Protein-protein interactions more conserved within species than across species

Experimental high-throughput studies of protein-protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another about 55,000 pairs of interacting proteins have been identified by more careful, detailed biochemical experiments. Most interactions are experimentally observed in prokaryotes and simple eukaryotes; very few interactions are observed in higher eukaryotes such as mammals. It is commonly assumed that pathways in mammals can be inferred through homology to model organisms, e.g. the experimental observation that two yeast proteins interact is transferred to infer that the two corresponding proteins in human also interact. Two pairs for which the interaction is conserved are often described as interologs. The goal of this investigation was a large-scale comprehensive analysis of such inferences, i.e. of the evolutionary conservation of interologs. Here, we introduced a novel score for measuring the overlap between protein-protein interaction data sets. This measure appeared to reflect the overall quality of the data and was the basis for our two surprising results from our large-scale analysis. Firstly, homology-based inferences of physical protein-protein interactions appeared far less successful than expected. In fact, such inferences were accurate only for extremely high levels of sequence similarity. Secondly, and most surprisingly, the identification of interacting partners through sequence similarity was significantly more reliable for protein pairs within the same organism than for pairs between species. Our analysis underlined that the discrepancies between different datasets are large, even when using the same type of experiment on the same organism. This reality considerably constrains the power of homology-based transfer of interactions. In particular, the experimental probing of interactions in distant model organisms has to be undertaken with some caution. More comprehensive images of protein-protein networks will require the combination of many high-throughput methods, including in silico inferences and predictions. http://www.rostlab.org/results/2006/ppi_homology/     

The distribution of positive and negative species interactions across environmental gradients on a dual-lattice model

There has been considerable recent interest in understanding the role of positive inter-specific interactions within ecology, and significant progress has been made both empirically and theoretically. Similarly, considerable progress has been made in improving our understanding of the mechanisms that limit species' ranges. In this contribution, we seek to understand the setting of species' borders when some species within the assemblage exhibit positive inter-specific interactions. We use a spatially explicit dual-lattice simulation model to explore the distribution of different interactions across environmental gradients. We first simulate community dynamics when there is either a gradient in reproductive rate or in mortality. We then consider what happens when gradients in reproduction and mortality run in parallel or perpendicular to one another. If the stress gradient impacts on reproductive potential, positive interactions are found where there is high abiotic stress. In this instance, the mutualists are able to tolerate an environment that the cheaters cannot. However, when the stress gradient influences mortality, we find that the mutualists occur as a stripe surrounded by cheaters both towards the better and the harsher ends of the gradient. Previous theory and most empirical evidence tend to indicate that net positive interactions are likely to occur in environments characterized by high abiotic stress. However, evidence from some stress gradients suggests that the distribution of positive and negative interactions can be more complex, with the most stressful environments being occupied by individuals engaging in negative rather than positive interactions. Our results provide a potential theoretical explanation for these recent field observation, and highlight the need for further theoretical and empirical work to better our understanding of how positive and negative interactions act to determine the limits to species' ranges.     

The evolution of species interactions across natural landscapes

Given the potential for rapid and microgeographical adaptation, ecologists increasingly are exploring evolutionary explanations for community patterns. Biotic selection can generate local adaptations that alter species interactions. Although some gene flow might be necessary to fuel local adaptation, higher gene flow can homogenise traits across regions and generate local maladaptation. Herein, I estimate the contributions of local biotic selection, gene flow and spatially autocorrelated biotic selection to among-population divergence in traits involved in species interactions across 75 studies. Local biotic selection explained 6.9% of inter-population trait divergence, an indirect estimate of restricted gene flow explained 0.1%, and spatially autocorrelated selection explained 9.3%. Together, biotic selection explained 16% of the variance in population trait means. Most biotic selection regimes were spatially autocorrelated. Hence, most populations receive gene flow from populations facing similar selection, which could allow for local adaptation despite moderate gene flow. Gene flow constrained adaptation in studies conducted at finer spatial scales as expected, but this effect was often confounded with spatially autocorrelated selection. Results indicate that traits involved in species interactions might often evolve across landscapes, especially when biotic selection is spatially autocorrelated. The frequent evolution of species interactions suggests that evolutionary processes might often influence community ecology.     

A quantitative genetic model for analyzing species differences in outcrossing species

A genetic model based on a two-level intra- and interspecific mating design is proposed to estimate the genetic architecture of species differences and heterosis for outcrossing species. The underlying genetic analyses make use of classical quantitative genetic theories and recent results from molecular genetic studies. Gene effects across different quantitative trait loci (QTL) can be approximated by a geometric series. Under natural selection, gene effects are often associated with allele frequencies in a particular way, which can be approximated by the gamma distribution. By incorporating these approximations into family structural analyses in the mating design, we are able to estimate a number of genetic parameters that contribute to quantitative genetic variation based on a nonlinear optimization approach. These parameters include the number of QTL, their gene effects, and their allele frequencies in the parental populations. We perform simulation studies and illustrate an example to demonstrate the statistical property and procedure of the method.     

A multiplicative-epistatic model for analyzing interspecific differences in outcrossing species

Epistasis may play an important role in evolution and speciation. Under multiplicative interactions between different loci, an analytical model is proposed to estimate genetic parameters at the individual locus level that contribute to interspecific differences in outcrossing species. The multiplicative epistasis model, inferred from a number of animal and plant experiments, suggests that genotypes at a pair of loci have genotypic values equal to the product of genotypic values at the two different loci. By considering the genetic property of outcrossing species (i.e., high polymorphisms) in the multilevel family structure analysis for an intra- and interspecific factorial mating design, a method is developed to provide estimates for allele frequencies and additive and dominant effects at individual loci in each of the two parental populations, the genotypic values of newly formed heterozygotes through species combination each with one allele from a parental population and the second from the other parental population, and the numbers of genetic factors that lead to species differentiation. Use of clones offers a tremendous power to test the adequacy of the model. However, the utilization of the model with species that cannot be cloned is also discussed. An example with interspecific hybrids of two forest tree species is used to demonstrate the model.     

The interplay of positive and negative species interactions across an environmental gradient: insights from an individual-based simulation model

Positive interspecific interactions are commonplace, and in recent years ecologists have begun to realize how important they can be in determining community and ecosystem dynamics. It has been predicted that net positive interactions are likely to occur in environments characterized by high abiotic stress. Although empirical field studies have started to support these predictions, little theoretical work has been carried out on the dynamic nature of these effects and their consequences for community structure. We use a simple patch-occupancy model to simulate the dynamics of a pair of species living on an environmental gradient. Each of the species can exist as either a mutualist or a cheater. The results confirm the prediction: a band of mutualists tends to occur in environmental conditions beyond the limits of the cheaters. The region between mutualists and cheaters is interesting: population density here is low. Mutualists periodically occupy this area, but are displaced by cheaters, who themselves go extinct in the absence of the mutualists. Furthermore, the existence of mutualists extends the area occupied by the cheaters, essentially increasing their realized niche. Our approach has considerable potential for improving our understanding of the balance between positive and negative interspecific interactions and for predicting the probable impacts of habitat loss and climate change on communities dominated by positive interspecific interactions.     

Evolution of abdominal pigmentation differences across species in the Drosophila dunni subgroup

The Drosophila dunni subgroup displays a nearly perfect latitudinal cline in abdominal pigmentation that likely resulted from selective forces acting in the habitat of each species during speciation. Here we characterize the nature of this clinal variation by developing a quantitative measure to assess variation in abdominal pigmentation within and between the D. dunni subgroup species. Using discriminant analysis, we confirm the existence of a cline and find that our quantitative measure of pigmentation distinguishes each of the species with singular efficacy. We then combine our quantitative phenotypic analysis of pigmentation with the phylogeny of the D. dunni subgroup species and map the species relationships into the three-dimensional morphological space defined by our pigmentation measures. In this manner, we can visualize how the species have traversed the morphological pigmentation space during the course of speciation. Our analysis reveals that natural selection has caused overall intensity of pigmentation among the northernmost species of the cline to converge. Along with this convergence in phenotype has been a relaxation in expression of sexual dimorphism in these species, indicating a possible shift in the relative intensity of natural and sexual selection. Our analysis indicates an accelerated rate of change in pigmentation for the darkest species in addition to this species evolving a novel abdominal pigmentation trait.     

Albumin-eicosanoid interactions. A model system to determine their attributes and inhibition

A model system was developed to (a) reflect the chemical attributes of the microenvironment involved in albumin-eicosanoid interactions and (b) determine the effects of other ligands on these interactions. Albumin-dependent modulation of prostaglandin stability was chosen as the basis for this system. 15-Ketoprostaglandin E2 (PGE2) was evaluated as a model ligand because under special conditions it decomposes with formation of a visible chromophore. Human serum albumin, in a concentration-dependent fashion, catalyzed the dehydration of 15-keto-PGE2 with the concurrent generation of this chromophore (lambda max = 505 nm, epsilon = 35,000). Since chromophore production from 15-keto-PGE2 in albumin-free solution occurs only at pH greater than 10, the results suggest that albumin-eicosanoid interactions involve a microenvironment with alkaline attributes. The effect of other ligands on albumin-15-keto-prostaglandin E2 interactions was determined by monitoring their ability to inhibit the spectral component of these interactions. Inhibition correlated with an affinity for specific binding sites on albumin. At mole ratios of ligand/albumin below 1, only phenylbutazone, its analogs, and warfarin inhibited chromophore development. Other ligands including fatty acids, steroids, tryptophan, and drugs with an affinity for other binding sites were ineffective inhibitors.     

How important are species richness,species evenness and interspecific differences to productivity? A mathematical model

We present a theoretical model to quantify the influence of diversity on productivity and nutrient acquisition in plant communities during exponential growth. The model fractionates diversity into three components, namely species richness ( S ), species evenness ( E ) and the degree of difference between species ( D ). The influence of each of these components is assessed individually: S is varied by changing the number of species, E by changing their population size, and D by changing the range of species traits critical to productivity (specific nutrient uptake rate, Σ _r , or nutrient use efficiency, NUE ). D was quantified as the coefficient of variation of Σ _r or NUE . All three components of diversity enhance the biomass and nutrient stocks in the community, but the response patterns are different. Species richness has a saturating influence, whereas effects of E and D are linear and exponential, respectively. In all cases the non-linear dependence of productivity and nutrient acquisition on Σ _r and NUE during exponential growth was the single mechanism underlying these effects. This causes the presence of plants with extreme traits to promote productivity, and S , E and D all affect the abundance and/or intensity of these extremes. The model offers a framework to explain differences between experimental observations, and suggests a concept of diversity where S and E are structural components and D a qualitative or functional component, which modulates the influence of the two others. We propose to explicitly recognise D as an integral constituent of plant diversity in future studies.     

Ulysses - an application for the projection of molecular interactions across species

We developed Ulysses as a user-oriented system that uses a process called Interolog Analysis for the parallel analysis and display of protein interactions detected in various species. Ulysses was designed to perform such Interolog Analysis by the projection of model organism interaction data onto homologous human proteins, and thus serves as an accelerator for the analysis of uncharacterized human proteins. The relevance of projections was assessed and validated against published reference collections. All source code is freely available, and the Ulysses system can be accessed via a web interface .     

遮阴对两种泥炭藓植物生长及相互作用的影响

以大泥炭藓和喙叶泥炭藓为材料,研究遮阴对其生长及植物相互作用的影响.结果表明:在单种群中,遮阴处理明显促进了大泥炭藓的高生长,但对喙叶泥炭藓的生长以及大泥炭藓生物量和分枝数未产生影响;在混合群中,喙叶泥炭藓抑制了大泥炭藓生物量和分枝数的增长,而大泥炭藓对喙叶泥炭藓的生长无影响.随遮阴胁迫的增加,邻体对喙叶泥炭藓竞争加剧,当胁迫进一步增强,邻体效应有转变为正相互作用的趋势,但邻体对大泥炭藓的效应始终为竞争,未随胁迫增加而变化.     

Spatial variability of hosts,parasitoids and their interactions across a homogeneous landscape

Species assemblages and their interactions vary through space, generating diversity patterns at different spatial scales. Here, we study the local‐scale spatial variation of a cavity‐nesting bee and wasp community (hosts), their nest associates (parasitoids), and the resulting antagonistic network over a continuous and homogeneous habitat. To obtain bee/wasp nests, we placed trap‐nests at 25 sites over a 32 km² area. We obtained 1,541 nests (4,954 cells) belonging to 40 host species and containing 27 parasitoid species. The most abundant host species tended to have higher parasitism rate. Community composition dissimilarity was relatively high for both hosts and parasitoids, and the main component of this variability was species turnover, with a very minor contribution of ordered species loss (nestedness). That is, local species richness tended to be similar across the study area and community composition tended to differ between sites. Interestingly, the spatial matching between host and parasitoid composition was low. Host β‐diversity was weakly (positively) but significantly related to geographic distance. On the other hand, parasitoid and host‐parasitoid interaction β‐diversities were not significantly related to geographic distance. Interaction β‐diversity was even higher than host and parasitoid β‐diversity, and mostly due to species turnover. Interaction rewiring between plots and between local webs and the regional metaweb was very low. In sum, species composition was rather idiosyncratic to each site causing a relevant mismatch between hosts and parasitoid composition. However, pairs of host and parasitoid species tended to interact similarly wherever they co‐occurred. Our results additionally show that interaction β‐diversity is better explained by parasitoid than by host β‐diversity. We discuss the importance of identifying the sources of variation to understand the drivers of the observed heterogeneity.     

Distinct longevity mechanisms across and within species and their association with aging

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A new herbarium-based method for reconstructing the phenology of plant species across large areas

Phenological data have recently emerged as particularly effective tools for studying the impact of climate change on plants, but long phenological records are rare. The lack of phenological observations can nevertheless be filled by herbarium specimens as long as some correction procedures are applied to take into account the different climatic conditions associated with sampling locations. In this study, we propose a new herbarium-based method for reconstructing the flowering dates of plant species that have been collected across large areas. Coltsfoot (Tussilago farfara L.) specimens from southern Quebec were used to test the method. Flowering dates for coltsfoot herbarium specimens were adjusted according to the date of disappearance of snow cover in the region where they were collected and compared using a reference point (the date of earliest snowmelt). In southern Quebec, coltsfoot blooms earlier at present (15-31 d) than during the first part of the 20th century. This phenomenon is likely associated with the climate warming trends recorded in this region in the last century, especially during the last three decades when the month of April became warmer, thereby favoring very early-flowering cases. The earlier flowering of coltsfoot is, however, only noticeable in large urban areas (Montreal, Quebec City), suggesting a strong urban heat island effect on the flowering of this plant. Herbarium specimens are useful phenological indicators; however, the databases should be carefully examined prior to analysis to detect biases or trends associated with sampling locations.     

A stochastic model for integrating changes in species richness and community similarity across spatial scales

Human activities have elevated the extinction of natural populations as well as the invasion of new areas by non-native species. These dual processes of invasion and extinction may change the richness and similarity of communities, but the form these changes take is likely to depend on the manner in which invasions and extinctions occur and the spatial scale at which the changes are measured. Here, we explore the influence of differing patterns of extinction and invasion on the similarity and richness of a meta-community. In particular, we model simple stochastic processes analogous to realistic modes of human-mediated introduction of non-native species and range expansion by native species. We show that different modes of invasion and extinction can produce very different changes in diversity, and that the relative magnitude of these changes depends both on where in the meta-community diversity is measured and the degree of initial species aggregation. At any spatial scale of measurement, changes in the richness and similarity of communities following invasion and extinction are not necessarily strongly coupled: relatively large increases in richness may or may not also be associated with relatively large increases in similarity among communities. Thus, in real systems, the influence of human-induced invasions and extinctions on diversity will depend on both the precise mode of these processes (especially invasion), and how species populations are distributed across space.     

Genetic and developmental analysis of abdominal pigmentation differences across species in the Drosophila dunni subgroup

Abdominal pigmentation pattern varies dramatically among the species of the Drosophila dunni subgroup across the islands of the Caribbean. Previously, we developed a quantitative measure of abdominal pigmentation to assess phenotypic variation within and between species of this group. In this paper, we use this quantitative measure in an interspecific genetic analysis to decipher the underlying genetic basis of pigmentation differences between one of the lightest and the darkest species in the group. Our analysis shows that pigmentation expression in different areas of the abdomen is under separate genetic control. For these different abdominal regions, we detected a wide range of genetic effects, including X-linked, autosomal additive, near single-gene dominant, and sex-specific effects. Combining these genetic results with our earlier phenotypic and phylogenetic analyses, we present a simple conceptual model to explain how change in the control of expression of pigmentation has evolved throughout the D. dunni subgroup.     

A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species

The evolution of complex organisms is a puzzle for evolutionary theory because beneficial mutations should be less frequent in complex organisms, an effect termed "cost of complexity." However, little is known about how the distribution of mutation fitness effects (f(s)) varies across genomes. The main theoretical framework to address this issue is Fisher's geometric model and related phenotypic landscape models. However, it suffers from several restrictive assumptions. In this paper, we intend to show how several of these limitations may be overcome. We then propose a model of f(s) that extends Fisher's model to account for arbitrary mutational and selective interactions among n traits. We show that these interactions result in f(s) that would be predicted by a much smaller number of independent traits. We test our predictions by comparing empirical f(s) across species of various gene numbers as a surrogate to complexity. This survey reveals, as predicted, that mutations tend to be more deleterious, less variable, and less skewed in higher organisms. However, only limited difference in the shape of f(s) is observed from Escherichia coli to nematodes or fruit flies, a pattern consistent with a model of random phenotypic interactions across many traits. Overall, these results suggest that there may be a cost to phenotypic complexity although much weaker than previously suggested by earlier theoretical works. More generally, the model seems to qualitatively capture and possibly explain the variation of f(s) from lower to higher organisms, which opens a large array of potential applications in evolutionary genetics.     

Two new species ofSporothrix and their relation toBlastobotrys nivea

Two new species ofSporothrix are described:S. cyanescens, isolated from human skin andS. fungorum from fungal carpophores. Both species may form secondary blastoconidia; they resembleBlastobotrys nivea in several respects. The latter species is distinct by the shape of the conidiophores.     

A set of EST‐SSRs isolated from peach fruit transcriptome and their transportability across Prunus species

Twenty‐one expressed sequence tag–simple sequence repeat (EST–SSR) markers were developed in peach from a mesocarp cDNA library. Eighteen of them gave successful amplification in 22 peach genotypes and produced one to three alleles each with an average of 1.8 alleles per locus. The average value of expected and observed heterozygosities was 0.24 and 0.20, respectively. All the primers gave successful amplification in other six Prunus species (almond, apricot, sweet cherry, Japanese plum, European plum and Prunus ferganensis).