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PubMed2004

Phylogenetic relationships of Plasmopara, Bremia and other genera of downy mildew pathogens with pyriform haustoria based on Bayesian analysis of partial LSU rDNA sequence data.

Bayesian and maximum parsimony phylogenetic analyses of 92 collections of the genera Basidiophora, Bremia, Paraperonospora, Phytophthora and Plasmopara were performed using nuclear large subunit ribosomal DNA sequences containing the D1 and D2 regions. In the Bayesian tree, two main clades were apparent: one clade containing Plasmopara pygmaea s. lat., Pl. sphaerosperma, Basidiophora, Bremia and Paraperonospora, and a clade containing all other Plasmopara species. Plasmopara is shown to be polyphyletic, and Pl. sphaerosperma is transferred to a new genus, Protobremia, for which also the oospore characteristics are described. Within the core Plasmopara clade, all collections originating from the same host family except from Asteraceae and Geraniaceae formed monophyletic clades; however, higher-level phylogenetic relationships lack significant branch support. A sister group relationship of Pl. sphaerosperma with Bremia lactucae is highly supported. Within Bremia lactucae s. l., three distinct clades are evident, which only partly conform to the published host specificity groups. All species of the genera Basidiophora, Bremia, Paraperonospora and Plasmopara included in the present study were investigated for haustorial morphology, and all had ellipsoid to pyriform haustoria, which are regarded as a diagnostic synapomorphy of the whole clade. Aspects of coevolution and cospeciation within the downy mildew pathogens with ellipsoid to pyriform haustoria are briefly discussed.

Bayes Theorem↗

PubMed2004

Male-female conflict and genitalia: failure to confirm predictions in insects and spiders.

Some recent models suggest a new role for evolutionary arms races between males and females in sexual selection. Female resistance to males is proposed to be driven by the direct advantage to the female of avoiding male-imposed reductions in the number of offspring she can produce, rather than by the indirect advantage of selecting among possible sires for her offspring, as in some traditional models of sexual selection by female choice. This article uses the massive but hitherto under-utilized taxonomic literature on genitalic evolution to test, in a two-step process, whether such new models of arms races between males and females have been responsible for rapid divergent evolution of male genitalia. The test revolves around the prediction that 'new arms races' are less likely to occur in species in which females are largely or completely protected from unwanted sexual attentions from males (e.g. species which mate in leks or in male swarms, in which males attract females from a distance, or in which females initiate contact by attracting males from a distance). The multiple possible mechanical functions of male genitalia are summarized, and functions of male genitalic structures in 43 species in 21 families of Diptera are compiled. Functions associated with intromission and insemination (e.g. seizing and positioning the female appropriately, pushing past possible barriers within the female, orienting within the female to achieve sperm transfer), which are unlikely to be involved in new arms races when females are protected, are shown to be common (> 50 % of documented cases). This information is then used to generate the new arms race prediction: differences in genitalic form among congeneric species in which females are protected should be less common than differences among congeneric species in which females are vulnerable to harassment by males. This prediction was tested using a sample of 361 genera of insects and spiders. The prediction clearly failed, even when the data were adjusted to take into account several possible biases. Comparative analyses within particular taxonomic groups also failed to show the predicted trends, as did less extensive data on other non-genitalic male display traits. Arms races, as defined in some recent models, seem to have been less important in male-female coevolution of genitalic structures than has been suggested. By elimination, alternative interpretations, such as traditional female choice, which do not predict associations between female protection from harassment and rapid divergent evolution, are strengthened.

Animals↗

PubMed2005

Complex interactions among mammalian carnivores in Australia, and their implications for wildlife management.

Mammalian carnivore populations are often intensively managed, either because the carnivore in question is endangered, or because it is viewed as a pest and is subjected to control measures, or both. Most management programmes treat carnivore species in isolation. However, there is a large and emerging body of evidence to demonstrate that populations of different carnivores interact with each other in a variety of complex ways. Thus, the removal or introduction of predators to or from a system can often affect other species in ways that are difficult to predict. Wildlife managers must consider such interactions when planning predator control programmes. Integrated predator control will require a greater understanding of the complex relationships between species. In many parts of the world, sympatric species of carnivores have coexisted over an evolutionary time scale so that niche differentiation has occurred, and competition is difficult to observe. Australia has experienced numerous introductions during the past 200 years, including those of the red fox (Vulpes vulpes) and the feral cat (Felis catus). These species now exist in sympatry with native mammalian predators, providing ecologists with the opportunity to study their interactions without the confounding effects of coevolution. Despite an increasing body of observational evidence for complex interactions among native and introduced predators in Australia, few studies have attempted to clarify these relationships experimentally, and the interactions remain largely unacknowledged. A greater understanding of these interactions would provide ecologists and wildlife managers world-wide with the ability to construct robust predictive models of carnivore communities, and to identify their broader effects on ecosystem functioning. We suggest that future research should focus on controlled and replicated predator removal or addition experiments. The dingo (Canis lupus dingo), as a likely keystone species, should be a particular focus of attention.

Animals↗

PubMed2003

Mitochondrial methionyl-tRNAfMet formyltransferase from Saccharomyces cerevisiae: gene disruption and tRNA substrate specificity.

Initiation of protein synthesis in bacteria, mitochondria, and chloroplasts involves a formylated methionyl-tRNA species. Formylation of this tRNA is catalyzed by a methionyl-tRNA(f)(Met) formyltransferase (formylase). Upon inactivation of the gene encoding formylase, the growth rate of Escherichia coli is severely decreased. This behavior underlines the importance of formylation to give tRNA(Met) an initiator identity. Surprisingly, however, recent data [Li, Y., Holmes, W. B., Appling, D. R., and RajBhandary, U. L. (2000) J. Bacteriol. 182, 2886-2892] showed that the respiratory growth of Saccharomyces cerevisiaewas not sensitive to deprivation of the mitochondrial formylase. In the present study, we report conditions of temperature or of growth medium composition in which inactivation of the formylase gene indeed impairs the growth of a S. cerevisiae haploid strain. Therefore, some selective advantage can eventually be associated to the existence of a formylating activity in the fungal mitochondrion under severe growth conditions. Finally, the specificity toward tRNA of S. cerevisiae mitochondrial formylase was studied using E. coli initiator tRNA and mutants derived from it. Like its bacterial counterpart, this formylase recognizes nucleotidic features in the acceptor stem of mitochondrial initiator tRNA. This behavior markedly distinguishes the mitochondrial formylase of yeast from that of animals. Indeed, it was shown that bovine mitochondrial formylase mainly recognizes the side chain of the esterified methionine plus a purine-pyrimidine base pair in the D-stem of tRNA [Takeuchi, N., Vial, L., Panvert, M., Schmitt, E., Watanabe, K., Mechulam, Y., and Blanquet, S. (2001) J. Biol. Chem. 276, 20064-20068]. Distinct tRNA recognition mechanisms adopted by the formylases of prokaryotic, fungal, or mammalian origins are likely to reflect coevolution of these enzymes with their tRNA substrate. Each mechanism appears well suited to an efficient selection of the substrate within the pool of all tRNAs.

Amino Acid Sequence↗

PubMed2004

Identification and activity of a lower eukaryotic serine proteinase inhibitor (serpin) from Cyanea capillata: analysis of a jellyfish serpin, jellypin.

Delineating the phylogenetic relationships among members of a protein family can provide a high degree of insight into the evolution of domain structure and function relationships. To identify an early metazoan member of the high molecular weight serine proteinase inhibitor (serpin) superfamily, we initiated a cDNA library screen of the cnidarian, Cyanea capillata. We identified one serpin cDNA encoding for a full-length serpin, jellypin. Phylogenetic analysis using the deduced amino acid sequence showed that jellypin was most similar to the platyhelminthe Echinococcus multiocularis serpin and the clade P serpins, suggesting that this serpin evolved approximately 1000 million years ago (MYA). Modeling of jellypin showed that it contained all the functional elements of an inhibitory serpin. In vitro biochemical analysis confirmed that jellypin was an inhibitor of the S1 clan SA family of serine proteinases. Analysis of the interactions between the human serine proteinases, chymotrypsin, cathepsin G, and elastase, showed that jellypin inhibited these enzymes in the classical serpin manner, forming a SDS stable enzyme/inhibitor complex. These data suggest that the coevolution of serpin structure and inhibitory function date back to at least early metazoan evolution, approximately 1000 MYA.

Amino Acid Sequence↗

PubMed2005

Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.

Information theory was used to identify nonconserved coevolving positions in multiple sequence alignments from a variety of protein families. Coevolving positions in these alignments fall into two general categories. One set is composed of positions that coevolve with only one or two other positions. These positions often display direct amino acid side-chain interactions with their coevolving partner. The other set comprises positions that coevolve with many others and are frequently located in regions critical for protein function, such as active sites and surfaces involved in intermolecular interactions and recognition. We find that coevolving positions are more likely to change protein function when mutated than are positions showing little coevolution. These results imply that information theory may be applied generally to find coevolving, nonconserved positions that are part of functional sites in uncharacterized protein families. We propose that these coevolving positions compose an important subset of the positions in an alignment, and may be as important to the structure and function of the protein family as are highly conserved positions.

Algorithms↗

PubMed2006

A structure-guided approach to an orthogonal estrogen-receptor-based gene switch activated by ligands suitable for in vivo studies.

A strategy to obtain a fully orthogonal estrogen-receptor-based gene switch responsive to molecules with acceptable pharmacological properties is presented. From a series of tetrahydrofluorenones active on the wild-type estrogen receptor (ER) an inactive analogue is chosen as a new lead compound. Coevolution of receptor mutants and ligands leads to an ER-based gene switch suitable for studies in animal models.

Binding Sites↗

PubMed2003

Community dynamics in a university environment.

Scholars have characterized academic communities of faculty, administration, and students in U.S. universities as "organized anarchies." In contrast, we offer evidence that the community structures of two representative public university systems are notably systematic by applying empirical phase-diagram techniques from the nonlinear dynamics literature to reconstruct low-dimensional deterministic behavior from historic data on the coevolution of faculty, administration, and student populations in each system. Ecological community models, fit with population data for each university, reproduce the essence of this behavior. The models offer novel explanations of how university resources obtained from enrollments and other sources are systematically partitioned among faculty, administration, and student populations interacting in shifting and well-defined community roles. This work offers empirical evidence that ecological principles, typically reserved for characterizing nonhuman interactions in biological systems, can shed light on human interactions in social systems.

Group Processes↗

PubMed2003

The early phases of genetic code origin: conjectures on the evolution of coded catalysis.

A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.

Amino Acids↗

PubMed1994

Parasitism, mutation accumulation and the maintenance of sex.

Two classes of models attempt to explain why obligate partheno-genesis only rarely replaces sexual reproduction in natural populations, in spite of the apparent reproductive advantage that parthenogens gain by producing only female offspring. The mutation-accumulation models suggest that sex is adaptive because it purges the genome of harmful recurrent mutations. The ecological genetic models postulate that sex is adaptive in variable environments, particularly when the relevant variation is generated by coevolutionary interactions with parasites. Both of these models have considerable merit, but would seem to have limitations. The mutation-accumulation models require high rates of mutation; the coevolutionary models require that parasites have severe fitness effects on their hosts. In addition, parasites could select for clonal diversity and thereby erode any advantage that sex gains by producing variable progeny. Here we consider the interaction between mutation accumulation and host-parasite coevolution. The results suggest that even moderate effects by parasites combined with reasonable rates of mutation could render sex evolutionarily stable against repeated invasion by clones.

Biological Evolution↗

PubMed1994

Co-evolution of ligand-receptor pairs.

Specific receptors for lutropin (luteinizing hormone; LH) and follitropin (follicle-stimulating hormone; FSH) mediate the actions of human chorionic gonadotropin (hCG) and FSH5 on the gonads. Here we report that short independent sequences of the beta-subunit enable hCG to distinguish between the receptors for FSH and LH. Residues between the 11th and 12th cysteines restrict FSH receptor binding; residues between the 10th and 11th cysteines and, to a much lesser extent, residues carboxy-terminal to the 12th cysteine also affect LH receptor binding. CF101-109, an hCG analogue containing hFSH beta residues between the 11th and 12th cysteines, had high affinity for both LH and FSH receptors. Modifications to CF101-109 that reduce binding to either LH or FSH receptors yield gonadotropin analogues having differing ratios of LH:FSH activity. Ligand-binding specificity of the LH receptor is determined by residues encoded by parts of exons 2-4 and 7-9 which prevent hFSH binding but have little effect on hCG binding. FSH receptor specificity is controlled primarily by residues encoded by exons 5 and 6 that prevent hCG binding but have little effect on hFSH binding. These determinants can be interchanged to create receptor analogues that bind hCG and hFSH. Our observations support a model in which distinct negative determinants restrict ligand-receptor interaction. This explains coevolution of binding specificity in families of homologous ligands and their receptors. Natural or designed manipulation of these determinants leads to the 'evolution' of new, specific protein-protein interactions.

Amino Acid Sequence↗

PubMed1996

Sexually antagonistic male adaptation triggered by experimental arrest of female evolution.

Each sex is part of the environment of the other sex. This may lead to perpetual coevolution between the sexes, when adaptation by one sex reduces fitness of the other. Indirect evidence comes from experiments with Drosophila melanogaster indicating that seminal fluid reduces the competitive ability of sperm from other males, thereby increasing male fitness. It also reduces a female's propensity to remate and increase her egg-laying rate. In contrast to these benefits to males, seminal fluid has substantial toxic side effects in females, with increasing quantity leading to decreasing female survival. Here I show that when female D. melanogaster are experimentally prevented from coevolving with males, males rapidly adapt to the static female phenotype. This male adaptation leads to a reduction in female survivorship, which is mediated by an increased rate of remating and increased toxicity of seminal fluid.

Adaptation, Physiological↗

PubMed1997

Conspecific sperm precedence in Drosophila.

Traits that influence the interactions between males and females can evolve very rapidly through sexual selection or sexually antagonistic coevolution. Rapid change in the fertilization systems of independent populations can give rise to reproductive incompatibilities between populations, and may contribute to speciation. Here I provide evidence for cryptic reproductive divergence among three sibling species of Drosophila that leads to a form of postmating isolation. When a female mates with both a conspecific and a heterospecific male, the conspecific sperm fertilize the vast majority of the eggs, regardless of the order of the matings. Heterospecific sperm fertilize fewer eggs after these double matings than after single matings. Experiments using spermless males show that the seminal fluid of the conspecific male is largely responsible for this conspecific sperm precedence. Moreover, when two males of the same species mate sequentially with a female from a different species, a highly variable pattern of sperm precedence replaces the second-male sperm precedence that is consistently found within species. These results indicate that females mediate sperm competition, and that second-male sperm precedence is not an automatic consequence of the mechanics of sperm storage.

Animals↗

PubMed2005

The effect of migration on local adaptation in a coevolving host-parasite system.

Antagonistic coevolution between hosts and parasites in spatially structured populations can result in local adaptation of parasites; that is, the greater infectivity of local parasites than foreign parasites on local hosts. Such parasite specialization on local hosts has implications for human health and agriculture. By contrast with classic single-species population-genetic models, theory indicates that parasite migration between subpopulations might increase parasite local adaptation, as long as migration does not completely homogenize populations. To test this hypothesis we developed a system-specific mathematical model and then coevolved replicate populations of the bacterium Pseudomonas fluorescens and a parasitic bacteriophage with parasite only, with host only or with no migration. Here we show that patterns of local adaptation have considerable temporal and spatial variation and that, in the absence of migration, parasites tend to be locally maladapted. However, in accord with our model, parasite migration results in parasite local adaptation, but host migration alone has no significant effect.

Adaptation, Physiological↗

PubMed2005

Evolutionary information for specifying a protein fold.

Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.

Algorithms↗

PubMed2004

Evolutionary innovation of the excretory system in Caenorhabditis elegans.

The evolution of complexity relies on changes that result in new gene functions. Here we show that the unique morphological and functional features of the excretory duct cell in C. elegans result from the gain of expression of a single gene. Our results show that innovation can be achieved by altered expression of a transcription factor without coevolution of all target genes.

Animals↗

PubMed2006

The innate signaling of dangers and the dangers of innate signaling.

The innate immune system of mammals has been forged by coevolution with microbes in response to the double constraint of preserving a symbiotic interaction with commensal flora and eliminating intrusion of those commensals or invasion by pathogens. Thus, a 'sensing' network, accompanied by or lacking inflammatory responses, is controlled by elaborate mechanisms of regulation that maintain balance in the basal state. A growing number of non-Toll-like innate immune receptors is recognized as part of this surveillance network.

Animals↗

PubMed2004

Molecular constraints to interspecies transmission of viral pathogens.

The successful replication of a viral pathogen in a host is a complex process involving many interactions. These interactions develop from the coevolution of pathogen and host and often lead to a species specificity of the virus that can make interspecies transmissions difficult. Nevertheless, viruses do sporadically cross species barriers into other host populations, including humans. In zoonotic infections, many of these interspecies transfer events are dead end, where transmission is confined only to the animal-to-human route but sometimes viruses adapt to enable spread from human to human. A pathogen must overcome many hurdles to replicate successfully in a foreign host. The viral pathogen must enter the host cell, replicate with the assistance of host factors, evade inhibitory host products, exit the first cell and move on to the next, and possibly leave the initial host and transmit to another. Each of these stages may require adaptive changes in the pathogen. Although the factors that influence each stage of the replication and transmission of most agents have not been resolved, the genomics of both hosts and pathogens are now at hand and we have begun to understand some of the molecular changes that enable some viruses to adapt to a new host.

Animals↗