Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

Background

While the conserved positions of a multiple sequence alignment (MSA) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. Different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones.

Methodology/Principal Findings

We have used two complementary approaches to test the efficacy of these methods. In the first approach, we have used a new program, MSAvolve, for the in silico evolution of MSAs, which records a detailed history of all covarying positions, and builds a global coevolution matrix as the accumulated sum of individual matrices for the positions forced to co-vary, the recombinant coevolution, and the stochastic coevolution. We have simulated over 1600 MSAs for 8 protein families, which reflect sequences of different sizes and proteins with widely different functions. The calculated coevolution matrices were compared with the coevolution matrices obtained for the same evolved MSAs with different coevolution detection methods. In a second approach we have evaluated the capacity of the different methods to predict close contacts in the representative X-ray structures of an additional 150 protein families using only experimental MSAs.

Conclusions/Significance

Methods based on the identification of global correlations between pairs were found to be generally superior to methods based only on local correlations in their capacity to identify coevolving residues using either simulated or experimental MSAs. However, the significant variability in the performance of different methods with different proteins suggests that the simulation of MSAs that replicate the statistical properties of the experimental MSA can be a valuable tool to identify the coevolution detection method that is most effective in each case.     

Coevolution and the Effects of Climate Change on Interacting Species

Background

Recent studies suggest that environmental changes may tip the balance between interacting species, leading to the extinction of one or more species. While it is recognized that evolution will play a role in determining how environmental changes directly affect species, the interactions among species force us to consider the coevolutionary responses of species to environmental changes.

Methodology/Principle Findings

We use simple models of competition, predation, and mutualism to organize and synthesize the ways coevolution modifies species interactions when climatic changes favor one species over another. In cases where species have conflicting interests (i.e., selection for increased interspecific interaction strength on one species is detrimental to the other), we show that coevolution reduces the effects of climate change, leading to smaller changes in abundances and reduced chances of extinction. Conversely, when species have nonconflicting interests (i.e., selection for increased interspecific interaction strength on one species benefits the other), coevolution increases the effects of climate change.

Conclusions/Significance

Coevolution sets up feedback loops that either dampen or amplify the effect of environmental change on species abundances depending on whether coevolution has conflicting or nonconflicting effects on species interactions. Thus, gaining a better understanding of the coevolutionary processes between interacting species is critical for understanding how communities respond to a changing climate. We suggest experimental methods to determine which types of coevolution (conflicting or nonconflicting) drive species interactions, which should lead to better understanding of the effects of coevolution on species adaptation. Conducting these experiments across environmental gradients will test our predictions of the effects of environmental change and coevolution on ecological communities.     

森林生态系统健康与野生动植物资源的可持续利用

研究了森林生态系统健康与野生动植物资源之间的关系,以及人类活动对森林生态系统健康的影响,提出了以下三个论点：(1)野生动植物资源是构成森林生态系统的基本物质内容。野生动植物资源对森林生态系统具有不可估量的影响和作用。(2)野生动植物资源的减少是森林生态系统健康状况下降的“显示器”。森林生态系统健康状况的下降或衰退,会导致野生动植物资源数量或种类的减少甚至种群灭绝。(3)森林生态系统是野生动植物资源与人类活动关系的集合体和反映体。人类与野生动植物资源是对立又统一的矛盾综合体,而森林生态系统健康与否就取决于这二者的关系。如果人类对野生动植物资源在保护的基础上进行合理的利用,就能保证森林生态系统的结构的完整和功能的良好,因此森林生态系统处于健康的状态;但若人类对野生动植物资源过度利用而不加保护,那么随着野生动植物资源的逐渐衰竭,森林生态系统将逐渐失去某些功能且变得支离破碎,也就无法保持健康的状态。提出了维持森林生态系统健康并实现野生动植物资源可持续利用的解决途径：(1)实行森林的可持续经营。森林可持续经营是指长期保持森林的生产力和可再生性,以及森林生态系统的物种和生物多样性。(2)发展“接近自然的林业”。近自然林业是在服从自然规律的前提下为人类的木材及林产品利用目的而设计的容许有一点偏离自然的森林模式,以森林生态健康为目标的建设方法。     

Coevolution Between Food-Rewarding Flowers and Their Pollinators

The concept of coevolution was first developed by Darwin, who used it to explain how pollinators and food-rewarding flowers involved in specialized mutualisms could, over time, develop long tongues and deep tubes, respectively. He famously predicted that Angraecum sesquipedale, a long-spurred Malagasy orchid, must be pollinated by a hawkmoth with an exceptionally long tongue. Darwin’s idea of a coevolutionary “race” was championed by contemporary naturalists, including Alfred Wallace, and a hawkmoth fitting the expected tongue-length profile was eventually discovered in Madagascar during the early twentieth century. However, strong empirical support for the mechanism behind Darwin’s coevolutionary model has been forthcoming only in the past two decades. It is now established that selection often strongly favors plants with floral tubes that exceed the length of their pollinator’s tongues. There is also evidence that pollinators gain an energetic benefit from having tongues that enable them to consume most or all of the nectar in deep tubular flowers. Alternative explanations for the evolution of long pollinator tongues, such as evasion of predators that use flowers as ambush sites, are considered much less compelling and lack quantitative support. Another important advance in coevolution research has been the development of approaches that explicitly predict a geographical mosaic of coevolution. The expectation that coevolution can lead to geographical diversification and trait covariation among strongly interacting organisms is strongly supported by studies of long-proboscid fly and oil-bee pollination systems in South Africa. Macro- and microevolutionary studies of pollination systems suggest that coevolution can operate alongside other one-sided evolutionary processes, such as shifts, in shaping plant and pollinator traits.     

Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure

Correlated mutation analysis (CMA) has been used to investigate protein functional sites. However, CMA has suffered from low signal-to-noise ratio caused by meaningless phylogenetic signals or structural constraints. We present a new method, Structure-based Correlated Mutation Analysis (SCMA), which encodes coevolution scores into a protein structure network. A path-based network model is adapted to describe information transfer between residues, and the statistical significance is estimated by network shuffling. This model intrinsically assumes that residues in physical contact have a more reliable coevolution score than distant residues, and that coevolution in distant residues likely arises from a series of contacting and coevolving residues. In addition, coevolutionary coupling is statistically controlled to remove the structural effects. When applied to the rhodopsin structure, the SCMA method identified a much higher percentage of functional residues than the typical coevolution score (61% vs. 22%). In addition, statistically significant residues are used to construct the coevolved residue-residue subnetwork. The network has one highly connected node (retinal bound Lys296), indicating that Lys296 can induce and regulate most other coevolved residues in a variety of locations. The coevolved network consists of a few modular clusters which have distinct functional roles. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.     

SUBTLEX-CH: Chinese Word and Character Frequencies Based on Film Subtitles

Background

Word frequency is the most important variable in language research. However, despite the growing interest in the Chinese language, there are only a few sources of word frequency measures available to researchers, and the quality is less than what researchers in other languages are used to.

Methodology

Following recent work by New, Brysbaert, and colleagues in English, French and Dutch, we assembled a database of word and character frequencies based on a corpus of film and television subtitles (46.8 million characters, 33.5 million words). In line with what has been found in the other languages, the new word and character frequencies explain significantly more of the variance in Chinese word naming and lexical decision performance than measures based on written texts.

Conclusions

Our results confirm that word frequencies based on subtitles are a good estimate of daily language exposure and capture much of the variance in word processing efficiency. In addition, our database is the first to include information about the contextual diversity of the words and to provide good frequency estimates for multi-character words and the different syntactic roles in which the words are used. The word frequencies are freely available for research purposes.     

Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

Background and Aims

ADP-glucose pyrophosphorylase (AGPase) is a key enzyme of starch biosynthesis. In the green plant lineage, it is composed of two large (LSU) and two small (SSU) sub-units encoded by paralogous genes, as a consequence of several rounds of duplication. First, our aim was to detect specific patterns of molecular evolution following duplication events and the divergence between monocotyledons and dicotyledons. Secondly, we investigated coevolution between amino acids both within and between sub-units.

Methods

A phylogeny of each AGPase sub-unit was built using all gymnosperm and angiosperm sequences available in databases. Accelerated evolution along specific branches was tested using the ratio of the non-synonymous to the synonymous substitution rate. Coevolution between amino acids was investigated taking into account compensatory changes between co-substitutions.

Key Results

We showed that SSU paralogues evolved under high functional constraints during angiosperm radiation, with a significant level of coevolution between amino acids that participate in SSU major functions. In contrast, in the LSU paralogues, we identified residues under positive selection (1) following the first LSU duplication that gave rise to two paralogues mainly expressed in angiosperm source and sink tissues, respectively; and (2) following the emergence of grass-specific paralogues expressed in the endosperm. Finally, we found coevolution between residues that belong to the interaction domains of both sub-units.

Conclusions

Our results support the view that coevolution among amino acid residues, especially those lying in the interaction domain of each sub-unit, played an important role in AGPase evolution. First, within SSU, coevolution allowed compensating mutations in a highly constrained context. Secondly, the LSU paralogues probably acquired tissue-specific expression and regulatory properties via the coevolution between sub-unit interacting domains. Finally, the pattern we observed during LSU evolution is consistent with repeated sub-functionalization under ‘Escape from Adaptive Conflict’, a model rarely illustrated in the literature.     

Coevolution in an Amazonian hummingbird-plant community

Relationships between hummingbirds and their food plants are often considered to have arisen through coevolution. However, while it is certainly the case that hummingbirds and plants are coevolved, it is not always clear to what extent coevolution has shaped community structure and the morphology of the birds and plants. Here I examine the hummingbird-plant community of a lowland Amazonian rainforest in southeastern Colombia and test hypotheses concerning coevolution and community structure. To determine the strength of interrelationships and the degree to which character displacement has occurred, the distributions of three floral traits (flowering phenology, nectar production and corolla length) and two hummingbird traits (culmen length and foraging ecology) have been statistically tested against random null models. Although the hummingbird-plant community at Matamatá is diverse and is highly likely to have a long shared evolutionary history, there is little evidence for pairwise coevolution. Instead, the community appears to have evolved through diffuse coevolution, resulting in guilds of hummingbirds and plants.     

An integrated system for studying residue coevolution in proteins

Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not much is known about their relative strengths and weaknesses. Also, subtle algorithmic details have discouraged implementing and comparing them. We addressed this issue by developing an integrated online system that enables comparative analyses with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods. A set of data preprocessing options are provided for improving the sensitivity and specificity of coevolution signal detection, including sequence weighting, residue grouping and the filtering of sequences, sites and site pairs. A total of more than 100 scoring variations are available. The system also provides facilities for studying the relationship between coevolution scores and inter-residue distances from a crystal structure if provided, which may help in understanding protein structures. AVAILABILITY: The system is available at http://coevolution.gersteinlab.org. The source code and JavaDoc API can also be downloaded from the web site.     

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.     

Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum.

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.     

ARMS RACE BETWEEN SELFISHNESS AND POLICING: TWO‐TRAIT QUANTITATIVE GENETIC MODEL FOR CASTE FATE CONFLICT IN EUSOCIAL HYMENOPTERA

Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two‐trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures’ propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures’ queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes.     

Obesity Research and Medical Journalism

With publication of the first number of volume 3 of OBESITY RESEARCH, the time is ripe to review where we have been and where we are going. There are now two widely accepted journals covering the field of obesity. It was not always so. Until 20 years ago only one journal had appeared with the word “obesity” in its title, and its publication was short lived (Table 1). The growth of medical journalism in this field over the past 20 years, as in other fields, is a reflection of the growth of scientific manpower and knowledge which had its beginnings in the scientific revolution more than 300 years ago. The frustration engendered by this steady and rapid growth of scientific journals has been reflected in the quotations from many scholars. Below are a few of these.     

Applications of sequence coevolution in membrane protein biochemistry

Recently, protein sequence coevolution analysis has matured into a predictive powerhouse for protein structure and function. Direct methods, which use global statistical models of sequence coevolution, have enabled the prediction of membrane and disordered protein structures, protein complex architectures, and the functional effects of mutations in proteins. The field of membrane protein biochemistry and structural biology has embraced these computational techniques, which provide functional and structural information in an otherwise experimentally-challenging field. Here we review recent applications of protein sequence coevolution analysis to membrane protein structure and function and highlight the promising directions and future obstacles in these fields. We provide insights and guidelines for membrane protein biochemists who wish to apply sequence coevolution analysis to a given experimental system.     

Rapidly fluctuating environments constrain coevolutionary arms races by impeding selective sweeps

Although pervasive, the impact of temporal environmental heterogeneity on coevolutionary processes is poorly understood. Productivity is a key temporally heterogeneous variable, and increasing productivity has been shown to increase rates of antagonistic arms race coevolution, and lead to the evolution of more broadly resistant hosts and more broadly infectious parasites. We investigated the effects of the grain of environmental heterogeneity, in terms of fluctuations in productivity, on bacteria–phage coevolution. Our findings demonstrate that environmental heterogeneity could constrain antagonistic coevolution, but that its effect was dependent upon the grain of heterogeneity, such that both the rate and extent of coevolution were most strongly limited in fine-grained, rapidly fluctuating heterogeneous environments. We further demonstrate that rapid environmental fluctuations were likely to have impeded selective sweeps of resistance alleles, which occurred over longer durations than the fastest, but not the slowest, frequency of fluctuations used. Taken together our results suggest that fine-grained environmental heterogeneity constrained the coevolutionary arms race by impeding selective sweeps.     

Phylogenetic analysis reveals a scattered distribution of autumn colours

Background and Aims

Leaf colour in autumn is rarely considered informative for taxonomy, but there is now growing interest in the evolution of autumn colours and different hypotheses are debated. Research efforts are hindered by the lack of basic information: the phylogenetic distribution of autumn colours. It is not known when and how autumn colours evolved.

Methods

Data are reported on the autumn colours of 2368 tree species belonging to 400 genera of the temperate regions of the world, and an analysis is made of their phylogenetic relationships in order to reconstruct the evolutionary origin of red and yellow in autumn leaves.

Key Results

Red autumn colours are present in at least 290 species (70 genera), and evolved independently at least 25 times. Yellow is present independently from red in at least 378 species (97 genera) and evolved at least 28 times.

Conclusions

The phylogenetic reconstruction suggests that autumn colours have been acquired and lost many times during evolution. This scattered distribution could be explained by hypotheses involving some kind of coevolutionary interaction or by hypotheses that rely on the need for photoprotection.Key words: Autumn colour, leaf colour, comparative analysis, coevolution, photoprotection, phylogenetic analysis     

Sexual Conflict and Sexually Antagonistic Coevolution in an Annual Plant

Background

Sexual conflict theory predicts sexually antagonistic coevolution of reproductive traits driven by conflicting evolutionary interests of two reproducing individuals. Most studies of the evolutionary consequences of sexual conflicts have, however, to date collectively investigated only a few species. In this study we used the annual herb Collinsia heterophylla to experimentally test the existence and evolutionary consequences of a potential sexual conflict over onset of stigma receptivity.

Methodology/Principal Findings

We conducted crosses within and between four greenhouse-grown populations originating from two regions. Our experimental setup allowed us to investigate male-female interactions at three levels of geographic distances between interacting individuals. Both recipient and pollen donor identity affected onset of stigma receptivity within populations, confirming previous results that some pollen donors can induce stigma receptivity. We also found that donors were generally better at inducing stigma receptivity following pollen deposition on stigmas of recipients from another population than their own, especially within a region. On the other hand, we found that donors did worse at inducing stigma receptivity in crosses between regions. Interestingly, recipient costs in terms of lowered seed number after early fertilisation followed the same pattern: the cost was apparent only if the pollen donor belonged to the same region as the recipient.

Conclusion/Significance

Our results indicate that recipients are released from the cost of interacting with local pollen donors when crossed with donors from a more distant location, a pattern consistent with a history of sexually antagonistic coevolution within populations. Accordingly, sexual conflicts may have important evolutionary consequences also in plants.     

Evaluating effects of divided hemispheric processing on word recognition in foveal and extrafoveal displays: the evidence from Arabic

Background

Previous studies have claimed that a precise split at the vertical midline of each fovea causes all words to the left and right of fixation to project to the opposite, contralateral hemisphere, and this division in hemispheric processing has considerable consequences for foveal word recognition. However, research in this area is dominated by the use of stimuli from Latinate languages, which may induce specific effects on performance. Consequently, we report two experiments using stimuli from a fundamentally different, non-Latinate language (Arabic) that offers an alternative way of revealing effects of split-foveal processing, if they exist.

Methods and Findings

Words (and pseudowords) were presented to the left or right of fixation, either close to fixation and entirely within foveal vision, or further from fixation and entirely within extrafoveal vision. Fixation location and stimulus presentations were carefully controlled using an eye-tracker linked to a fixation-contingent display. To assess word recognition, Experiment 1 used the Reicher-Wheeler task and Experiment 2 used the lexical decision task.

Results

Performance in both experiments indicated a functional division in hemispheric processing for words in extrafoveal locations (in recognition accuracy in Experiment 1 and in reaction times and error rates in Experiment 2) but no such division for words in foveal locations.

Conclusions

These findings from a non-Latinate language provide new evidence that although a functional division in hemispheric processing exists for word recognition outside the fovea, this division does not extend up to the point of fixation. Some implications for word recognition and reading are discussed.     

Predicting protein domain interactions from coevolution of conserved regions

The knowledge of protein and domain interactions provide crucial insights into their function within a cell. Several computational methods have been proposed to detect interactions between proteins and their constitutive domains. In this work, we focus on approaches based on correlated evolution (coevolution) of sequences of interacting proteins. In this type of approach, often referred to as the mirrortree method, a high correlation of evolutionary histories of two proteins is used as an indicator to predict protein interactions. Recently, it has been observed that subtracting the underlying speciation process by separating coevolution due to common speciation divergence from that due to common function of interacting pairs greatly improves the predictive power of the mirrortree approach. In this article, we investigate possible improvements and limitations of this method. In particular, we demonstrate that the performance of the mirrortree method that can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions). We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins.     

Plant coevolution: evidences and new challenges

Abstract

Coevolution has been defined as the reciprocal genetic change in interacting species owing to natural selection imposed by each on the other. The process of coevolution between plants and the surrounding biota – including viruses, fungi, bacteria, nematodes, insects, and mammals – is considered by many biologists to have generated much of the earth's biological diversity. While much of the discussion on plant coevolution focuses on single plant–enemy interactions, a wide array of other micro and macro coevolutive processes co-occur in the same individual plant, posing the question whether we should talk about plant coevolutions. In this review article, I begin by briefly discussing the framework of coevolution theory and explore the complexities of studying coevolution in natural conditions. Then I analyze the difference between plants, microbes and animal coevolution, by exploring the above- and below-ground behaviors.