Cooperation and competition in pathogenic bacteria

Explaining altruistic cooperation is one of the greatest challenges for evolutionary biology. One solution to this problem is if costly cooperative behaviours are directed towards relatives. This idea of kin selection has been hugely influential and applied widely from microorganisms to vertebrates. However, a problem arises if there is local competition for resources, because this leads to competition between relatives, reducing selection for cooperation. Here we use an experimental evolution approach to test the effect of the scale of competition, and how it interacts with relatedness. The cooperative trait that we examine is the production of siderophores, iron-scavenging agents, in the pathogenic bacterium Pseudomonas aeruginosa. As expected, our results show that higher levels of cooperative siderophore production evolve in the higher relatedness treatments. However, our results also show that more local competition selects for lower levels of siderophore production and that there is a significant interaction between relatedness and the scale of competition, with relatedness having less effect when the scale of competition is more local. More generally, the scale of competition is likely to be of particular importance for the evolution of cooperation in microorganisms, and also the virulence of pathogenic microorganisms, because cooperative traits such as siderophore production have an important role in determining virulence.     

Evolution of an obligate social cheater to a superior cooperator

Obligate relationships have evolved many times and can be parasitic or mutualistic. Obligate organisms rely on others to survive and thus coevolve with their host or partner. An important but little explored question is whether obligate status is an evolutionarily terminal condition or whether obligate lineages can evolve back to an autonomous lifestyle. The bacterium Myxococcus xanthus survives starvation by the social development of spore-bearing fruiting bodies. Some M. xanthus genotypes defective at fruiting body development in isolation can nonetheless exploit proficient genotypes in chimaeric groups. Here we report an evolutionary transition from obligate dependence on an altruistic host to an autonomous mode of social cooperation. This restoration of social independence was caused by a single mutation of large effect that confers fitness superiority over both ancestral genotypes, including immunity from exploitation by the ancestral cheater. Thus, a temporary state of obligate cheating served as an evolutionary stepping-stone to a novel state of autonomous social dominance.     

Monkeys reject unequal pay

During the evolution of cooperation it may have become critical for individuals to compare their own efforts and pay-offs with those of others. Negative reactions may occur when expectations are violated. One theory proposes that aversion to inequity can explain human cooperation within the bounds of the rational choice model, and may in fact be more inclusive than previous explanations. Although there exists substantial cultural variation in its particulars, this 'sense of fairness' is probably a human universal that has been shown to prevail in a wide variety of circumstances. However, we are not the only cooperative animals, hence inequity aversion may not be uniquely human. Many highly cooperative nonhuman species seem guided by a set of expectations about the outcome of cooperation and the division of resources. Here we demonstrate that a nonhuman primate, the brown capuchin monkey (Cebus apella), responds negatively to unequal reward distribution in exchanges with a human experimenter. Monkeys refused to participate if they witnessed a conspecific obtain a more attractive reward for equal effort, an effect amplified if the partner received such a reward without any effort at all. These reactions support an early evolutionary origin of inequity aversion.     

Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae

Cooperation is central to many major transitions in evolution, including the emergence of eukaryotic cells, multicellularity and eusociality. Cooperation can be destroyed by the spread of cheater mutants that do not cooperate but gain the benefits of cooperation from others. However, cooperation can be preserved if cheaters are facultative, cheating others but cooperating among themselves. Several cheater mutants have been studied before, but no study has attempted a genome-scale investigation of the genetic opportunities for cheating. Here we describe such a screen in a social amoeba and show that cheating is multifaceted by revealing cheater mutations in well over 100 genes of diverse types. Many of these mutants cheat facultatively, producing more than their fair share of spores in chimaeras, but cooperating normally when clonal. These findings indicate that phenotypically stable cooperative systems may nevertheless harbour genetic conflicts. The opportunities for evolutionary moves and countermoves in such conflicts may select for the involvement of multiple pathways and numerous genes.     

Evolution of cooperation and conflict in experimental bacterial populations

A fundamental problem in biology is the evolutionary transition from single cells to multicellular life forms. During this transition the unit of selection shifts from individual cells to groups of cooperating cells. Although there is much theory, there are few empirical studies. Here we describe an evolutionary transition that occurs in experimental populations of Pseudomonas fluorescens propagated in a spatially heterogeneous environment. Cooperating groups are formed by over-production of an adhesive polymer, which causes the interests of individuals to align with those of the group. The costs and benefits of cooperation, plus evolutionary susceptibility to defecting genotypes, were analysed to determine conformation to theory. Cooperation was costly to individuals, but beneficial to the group. Defecting genotypes evolved in populations founded by the cooperating type and were fitter in the presence of this type than in its absence. In the short term, defectors sabotaged the viability of the group; but these findings nevertheless show that transitions to higher orders of complexity are readily achievable, provide insights into the selective conditions, and facilitate experimental analysis of the evolution of individuality.     

Developmental cheating in the social bacterium Myxococcus xanthus

Cheating is a potential problem in any social system that depends on cooperation and in which actions that benefit a group are costly to individuals that perform them. Genetic mutants that fail to perform a group-beneficial function but that reap the benefits of belonging to the group should have a within-group selective advantage, provided that the mutants are not too common. Here we show that social cheating exists even among prokaryotes. The bacterium Myxococcus xanthus exhibits several social behaviours, including aggregation of cells into spore-producing fruiting bodies during starvation. We examined a number of M. xanthus genotypes that were defective for fruiting-body development, including several lines that evolved for 1,000 generations under asocial conditions and others carrying defined mutations in developmental pathways, to determine whether they behaved as cheaters when mixed with their developmentally proficient progenitor. Clones from several evolved lines and two defined mutants exhibited cheating during development, being overrepresented among resulting spores relative to their initial frequency in the mixture. The ease of finding anti-social behaviours suggests that cheaters may be common in natural populations of M. xanthus.     

“一带一路”背景下基于知识溢出视角的企业动态合作行为演化博弈分析

"一带一路"战略的逐步推进使得企业与企业之间的合作突破了地域、国别和文化的限制。在此背景下,基于知识溢出视角,针对企业间复杂动态合作行为演化问题,在有限理性的前提下,运用演化博弈理论,通过构建演化博弈模型,对企业动态合作行为演化路径进行了分析,对影响企业合作策略选择的作用机理进行了研究。研究发现:合作双方的策略选择与初始支付矩阵有关,也与支付矩阵的初始参数设置有关。其中,在一定范围内,增大合作收益系数,减小合作风险,降低合作成本有利于企业展开合作活动,实现合作共赢的最终目标。最后根据本文研究结果,对政府及企业提出了相关政策建议。     

Social diversity promotes the emergence of cooperation in public goods games

Humans often cooperate in public goods games and situations ranging from family issues to global warming. However, evolutionary game theory predicts that the temptation to forgo the public good mostly wins over collective cooperative action, and this is often also seen in economic experiments. Here we show how social diversity provides an escape from this apparent paradox. Up to now, individuals have been treated as equivalent in all respects, in sharp contrast with real-life situations, where diversity is ubiquitous. We introduce social diversity by means of heterogeneous graphs and show that cooperation is promoted by the diversity associated with the number and size of the public goods game in which each individual participates and with the individual contribution to each such game. When social ties follow a scale-free distribution, cooperation is enhanced whenever all individuals are expected to contribute a fixed amount irrespective of the plethora of public goods games in which they engage. Our results may help to explain the emergence of cooperation in the absence of mechanisms based on individual reputation and punishment. Combining social diversity with reputation and punishment will provide instrumental clues on the self-organization of social communities and their economical implications.     

Transformation and diversification in early mammal evolution

Evolution of the earliest mammals shows successive episodes of diversification. Lineage-splitting in Mesozoic mammals is coupled with many independent evolutionary experiments and ecological specializations. Classic scenarios of mammalian morphological evolution tend to posit an orderly acquisition of key evolutionary innovations leading to adaptive diversification, but newly discovered fossils show that evolution of such key characters as the middle ear and the tribosphenic teeth is far more labile among Mesozoic mammals. Successive diversifications of Mesozoic mammal groups multiplied the opportunities for many dead-end lineages to iteratively evolve developmental homoplasies and convergent ecological specializations, parallel to those in modern mammal groups.     

The coevolution of choosiness and cooperation

Explaining the rise and maintenance of cooperation is central to our understanding of biological systems and human societies. When an individual's cooperativeness is used by other individuals as a choice criterion, there can be competition to be more generous than others, a situation called competitive altruism. The evolution of cooperation between non-relatives can then be driven by a positive feedback between increasing levels of cooperativeness and choosiness. Here we use evolutionary simulations to show that, in a situation where individuals have the opportunity to engage in repeated pairwise interactions, the equilibrium degree of cooperativeness depends critically on the amount of behavioural variation that is being maintained in the population by processes such as mutation. Because our model does not invoke complex mechanisms such as negotiation behaviour, it can be applied to a wide range of species. The results suggest an important role of lifespan in the evolution of cooperation.     

Spatial structure often inhibits the evolution of cooperation in the snowdrift game

Understanding the emergence of cooperation is a fundamental problem in evolutionary biology. Evolutionary game theory has become a powerful framework with which to investigate this problem. Two simple games have attracted most attention in theoretical and experimental studies: the Prisoner's Dilemma and the snowdrift game (also known as the hawk-dove or chicken game). In the Prisoner's Dilemma, the non-cooperative state is evolutionarily stable, which has inspired numerous investigations of suitable extensions that enable cooperative behaviour to persist. In particular, on the basis of spatial extensions of the Prisoner's Dilemma, it is widely accepted that spatial structure promotes the evolution of cooperation. Here we show that no such general predictions can be made for the effects of spatial structure in the snowdrift game. In unstructured snowdrift games, intermediate levels of cooperation persist. Unexpectedly, spatial structure reduces the proportion of cooperators for a wide range of parameters. In particular, spatial structure eliminates cooperation if the cost-to-benefit ratio of cooperation is high. Our results caution against the common belief that spatial structure is necessarily beneficial for cooperative behaviour.     

企业-科研机构合作创新的演化博弈分析

企业与科研机构的合作创新是企业获取技术的一种重要手段。该文运用演化博弈基本理论和模型对企业与科研机构间合作创新问题进行研究,分析了企业面临科研机构不同价值类型的科研成果在技术交易与商业化协作2种合作方式之间的策略选择趋势;以及科研机构为应付企业的2种合作方式对科研成果价值类型的策略选择;并进一步说明了我国高风险科研项目合作困难的深层次原因。     

复杂系统中的合作演化与自组织斑图

目前,复杂系统中大量个体的集体行为在社会学、生物学和物理学领域备受关注.对这些集体行为的研究中,合作涌现和自组织斑图的研究尤为瞩目.基于此,简要介绍国内这一领域的相关研究进展,包括基于演化博弈探讨自私个体间的合作行为和相互竞争物种间的自组织斑图.     

活跃连接下两个水平上的合作进化

本文研究活跃链接下两个水平（即组选择）的合作进化动态．给出了弱选择下策略的固定概率及策略更有优势的条件．然后以囚徒困境为例讨论了促进合作行为进化的条件，即如果支付收益比与总体内组数、组容量及各策略间接触率满足一定的不等式，则有利于合作行为的进化．最后，本文对模型进行了数值模拟，结果表明，本文模型可以有效促进合作行为的进化．     

基于二阶声誉测度的自组织网络合作激励机制

将二阶声誉测度Standing应用到自组织网络的合作激励机制中,设计了一种基于Standing的包括服务和声誉管理的分布式合作管理协议,克服了间接互惠所面临的二阶搭便车问题.数学分析和模拟实验表明,在二阶声誉作用下,区分策略是演化博弈惟一的进化稳定策略,从而促进了用户的合作.同时,采用完全的分布方式所构建的可信第三方架构能够有效应对合谋、虚假的声誉反馈与声誉提供等欺骗行为.该合作机制在一般的动态环境中具有良好的适应性.     

完全信息与不完全信息下供应链合作伙伴演化

运用间接演化方法对完全信息和不完全信息情况下供应链合作伙伴(supply chain partner-ships,SCP)系统的演化过程进行了研究.首先把SCP系统企业声誉引入企业效用函数,提出了完全信息和不完全信息情况下SCP系统企业合作偏好度演化模型.然后,基于演化博弈中演化稳定策略概念,运用间接演化方法分别研究了完全信息和不完全信息情况下SCP系统企业合作偏好度的内在演化机制.结果发现,SCP系统的演化过程与企业群体是否具有完全信息相关.完全信息情况下SCP系统将演化成为链状模型,不完全信息情况下SCP系统将演化成为网状模型,并且企业合作偏好度随着企业的生产技术水平和企业的相关程度的不同而变化.     

Birds have paedomorphic dinosaur skulls

The interplay of evolution and development has been at the heart of evolutionary theory for more than a century. Heterochrony—change in the timing or rate of developmental events—has been implicated in the evolution of major vertebrate lineages such as mammals, including humans. Birds are the most speciose land vertebrates, with more than 10,000 living species representing a bewildering array of ecologies. Their anatomy is radically different from that of other vertebrates. The unique bird skull houses two highly specialized systems: the sophisticated visual and neuromuscular coordination system allows flight coordination and exploitation of diverse visual landscapes, and the astonishing variations of the beak enable a wide range of avian lifestyles. Here we use a geometric morphometric approach integrating developmental, neontological and palaeontological data to show that the heterochronic process of paedomorphosis, by which descendants resemble the juveniles of their ancestors, is responsible for several major evolutionary transitions in the origin of birds. We analysed the variability of a series of landmarks on all known theropod dinosaur skull ontogenies as well as outgroups and birds. The first dimension of variability captured ontogeny, indicating a conserved ontogenetic trajectory. The second dimension accounted for phylogenetic change towards more bird-like dinosaurs. Basally branching eumaniraptorans and avialans clustered with embryos of other archosaurs, indicating paedomorphosis. Our results reveal at least four paedomorphic episodes in the history of birds combined with localized peramorphosis (development beyond the adult state of ancestors) in the beak. Paedomorphic enlargement of the eyes and associated brain regions parallels the enlargement of the nasal cavity and olfactory brain in mammals. This study can be a model for investigations of heterochrony in evolutionary transitions, illuminating the origin of adaptive features and inspiring studies of developmental mechanisms.     

生产商、批发商和销售商信息合作行为的演化博弈

针对低碳农产品供应链信息共享机制不完全与合作商之间存在博弈的现象,提出生产商、批发商和销售商信息合作演化路径,为了探究供应商信息合作的因素和利益关系,构建 3 种信息合作演化博弈模 型;首先,求解出生产商与批发商合作模型和批发商与销售商合作模型以及 3 方信息合作模型下的演化博弈 均衡解,通过对模型稳定性的分析,得到在供应链成员行为决策和期望利润驱使下系统整体随时间变化的动 态趋势;然后,将不同信息合作下的决策行为进行仿真分析,并对比3种模型,探索得出均衡策略和影响因素 的作用原理;最后研究结论表明:选择合作收益大于非合作情况下的收益,并且演化博弈系统最终趋向于合 作博弈策略,使总体和个体达到收益最大化。     

The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ～94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.     

农户环保合作的演化博弈分析

通过演化博弈理论分析农户环保博弈系统的演化过程与均衡状态, 首先建立复制者动态方程, 分析系统的演化稳定性; 然后讨论影响系统的随机因素, 在此基础上建立随机演化博弈模型, 分析系统的随机演化动态和随机稳定性。结果表明, 环保合作能否成为系统演化的结果, 取决于两方面: 1) 农户在考虑环保行为的成本、收益以及农户认为环保行为的正外部性给自身造成的损失后, 所得到的净收益; 2) 博弈过程的惯例。因此要促进制度向农户环保合作制度演进, 可以采取选择性激励措施, 增加采取环保行为农户的收益, 选择性激励措施的供给者承担制度变迁的主要成本; 同时建立行为重复机制, 使有记忆的博弈中环保合作成为唯一惯例, 行为重复机制的提供者承担制度变迁的主要成本。