Reciprocal Selection Research Articles

The human protein coevolution network

Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cellular function. Prediction of interaction partners from different protein families exploits the property that interacting proteins can follow similar patterns and relative rates of evolution. Current methods for detecting coevolution based on the similarity of phylogenetic trees or evolutionary distance matrices have, however, been limited by requiring coevolution over the entire evolutionary history considered and are inaccurate in the presence of paralogous copies. We present a novel method for determining coevolving protein partners by finding the largest common submatrix in a given pair of distance matrices, with the size of the largest common submatrix measuring the strength of coevolution. This approach permits us to consider matrices of different size and scale, to find lineage-specific coevolution, and to predict multiple interaction partners. We used MatrixMatchMaker to predict protein-protein interactions in the human genome. We show that proteins that are known to interact physically are more strongly coevolving than proteins that simply belong to the same biochemical pathway. The human coevolution network is highly connected, suggesting many more protein-protein interactions than are currently known from high-throughput and other experimental evidence. These most strongly coevolving proteins suggest interactions that have been maintained over long periods of evolutionary time, and that are thus likely to be of fundamental importance to cellular function.

Darwinism renewed: contemporary studies of plant adaptation

Darwinism renewed: contemporary studies of plant adaptation

Reduced Bloch mode expansion for periodic media band structure calculations

Reduced Bloch mode expansion (RBME) is presented for fast periodic media band structure calculations. The expansion employs a natural basis composed of a selected reduced set of Bloch eigenfunctions. The reduced basis is selected within the irreducible Brillouin zone at high symmetry points determined by the medium’s crystal structure and group theory (and possibly at additional related points). At each of the reciprocal lattice selection points, a number of Bloch eigenfunctions are selected up to the frequency/energy range of interest for the band structure calculations. As it is common to initially discretize the periodic unit cell and solution field using some choice of basis, RBME is practically a secondary expansion that uses a selected set of Bloch eigenvectors. Such expansion therefore keeps, and builds on, any favourable attributes a primary expansion approach might exhibit. Being in line with the well-known concept of modal analysis, the proposed approach maintains accuracy while reducing the computation time by up to two orders of magnitudes or more depending on the size and extent of the calculations. Results are presented for phononic, photonic and electronic band structures.

Source Populations Act as Coevolutionary Pacemakers in Experimental Selection Mosaics Containing Hotspots and Coldspots

Natural populations of hosts and their enemies are often spatially structured, with patches that vary in the strength of reciprocal selection, so-called coevolutionary hotspots and coldspots with strong or weak reciprocal selection, respectively. Theory predicts that dispersal from hotspots should intensify coevolution in coldspots, whereas dispersal from coldspots should weaken coevolution in hotspots; however, there have been few empirical tests. We addressed this using paired populations of the bacterium Pseudomonas fluorescens and the phage SBW25Phi2 linked by one-way dispersal. Within each population, the strength of reciprocal selection was manipulated by altering the bacteria-phage encounter rate, which changes the rate of coevolution without affecting environmental productivity. We observed that dispersal from hotspots accelerated coevolution in coldspots, while dispersal from coldspots decelerated coevolution in hotspots. These results confirm theoretical predictions and suggest that source populations can act as coevolutionary "pacemakers" for recipient populations, overriding local conditions.

Ecological modules and roles of species in heathland plant–insect flower visitor networks

1. Co-existing plants and flower-visiting animals often form complex interaction networks. A long-standing question in ecology and evolutionary biology is how to detect nonrandom subsets (compartments, blocks, modules) of strongly interacting species within such networks. Here we use a network analytical approach to (i) detect modularity in pollination networks, (ii) investigate species composition of modules, and (iii) assess the stability of modules across sites. 2. Interactions between entomophilous plants and their flower-visitors were recorded throughout the flowering season at three heathland sites in Denmark, separated by >or= 10 km. Among sites, plant communities were similar, but composition of flower-visiting insect faunas differed. Visitation frequencies of visitor species were recorded as a measure of insect abundance. 3. Qualitative (presence-absence) interaction networks were tested for modularity. Modules were identified, and species classified into topological roles (peripherals, connectors, or hubs) using 'functional cartography by simulated annealing', a method recently developed by Guimerà & Amaral (2005a). 4. All networks were significantly modular. Each module consisted of 1-6 plant species and 18-54 insect species. Interactions aggregated around one or two hub plant species, which were largely identical at the three study sites. 5. Insect species were categorized in taxonomic groups, mostly at the level of orders. When weighted by visitation frequency, each module was dominated by one or few insect groups. This pattern was consistent across sites. 6. Our study adds support to the conclusion that certain plant species and flower-visitor groups are nonrandomly and repeatedly associated. Within a network, these strongly interacting subgroups of species may exert reciprocal selection pressures on each other. Thus, modules may be candidates for the long-sought key units of co-evolution.

The Coevolving Web of Life(American Society of Naturalists Presidential Address)

Coevolution--reciprocal evolutionary change in interacting species--is one of the central biological processes organizing the web of life, and most species are involved in one or more coevolved interactions. We have learned in recent years that coevolution is a highly dynamic process that continually reshapes interactions among species across ecosystems, creating geographic mosaics over timescales sometimes as short as thousands or even hundreds of years. If we take that as our starting point, what should we now be asking about the coevolutionary process? Here I suggest five major questions that we need to answer if we are to understand how coevolution shapes the web of life. How evolutionarily dynamic is specialization to other species, and what is the role of coevolutionary alternation in driving those dynamics? Does the geographic mosaic of coevolution shape adaptation in fundamentally different ways in different forms of interaction? How does the geographic mosaic of coevolution shape speciation? How does the structure of reciprocal selection change during the assembly of large webs of interacting species? How important are genomic events such as whole-genome duplication (i.e., polyploidy) and whole-genome capture (i.e., hybridization) in generating novel webs of interacting species? I end by suggesting four points about coevolution that we should tell every new student or researcher in biology.

FLIES AND FLOWERS IN DARWIN'S RACE

The idea of coevolution originated with Darwin's proposal that long-proboscid pollinators and long-tubed flowers might be engaged in reciprocal selection, but this has not been demonstrated. Here we test key aspects of Darwin's hypothesis of reciprocal selection in an experiment with naturally interacting populations of extremely long-proboscid flies (Moegistorhynchus longirostris: Nemestinidae) and long-tubed irises (Lapeirousia anceps: Iridaceae). We show that the benefit derived by both the fly (volume of nectar consumed) and the plant (number pollen grains received) depends on the relative length of their interacting organs. Each trait is shown to act both as agent and target in directional reciprocal selection, potentially leading to a race. This understanding of how fitness in both species varies in relation to the balance of their armament allows us to make tentative predictions about the nature of selection across multiple communities. We find that in each community a core group of long-tubed plant species might together be involved in diffuse coevolution with the fly. In poorly matched populations, the imbalance in armament is too great to allow reciprocal selection to act, and these species might instead experience one-sided selection that leads to convergence with the core species. Reciprocal selection drives the evolution of the community, then, additional species become attached to the network of interacting mutualists by convergence.

Predators Make (Temporary) Escape from Coevolutionary Arms Race

Predators Make (Temporary) Escape from Coevolutionary Arms Race

Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race.

Local Adaptation and Vector-Mediated Population Structure in Plasmodium vivax Malaria

Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control.

THE GEOGRAPHIC SELECTION MOSAIC FOR PONDEROSA PINE AND CROSSBILLS: A TALE OF TWO SQUIRRELS

Recent research demonstrates how the occurrence of a preemptive competitor (Tamiasciurus) gives rise to a geographic mosaic of coevolution for crossbills (Loxia) and conifers. We extend these studies by examining ponderosa pine (Pinus ponderosa), which produces more variable annual seed crops than the conifers in previous studies and often cooccurs with tree squirrels in the genus Sciurus that are less specialized than Tamiasciurus on conifer seed. We found no evidence of seed defenses evolving in response to selection exerted by S. aberti, which was apparently overwhelmed by selection resulting from inner bark feeding that caused many developing cones to be destroyed. In the absence of S. aberti, defenses directed at crossbills increased, favoring larger-billed crossbills and causing stronger reciprocal selection between crossbills and ponderosa pine. However, crossbill nomadism in response to cone crop fluctuations prevents localized reciprocal adaptation by crossbills. In contrast, evolution in response to S. griseus has incidentally defended cones against crossbills, limiting the geographic range of the interaction between crossbills and ponderosa pine. Our results suggest that annual resource variation does not prevent competitors from shaping selection mosaics, although such fluctuations likely prevent fine-scale geographic differentiation in predators that are nomadic in response to resource variability.

Discovery of inhibitors of the pentein superfamily protein dimethylarginine dimethylaminohydrolase (DDAH), by virtual screening and hit analysis

An efficient process for the discovery of inhibitors of DDAH enzymes, without the requirement for high throughput screening, is described. Physicochemical filtering of a 308,000-compound library according to drug likeness followed by reciprocal nearest neighbour selection produced a representative subset of 35,000 compounds. Virtual screening on a dual processor PC using FlexX, followed by biological screening, identified two hit series. Similarity searches of commercial databases and chemical re-synthesis of pure compounds resulted in SR445 as an inhibitor of Pseudomonas aeruginosa DDAH at 2 μM.

Consolidation of the Thioredoxin Fold by Peptide Recognition: Interaction between E. coli Thioredoxin Fragments 1−93 and 94−108

Escherichia coli thioredoxin (TRX) catalyzes redox reactions via the reversible oxidation of the conserved active center WCGPC. TRX is a monomeric alpha/beta protein with a fold characterized by a central beta-sheet surrounded by alpha-helical elements. The interaction of the C-terminal alpha-helix (helix 5) of TRX against the remainder of the protein involves the close packing of hydrophobic surfaces, opening the possibility of studying a fine-tuned molecular recognition phenomenon. To evaluate the relevance of this interaction on the folding mechanism of TRX, we characterize TRX1-93, a truncated variant of TRX devoid of the last stretch of 15 amino acid residues that includes helix 5. TRX1-93 may possibly represent a molecular form where the folding process becomes interrupted, giving rise to a structure exhibiting the features of a molten globule state. This was assessed by circular dichroism, intrinsic fluorescence, binding of the probe ANS, size-exclusion chromatography, limited proteolysis, and calorimetry. Remarkably, fragment TRX1-93 interacts with peptide TRX94-108 (KD approximately 2-12 microM), bringing forth the restoration of native-like signatures and enzymic function. This represents a molecular event of reciprocal structure selection where both partners gain order, thus leading to long-range consequences on conformation. In this context, the binding of the C-terminal helix could signify a late event in the consolidation of the overall TRX fold.

POLYGENIC TRAITS AND PARASITE LOCAL ADAPTATION

The extent to which parasites are locally adapted to their hosts has important implications for human health and agriculture. A recently developed conceptual framework--the geographic mosaic theory of coevolution--predicts that local maladaptation should be common and largely determined by the interplay between gene flow and spatially variable reciprocal selection. Previous investigation of this theory has predominately focused on genetic systems of infection and resistance characterized by few genes of major effect and particular forms of epistasis. Here we extend existing theory by analyzing mathematical models of host-parasite interactions in which host resistance to parasites is mediated by quantitative traits with an additive polygenic basis. In contrast to previous theoretical studies predicated upon major gene mechanisms, we find that parasite local maladaptation is quite uncommon and restricted to one specific functional form of host resistance. Furthermore, our results show that local maladaptation should be rare or absent in studies that measure local adaptation using reciprocal transplant designs conducted in natural environments. Our results thus narrow the scope over which the predictions of the geographic mosaic theory are likely to hold and provide novel and readily testable predictions about when and where local maladaptation is expected.

Spatial mosaic evolution of snail defensive traits.

BackgroundRecent models suggest that escalating reciprocal selection among antagonistically interacting species is predicted to occur in areas of higher resource productivity. In a putatively coevolved interaction between a freshwater snail (Mexipyrgus churinceanus) and a molluscivorous cichlid (Herichthys minckleyi), we examined three components of this interaction: 1) spatial variation in two putative defensive traits, crushing resistance and shell pigmentation; 2) whether abiotic variables or frequency of molariform cichlids are associated with spatial patterns of crushing resistance and shell pigmentation and 3) whether variation in primary productivity accounted for small-scale variation in these defensive traits.ResultsUsing spatial autocorrelation to account for genetic and geographic divergence among populations, we found no autocorrelation among populations at small geographic and genetic distances for the two defensive traits. There was also no correlation between abiotic variables (temperature and conductivity) and snail defensive traits. However, crushing resistance and frequency of pigmented shells were negatively correlated with molariform frequency. Crushing resistance and levels of pigmentation were significantly higher in habitats dominated by aquatic macrophytes, and both traits are phenotypically correlated.ConclusionCrushing resistance and pigmentation of M. churinceanus exhibit striking variation at small spatial scales often associated with differences in primary productivity, substrate coloration and the frequency of molariform cichlids. These local geographic differences may result from among-habitat variation in how resource productivity interacts to promote escalation in prey defenses.

Qualitative and Quantitative Evolution of Selected Oil Palm Seed Production at La Dibamba Specialised Centre on Oil Palm Research (Cameroon)

The La Dibamba Specialised Centre on Oil Palm Research (CEREPAH) is a member of CIRAD’s “network” that includes CNRA La Mé (Côte d’Ivoire), Embrapa Rio Urubu Station (Brazil), SRPH Pobè Station (Benin), P T Socfindo (Indonesia) and CIRAD (France). Sustainable high yielding oil palm breeding is based on a recurrent selection scheme (RRS). The major advantage is the capacity to produce new planting materials as soon as the value of the crosses or the parents tested obtained from progeny tests is known. At the end of the first cycle, 18 per cent improvement in oil yield was achieved. An average yield increase of 36 per cent was achieved over two cycles of recurrent reciprocal selection. At La Dibamba the production of first selection cycle planting materials started in 1985, while that of the second in 1991 which progressively took over the first selection cycle planting materials. Since 2003, 98 per cent of seeds produced are of the second selection cycle. The number of dura parents, the potential number of pisifera parents and the seed production potential are high. The gap existing between the seed production potential and the quantity of seeds produced yearly is explained. Keywords: Oil palm, seed production, dura parent, pisifera parent, category, potential, La Dibamba.

Diversity begets diversity: host expansions and the diversification of plant-feeding insects

BackgroundPlant-feeding insects make up a large part of earth's total biodiversity. While it has been shown that herbivory has repeatedly led to increased diversification rates in insects, there has been no compelling explanation for how plant-feeding has promoted speciation rates. There is a growing awareness that ecological factors can lead to rapid diversification and, as one of the most prominent features of most insect-plant interactions, specialization onto a diverse resource has often been assumed to be the main process behind this diversification. However, specialization is mainly a pruning process, and is not able to actually generate diversity by itself. Here we investigate the role of host colonizations in generating insect diversity, by testing if insect speciation rate is correlated with resource diversity.ResultsBy applying a variant of independent contrast analysis, specially tailored for use on questions of species richness (MacroCAIC), we show that species richness is strongly correlated with diversity of host use in the butterfly family Nymphalidae. Furthermore, by comparing the results from reciprocal sister group selection, where sister groups were selected either on the basis of diversity of host use or species richness, we find that it is likely that diversity of host use is driving species richness, rather than vice versa.ConclusionWe conclude that resource diversity is correlated with species richness in the Nymphalidae and suggest a scenario based on recurring oscillations between host expansions – the incorporation of new plants into the repertoire – and specialization, as an important driving force behind the diversification of plant-feeding insects.

Host-Parasite Relationships inCannabis

Abstract Plant taxonomy is primarily based on patterns of morphological variation and geographical distribution. Plant-parasite relationships can also offer clues regarding the phylogeny of the host plant. Many obligate parasites coevolve with their hosts, eventually becoming restricted to an individual taxon. Host restriction may take place at different taxonomic ranks, i.e., parasites may become restricted to one host genus within a plant family, to one species within a genus, or to one infraspecific taxon within a species. This phylogenetic congruence between plants and their parasites may be due to cospeciation or due to co-adaptation (reciprocal adaptive selection). Our study reviewed plant-parasite interactions with regard to putative Cannabis taxa. The results Curators of the following herbaria are thanked for loaning collections: BPI, IMI, FH, GH, BR, ILLS, MICH, VT. suggest that certain parasites may have co-evolved with putative species and biotypes within the Cannabisgenus.

Microsatellite analysis reveals strong but differential impact of a social parasite on its two host species

The speed and the dynamics of the co-evolutionary process strongly depend on the relative strengths of reciprocal selection pressures exerted by the interacting species. Here, we investigate the influence of an obligate social parasite, the slave-making ant Harpagoxenus sublaevis, on populations of the two main host species Leptothorax acervorum and Leptothorax muscorum from a German ant community. A combination of genetic and demographic data allowed us to analyse the consequences of raiding pressure on the hosts' life history and possible host preferences of the parasite. We can demonstrate that slave raids during which the social parasite pillages brood from neighbouring host colonies are both frequent and extremely destructive for both host species. Microsatellite analysis showed that, on average, a single slave-maker colony conducts more than three raids per year and that host colonies mostly perish in the aftermath of these parasite attacks. Only in few cases, surviving nests of previously raided host colonies were found in the surroundings of slave-maker colonies. As a consequence of the high prevalence of parasites and their recurrent and devastating slave raids on host colonies, the life expectancy of host colonies was severely reduced. Combining our results on host-specific parasitic colony founding and raiding frequencies with the post-raid survival rate, we can demonstrate an overall higher mortality rate for the smaller host species L. muscorum. This might be caused by a preference of H. sublaevis for this secondary host species as demographic data on host species usage indicate.

Temporally persistent patterns of incidence and abundance in a pollinator guild at annual and decadal scales: the bees of Larrea tridentata

A recent alternative model to conventional coevolution, the geographic mosaic theory of coevolution, posits that reciprocal selection is episodic and local, rather than persistent and spatially extensive. However, little empirical evidence addresses this model's tenets, in particular the temporal stability of local plant–pollinator interactions. We evaluated this tenet using the richly diverse guild of bees at creosote bush (Larrea tridentata), a generalist plant that hosts many specialist bees. We systematically resampled over 2–5 years at 11 sites across the south-western USA. Incidence and abundance also were compared for survey sites sampled 20 ± 2 years earlier. Average Morisita-Horn faunal similarities of local bee guilds was 87% for sequential years and 36% after 20 years. Similarities in taxonomic composition of resampled local bee guilds could be statistically represented as a random assemblage drawn from the regional source pool of 54–68 bee species that could be expected at Larrea, weighted by regional abundance. At every site, only the minority of abundant bee species was typically persistent in local guilds, even after > 20 years. Most bee species in the Larrea guild were chronically uncommon, geographically sporadic and temporally unpredictable, attributes that render them numerically inconsequential as pollinators in their local guild. Persistence among abundant bee species in local pollinator assemblages satisfies one condition by which reciprocal selection could act locally. The well-being of these more abundant core species, and not bee diversity per se, may better characterize the health of such plant–pollinator associations. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 319–329.