substitution models preferable in some circumstances. We describe a method to estimate correlations of pairwise evolutionary distances, which adjusts for non-independent correlations due to shared evolutionary history. Associations of proteins based on their edge-length vectors are visualized and assessed using a variety of hierarchical clustering and multidimensional scaling methods. New formula for estimating the fit of data to model, including the average percent standard deviation of distances on least squares trees, are presented. Use of edge-length vectors is compared and contrasted with correlated distance methods, correlated rates methods, and site-specific evidence of coevolution.

Cluster Analysis↗