Coevolution is a short-distance force at the protein interaction level and correlates with the modular organization of protein networks

We investigated what roles coevolution plays in shaping yeast protein interaction network (PIN). We found that the extent of coevolution between two proteins decreases rapidly as their interacting distance on the PIN increases, suggesting coevolutionary constraint is a short-distance force at the molecular level. We also found that protein-protein interactions (PPIs) with strong coevolution tend to be enriched in interconnected clusters, whereas PPIs with weak coevolution are more frequently present at inter-cluster region. The findings indicate the close relationship between coevolution and modular organization of PINs, and may provide insights into evolution and modularity of cellular networks.     

Cranial modularity shifts during mammalian evolution

The mammalian skull has been studied as several separate functional components for decades, but the study of modularity is a more recent, integrative approach toward quantitative examination of independent subsets of highly correlated traits, or modules. Although most studies of modularity focus on developmental and genetic systems, phenotypic modules have been noted in many diverse morphological structures. However, few studies have provided empirical data for comparing modules across higher taxonomic levels, limiting the ability to assess the broader evolutionary significance of modularity. This study uses 18-32 three-dimensional cranial landmarks to analyze phenotypic modularity in 106 mammalian species and demonstrates that cranial modularity is generally conserved in the evolution of therian mammals (marsupials and placentals) but differs between therians and monotremes, the two extant subclasses of Mammalia. Within therians, cluster analyses identify six distinct modules, but only three modules display significant integration in all species. Monotremes display only two highly integrated modules. Specific hypotheses of functional and developmental influences on cranial bones were tested. Theoretical correlation matrices for bones were constructed on the basis of shared function, tissue origin, or mode of ossification, and all three of these models are significantly correlated with observed correlation matrices for the mammalian cranium.     

Rapid divergent evolution of sexual morphology: comparative tests of antagonistic coevolution and traditional female choice

Male structures specialized to contact females during sexual interactions often diverge relatively rapidly over evolutionary time. Previous explanations for this pattern invoked sexual selection by female choice, but new ideas emphasize possible sexually antagonistic coevolution resulting from male-female conflict over control of fertilization. The two types of selection have often not been carefully distinguished. They do not theoretically exclude one another, but they have not necessarily had equally important roles in producing rapid evolutionary divergence. To date, most recent empirical studies of antagonistic coevolution have emphasized only a few taxa. This study uses the abundant but little-used data in the taxonomic literature on morphology to evaluate the roles of antagonistic coevolution and traditional female choice over a wide taxonomic spectrum (61 families of arthropods, mostly insects and spiders). Groups with species-specific male structures that contact females were checked for coevolution of species-specific female structures that are contacted by the male and that have mechanical properties that could potentially defend her against the male. Facultatively deployable, species-specific female defensive structures, a design that would seem likely to evolve frequently under the sexually antagonistic coevolution hypothesis, were completely absent (0% of 106 structures in 84 taxonomic groups). Although likely cases of sexually antagonistic coevolution exist, using conservative criteria, 79.2% of the 106 structures lacked even potentially defensive female coevolution. A common pattern (53.8% of 106) was a nearly complete absence of female change in areas contacted by species-specific male structures. Post-hoc arguments invoking possible coevolution of defensive female behavior instead of morphology, or of female sensitivities and responses to male sensory traps, could enable the sexually antagonistic coevolution hypothesis to explain these data. No case of such coevolution of female behavior or sensitivities has been demonstrated, and there are additional reasons to doubt that they are general explanations for the data presented here. Detailed studies of female resistance behavior could help illuminate several issues. The possibility of a greater role for antagonistic coevolution in reproductive physiology than in morphology and the possibility that female choice and sexually antagonistic coevolution have both been important in some lineages are discussed.     

Modularity and the units of evolution

Summary While many developmental processes (e. g., gene networks or signaling pathways) are astonishingly conserved during evolution, they may be employed differently in different metazoan taxa or may be used multiply in different contexts of development. This suggests that these processes belong to building blocks or modules, viz., highly integrated parts of the organism, which develop and/or function relatively independent from other parts. Such modules may be relatively easy to dissociate from other modules and, therefore, could also serve as units of evolution. However, in order to further explore the implications of modularity for evolution, the vague notion of “modularity” as well as its relation to concepts like “unit of evolution” need to be more precisely specified. Here, a module is characterized as a certain type of dynamic pattern of couplings among the constituents of a process. It may or may not form a spatially contiguous unit. A unit of selection is defined as a unit of those constituents of a reproducing process/system, which exists in different variants and acts as a non-decomposable unit of fitness and variant reproduction during a particular selection process. The more general notion of a unit of evolution is characterized as a nondecomposable unit of constituents with reciprocal fitness dependence, be it due to fitness epistasis or due to the lack of independent variability. Because such fitness dependence may only be observed for some combinations of variants, several constituents may act as a unit of evolution only with a certain probability (coevolution probability). It is argued, that under certain conditions modules are likely to act as units of evolution with high coevolution probabilities, because there is likely to be a close tie between the pattern of couplings of the constituents of a reproducing system and their interdependent fitness contributions. Moreover and contrary to the traditional dichotomy of genes versus organisms as units of selection, modules tend to be more important in delimiting actual units of selection than either organisms or genes, because they are less easily disrupted by recombination than organisms, while having less contextsensitive fitness values than genes. Finally, it is suggested that the evolution of modularity is self-reinforcing, because the flexibility of intermodular connections facilitates the recombination among modules and their multiple employment in new contexts.     

Metabolic network modularity in archaea depends on growth conditions

Network modularity is an important structural feature in metabolic networks. A previous study suggested that the variability in natural habitat promotes metabolic network modularity in bacteria. However, since many factors influence the structure of the metabolic network, this phenomenon might be limited and there may be other explanations for the change in metabolic network modularity. Therefore, we focus on archaea because they belong to another domain of prokaryotes and show variability in growth conditions (e.g., trophic requirement and optimal growth temperature), but not in habitats because of their specialized growth conditions (e.g., high growth temperature). The relationship between biological features and metabolic network modularity is examined in detail. We first show the absence of a relationship between network modularity and habitat variability in archaea, as archaeal habitats are more limited than bacterial habitats. Although this finding implies the need for further studies regarding the differences in network modularity, it does not contradict previous work. Further investigations reveal alternative explanations. Specifically, growth conditions, trophic requirement, and optimal growth temperature, in particular, affect metabolic network modularity. We have discussed the mechanisms for the growth condition-dependant changes in network modularity. Our findings suggest different explanations for the changes in network modularity and provide new insights into adaptation and evolution in metabolic networks, despite several limitations of data analysis.     

On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms

Analyses of effects of mutants on many traits have enabled estimates to be obtained of the magnitude of pleiotropy, and in reviews of such data others have concluded that the degree of pleiotropy is highly restricted, with implications on the evolvability of complex organisms. We show that these conclusions are highly dependent on statistical assumptions, for example significance levels. We analyze models with pleiotropic effects on all traits at all loci but by variable amounts, considering distributions of numbers of traits declared significant, overall pleiotropic effects, and extent of apparent modularity of effects. We demonstrate that these highly pleiotropic models can give results similar to those obtained in analyses of experimental data and that conclusions on limits to evolvability through pleiotropy are not robust.     

Experimental evolution reveals divergence in female genital teeth morphology in response to sexual conflict intensity in a moth

The rapid evolutionary divergence of male genital structures under sexual selection is well documented. However, variation in female genital traits and the potential for sexual conflict to drive the coevolution between male and female traits has only recently received attention. In many lepidopterans, females possess genital teeth (collectively, signa). Comparative studies suggest these teeth, involved in the deflation of spermatophores, may have coevolved with male spermatophore thickness via sexually antagonistic coevolution in a contest over the rate of deflation of spermatophores within the reproductive tract. We tested the hypothesis that sexual conflict should generate coevolution between genital teeth and spermatophore morphology by examining these traits under experimental manipulation of sexual conflict intensity. Using micro‐CT scanning, we examined spermatophore and teeth morphology in populations of the Indian moth, Plodia interpunctella, which had been evolving for 110 generations under different adult sex‐ratio biases. We found divergence in female signa morphology in response to sexual conflict: females from female‐biased populations (reduced sexual conflict) developed wider signa. However, we found no evidence of coevolution between signa traits and spermatophore thickness as reported from comparative studies.     

Studying morphological integration and modularity at multiple levels: concepts and analysis

Although most studies on integration and modularity have focused on variation among individuals within populations or species, this is not the only level of variation for which integration and modularity exist. Multiple levels of biological variation originate from distinct sources: genetic variation, phenotypic plasticity resulting from environmental heterogeneity, fluctuating asymmetry from random developmental variation and, at the interpopulation or interspecific levels, evolutionary change. The processes that produce variation at all these levels can impart integration or modularity on the covariance structure among morphological traits. In turn, studies of the patterns of integration and modularity can inform about the underlying processes. In particular, the methods of geometric morphometrics offer many advantages for such studies because they can characterize the patterns of morphological variation in great detail and maintain the anatomical context of the structures under study. This paper reviews biological concepts and analytical methods for characterizing patterns of variation and for comparing across levels. Because research comparing patterns across level has only just begun, there are relatively few results, generalizations are difficult and many biological and statistical questions remain unanswered. Nevertheless, it is clear that research using this approach can take advantage of an abundance of new possibilities that are so far largely unexplored.     

Two-step infection processes can lead to coevolution between functionally independent infection and resistance pathways

There is growing evidence that successful infection of hosts by pathogens requires a series of independent steps. However, how multistep infection processes affect host-pathogen coevolution is unclear. We present a coevolutionary model, inspired by empirical observations from a range of host-pathogen systems, where the infection process consists of the following two steps: the first is for the pathogen to recognize and locate a suitable host, and the second is to exploit the host while evading immunity. Importantly, these two steps conform to different models of infection genetics: inverse-gene-for-gene (IGFG) and gene-for-gene (GFG), respectively. We show that coevolution under this scenario can lead to coupled gene frequency changes across these two systems. In particular, selection often favors pathogens that are infective at the first, IGFG, step and hosts that are resistant at the second, GFG, step. Hence, there may be signals of positive selection between functionally independent systems whenever there are multistep processes determining resistance and infectivity. Such multistep infection processes are a fundamental, but overlooked feature of many host-pathogen interactions, and have important consequences for our understanding of host-pathogen coevolution.     

Two modes of host–enemy coevolution

The process of coevolution between host and enemy has traditionally been viewed as an evolutionary arms race between resistance and counterresistance. The arms-race metaphor of coevolution is widely accepted because it explains the evolution of many characters in species involved in host–enemy interactions. However, molecular work in plant–pathogen systems suggests a coevolutionary interplay between plant recognition of an attacking pathogen and pathogen evasion from recognition. We refer to this process as information coevolution, and contrast this with arms race coevolution to show that these two processes result in very different patterns of host resistance and enemy virulence at the population level. First, information coevolution results in a lower proportion of hosts that are susceptible to enemy attack within a population. Second, information coevolution produces a pattern of local maladaptation of enemy on host, a naturally occurring phenomenon that is difficult to explain under arms race coevolution. We then conduct a literature review to survey the empirical support for either mode of coevolution using the predicted patterns of host resistance and enemy virulence. Evidence supports both modes of coevolution in plant–enemy interactions, whereas no support is found for information coevolution in vertebrate–parasite and invertebrate–parasite systems.     

The measurement of coevolution in the wild

Coevolution has long been thought to drive the exaggeration of traits, promote major evolutionary transitions such as the evolution of sexual reproduction and influence epidemiological dynamics. Despite coevolution’s long suspected importance, we have yet to develop a quantitative understanding of its strength and prevalence because we lack generally applicable statistical methods that yield numerical estimates for coevolution’s strength and significance in the wild. Here, we develop a novel method that derives maximum likelihood estimates for the strength of direct pairwise coevolution by coupling a well‐established coevolutionary model to spatially structured phenotypic data. Applying our method to two well‐studied interactions reveals evidence for coevolution in both systems. Broad application of this approach has the potential to further resolve long‐standing evolutionary debates such as the role species interactions play in the evolution of sexual reproduction and the organisation of ecological communities.     

Increasing productivity accelerates host-parasite coevolution

Host-parasite coevolution is believed to influence a range of evolutionary and ecological processes, including population dynamics, evolution of diversity, sexual reproduction and parasite virulence. The impact of coevolution on these processes will depend on its rate, which is likely to be affected by the energy flowing through an ecosystem, or productivity. We addressed how productivity affected rates of coevolution during a coevolutionary arms race between experimental populations of bacteria and their parasitic viruses (phages). As hypothesized, the rate of coevolution between bacterial resistance and phage infectivity increased with increased productivity. This relationship can in part be explained by reduced competitiveness of resistant bacteria in low compared with high productivity environments, leading to weaker selection for resistance in the former. The data further suggest that variation in productivity can generate variation in selection for resistance across landscapes, a result that is crucial to the geographic mosaic theory of coevolution.     

Diversification and coevolution in brood pollination mutualisms: Windows into the role of biotic interactions in generating biological diversity

Brood pollination mutualisms—interactions in which specialized insects are both the pollinators (as adults) and seed predators (as larvae) of their host plants—have been influential study systems for coevolutionary biology. These mutualisms include those between figs and fig wasps, yuccas and yucca moths, leafflowers and leafflower moths, globeflowers and globeflower flies, Silene plants and Hadena and Perizoma moths, saxifrages and Greya moths, and senita cacti and senita moths. The high reciprocal diversity and species‐specificity of some of these mutualisms have been cited as evidence that coevolution between plants and pollinators drives their mutual diversification. However, the mechanisms by which these mutualisms diversify have received less attention. In this paper, we review key hypotheses about how these mutualisms diversify and what role coevolution between plants and pollinators may play in this process. We find that most species‐rich brood pollination mutualisms show significant phylogenetic congruence at high taxonomic scales, but there is limited evidence for the processes of both cospeciation and duplication, and there are no unambiguous examples known of strict‐sense contemporaneous cospeciation. Allopatric speciation appears important across multiple systems, particularly in the insects. Host‐shifts appear to be common, and widespread host‐shifts by pollinators may displace other pollinator lineages. There is relatively little evidence for a “coevolution through cospeciation” model or that coevolution promotes speciation in these systems. Although we have made great progress in understanding the mechanisms by which brood pollination mutualisms diversify, many opportunities remain to use these intriguing symbioses to understand the role of biotic interactions in generating biological diversity.     

Coevolving protein residues: maximum likelihood identification and relationship to structure

The identification of protein sites undergoing correlated evolution (coevolution) is of great interest due to the possibility that these pairs will tend to be adjacent in the three-dimensional structure. Identification of such pairs should provide useful information for understanding the evolutionary process, predicting the effects of site-directed substitution, and potentially for predicting protein structure. Here, we develop and apply a maximum likelihood method with the aim of improving detection of coevolution. Unlike previous methods which have had limited success, this method allows for correlations induced by phylogenetic relationships and for variation in rate of evolution along branches, and does not rely on accurate reconstruction of ancestral nodes. In order to reduce the complexity of coevolutionary relationships and identify the primary component of pairwise coevolution between two sites, we reduce the data to a two-state system at each site, regardless of the actual number of residues observed at that site. Simulations show that this strategy is good at identifying simple correlations and at recognizing cases in which the data are insufficient to distinguish between coevolution and spurious correlations. The new method was tested by using size and charge characteristics to group the residues at each site, and then evaluating coevolution in myoglobin sequences. Grouping based on physicochemical characteristics allows categorization of coevolving sites into positive and negative coevolution, depending on the correlation between equilibrium state frequencies. We detected a striking excess of negative coevolution (corresponding to charge) at sites brought into proximity by the periodicity of the alpha-helix, and there was also a tendency for sites with significant likelihood ratios to be close in the three-dimensional structure. Sites on the surface of the protein appear to coevolve both when they are close in the structure, and when they are distant, implying a role for folding and/or avoidance of quaternary structure in the coevolution process.     

Cranial Suture Closure Patterns in Sciuridae: Heterochrony and Modularity

Studies of sequence heterochrony in mammalian evolution have revealed differences in bone ossification between and within major clades. Sequences of late stage developmental events have been less well studied, and the relation of modularity to sequence heterochrony at these stages has not been explicitly tested. Here, the first data on cranial suture closure are provided for members of Sciuridae. Sequence heterochrony is quantified using the recently developed Parsimov-based genetic inference (PGi) algorithm to identify shifts in suture closure sequence, and modularity in heterochronic shifts is tested. Results indicate that suture closure pattern was quite variable among sciurids, and interspecific correspondence in closure sequence was generally lower than has been found for other rodents, and for carnivorans. A number of sequence heterochronies were detected for inclusive clades, and these were not randomly distributed but mainly concentrated among sutures that exhibited high rank variability and belonged to the orbit and cranial vault modules, suggesting that some regions of the cranium exhibited a greater capacity for variation in suture closure. Heterchronies were not detected for sutures belonging to the basicranium, or anterior orbit-nasal modules, both of which are recognized as highly integrated modules based on landmark data. Modularity of suture closure sequence was not significant for any modules following multiple-comparison correction, which contrasts with modularity that has been recovered in early stage, ossification sequence events among other mammals.     

Failure to cospeciate: an unsorted tale of millipedes and mites

Mites form symbiotic relationships with many animal taxa, including fish, amphibians, reptiles, birds, mammals, mollusks and arthropods. They are often found living on millipedes and it has often been speculated that these two groups of arthropods have, in some cases, undergone coevolution. However, this hypothesis has never been formally tested. Millipedes of the family Xystodesmidae Cook 1895 (Diplopoda: Polydesmida) and their symbiotic mites of the genus Stylochyrus Canestrini & Canestrini 1882 were collected in broadleaf forests of the eastern USA. The DNA from two mitochondrial regions (16S/12S and cox1) was sequenced for all collected millipede and mite specimens. Phylogenetic trees were reconstructed for both millipede and mite taxa using Bayesian inference. Pairwise distance data were used in distance‐based coevolutionary analyses and reconstructed phylogenies were used in tree‐based coevolutionary analyses. The phylogenetic analyses indicate Stylochyrus and xystodesmid millipede evolutionary history is incongruent. Moreover, the evolutionary relationships among mite individuals and populations have very low support values and indicate little to no geographic structuring. The coevolutionary analyses likewise detected no pattern of coevolution among these millipede and mite lineages. Unlike many arthropod species, Stylochyrus mites appear to be highly vagile. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 272–287.     

Ecological niches of ectoparasites

On mammals and birds communities of ectoparasites are present, which can include scores of ticks, mites and insects species. The parasitizing of arthropods terrestrial vertebrates appeared as far back a the Cretaceous period, and after 70-100 mil. years of the coevolution ectoparasites have assimilated all food resources and localities of the hosts' bodies. To the present only spatial and (to the less extent) trophic niches of parasitic insects, ticks and mites are studied completely enough. The main results these investigations are discussed in the present paper. A high abundance of the communities is reached because of their partition into the number of ecological niches. Host is complex of ecological niches for many ectoparasites species. These niches reiterate in the populations of a species closely related species of hosts and repeat from generation to generation. The each part of host (niche) being assimilated be certain parasite species is available potentially for other species. The partition of host into ecological niches is clearer than the structure of ecosystems including free-living organisms. A real extent of the ecological niches occupation by different species of ticks, mites and insects is considerably lower than a potential maximum. The degree of ecological niches saturation depends on the history of the coevolution of parasites community components, previous colonization be new ectoparasite species and many other ecological factors affecting host-parasite system. The use of the ecological niche conception in parasitology is proved to be rather promising. Ectoparasites communities because of their species diversity, different types of feeding and a number of habitats on host represent convenient models and study of them can contribute significantly to the developmeht of the general conception of ecological niche.     

The evolution of ecologically important characters in Heliconius butterflies (Lepidoptera: Nymphalidae): a cladistic review

The biology of Heliconius butterflies has provided a rich source of data to test theories of ecological genetics, coevolution and community ecology. Many putatively adaptive characters have been discussed with reference to a phylogenetic hypothesis based on a variety of morphological and life-history traits interpreted from an evolutionary taxonomic perspective. Here, alternate interpretations of characters on the traditional tree and a more recent mitochondrial DNA cladogram with a substantially different topology are compared and contrasted. It is shown that many characters ostensibly providing support for the traditional phylogenetic hypothesis are almost equally parsimoniously distributed and in some cases more parsimoniously distributed on the mtDNA tree than on the tree inferred from those characters. Discussion of alternate evolutionary scenarios based on the mDNA-based topology is presented for pupal mating, pollen feeding, foodplant coevolution, and other ecologically significant features.     

Host-bacterial coevolution and the search for new drug targets

Understanding the coevolution between humans and our microbial symbionts and pathogens requires complementary approaches, ranging from community analysis to in-depth analysis of individual genomes. Here we review the evidence for coevolution between symbionts and their hosts, the role of horizontal gene transfer in coevolution, and genomic and metagenomic approaches to identify drug targets. Recent studies have shown that our symbiotic microbes confer many metabolic capabilities that our mammalian genomes lack, and that targeting mechanisms of horizontal gene transfer is a promising new direction for drug discovery. Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities.