Darwin’s Necessary Misfit and the Sloshing Bucket: The Evolutionary Biology of Emerging Infectious Diseases

Evolutionary studies suggest that the potential for rapid emergence of novel host–parasite associations is a “built-in feature” of the complex phenomenon that is Darwinian evolution. The current Emerging Infectious Disease (EID) crisis is thus a new manifestation of an old and repeating phenomenon. There is evidence that previous episodes of global climate change and ecological perturbation, broadly defined, throughout earth history have been associated with environmental disruptions that produce episodic bursts of new host–parasite associations, each of which would have been called an EID at the time of its first appearance. This perspective implies that there are many evolutionary accidents waiting to happen, requiring only the catalyst of climate change, species introductions, and the intrusion of humans into areas they have never inhabited before.     

Evolutionary epistemology as science

What credentials does evolutionary epistemology have as science? A judgement based on past performance, both in terms of advancing an empirical programme and further ng theory construction, is not much. This paper briefly outlines some of the research areas, both theoretical and empirical, that can be developed and that might secure for evolutionary epistemology a future in evolutionary biology.     

Evolutionary Theory and the Social uses of Biology

Stephen Jay Gould is rightly remembered for many different kinds of contributions to our intellectual life. I focus on his criticisms of uses of evolutionary ideas to defend inegalitarian doctrines and on his attempts to expand the framework of Darwinian evolutionary theory. I argue that his important successes in the former sphere are applications of the idea of local critique, grounded in careful attention to the details of the inegalitarian proposals. As he became more concerned with the second project, Gould was inclined to suggest that the abuses of evolutionary ideas rested on an insufficiently expanded Darwinism. I suggest that what is valuable in Gould's contribution to general evolutionary theory is the original claim about punctuated equilibrium (advanced, with Niles Eldredge in1972), and the careful defense of that claim through the accumulation of paleontological evidence. I try to show that the more ambitious program of a hierarchical expansion of neo-Darwinism is misguided, and that the endeavor to go beyond local critique fails.     

Evolutionary graph theory: breaking the symmetry between interaction and replacement

We study evolutionary dynamics in a population whose structure is given by two graphs: the interaction graph determines who plays with whom in an evolutionary game; the replacement graph specifies the geometry of evolutionary competition and updating. First, we calculate the fixation probabilities of frequency dependent selection between two strategies or phenotypes. We consider three different update mechanisms: birth-death, death-birth and imitation. Then, as a particular example, we explore the evolution of cooperation. Suppose the interaction graph is a regular graph of degree h, the replacement graph is a regular graph of degree g and the overlap between the two graphs is a regular graph of degree l. We show that cooperation is favored by natural selection if b/c>hg/l. Here, b and c denote the benefit and cost of the altruistic act. This result holds for death-birth updating, weak-selection and large population size. Note that the optimum population structure for cooperators is given by maximum overlap between the interaction and the replacement graph (g=h=l), which means that the two graphs are identical. We also prove that a modified replicator equation can describe how the expected values of the frequencies of an arbitrary number of strategies change on replacement and interaction graphs: the two graphs induce a transformation of the payoff matrix.     

车前属(Plantago L.)植物生态与进化生物学研究进展

车前属植物是理论生态学、生理生态学、进化生物学研究的理想材料。本文综述了近年来国内外学者在车前属生态学、进化生物学、系统分类学方面的研究概况。     

Proposal for Teaching Evolutionary Biology: A bridge between research and educational practice

We present quantitative results for the doctoral thesis of the first-named author of this article. The objective was to recommend and test a teaching proposal for core knowledge of evolutionary biology in secondary education. The focus of the study is ‘Problem cores in teaching’. The ‘Weaving evolutionary thinking’ teaching unit, designed for and tested in this study, entailed: selecting basic evolutionary knowledge from the model of evolution through variation and natural selection; designing a coordinated set of activities, teaching resources and evaluation tools; leading a process of teacher training; and building bridges between: the teaching model, research into the teaching of evolutionary biology, our own teaching experience and that of the secondary school teacher who participated in the project. The data collected through questionnaires show significant differences in favour of the experimental group, which means that the proposal may be favourably assessed in the context of Mexican education, in terms of feasibility, relevance and the pedagogical transformation of knowledge.     

Evolutionary dynamics of biological auctions

Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.     

Pharmacology,Genomics, and the Evolutionary Biology of Ageing

Aging is a multifold process affected by many genes and thus many biochemical pathways. This conclusion is underscored by the failure to find simple central controls for the aging process during the 20th Century. This situation poses a fundamental challenge to anti-aging medicine: how to develop effective therapies for a genomically complex pathology. We propose such a strategy. As a first step, we recommend the use of model systems in which significant genetic intervention is not proscribed or impractical. Second, we propose that work with such model systems begin with selected lines that have genetic enhancements that allow increased lifespan. Third, genomic methods should be used to identify a number of biochemical pathways for increasing lifespan. Fourth, biochemical pathways that have been identified in model systems would then be available for pharmaceutical development, first in rodents, eventually in a clinical human population. This may seem to be a cumbersome R&D strategy, but starting with human populations or inadequately pre-screened compounds would be unlikely to succeed because of the complexity of the aging problem.     

Evolutionary morphology and Evo-devo: Hierarchy and novelty

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology.     

芸薹属自交不亲和基因的分子生物学及进化模式

芸薹属的自交不亲和性是受单基因座、复等位基因控制的孢子体控制型。自交不亲和基因座位(S-locus)是由多个基因组成的复杂区域,称之为S多基因家族,其大多数成员分布于芸薹属的整个染色体组。目前已鉴定出100多个S等位基因,它们的起源分化始于一千万年前。S-座位上存在的多基因有3种：SRK,SLG和SCR／SPII;SRK和SLG在柱头中表达,SCR／SPII在雄蕊中表达。SRK蛋白在识别同类花粉的过程中起主要作用,而SLG蛋白增强了这种自交不亲和反应。SLG与SRK基因中编码S-结构域的核苷酸序列相似性程度高达85％～98％。基因转换可能是SLG和SRK的高度同源性能够得以保持的原因。SRK,SLG和SCR基因紧密相连,并表现出高水平的序列多样性。SRK与SLG基因间的距离很近,在20～25kb之间。在柱头和花粉中,自交不亲和等位基因之间的共显性关系要比显性和隐性关系更加普遍,这是芸薹属自交不亲和性的一大特点。自交不亲和基因的进化模式存在两种假说：双基因进化模式和中性变异体进化模式;可能存在几种不同的进化方式,它们共同在自然群体中新的S等位基因进化过程中起作用。     

Settlement Hierarchies and Political Complexity in Nonmarket Societies: The Formative Period of the Valley of Mexico

Archaeologists have long recognized that increases in political centralization often coincide with the growth of regional settlement hierarchies. Here I develop a theoretical model which explicitly relates certain aspects of political complexity to variation in settlement size. This model applies specifically to hierarchical societies without well-developed market economies—societies which Service would classify as chiefdoms and (perhaps) simple states. Using settlement data from the Formative Period Valley of Mexico, I show how this model is useful in measuring (1) the number of levels in a regional hierarchy, (2) the degree of political centralization, and (3) the relative amount of surplus food mobilized to support the political establishment.     

Evolutionary Developmental Biology: the Interaction of Developmental Biology,Evolutionary Biology,Paleontology, and Genomics

Paleontological Journal - Evolutionary developmental biology (evo-devo) formed due to the interactions of evolutionary biology, paleontology, and comparative genomics, analyzes the interrelations...     

Evolutionary synthesis from a cosmopolitan point of view: a commentary on the ideas of Reif, Junker and Hossfeld

Summary The analysis of the Evolutionary Synthesis by Reif, Junker and Hossfeld (2000, Theory in Biosciences 119: 41–91) draws attention to language barriers that however important are far from impenetrable. The Synthesis is better viewed as a restoration than a revolution, and as something that occurred gradually, with no particular goal.     

Measuring Evolutionary Constraints Through the Dimensionality of the Phenotype: Adjusted Bootstrap Method to Estimate Rank of Phenotypic Covariance Matrices

The potential and direction of phenotypic evolution is constrained by the distribution of genetic variation for the traits as described by the phenotypic (P) and genetic covariance matrices (G). The rank of the covariance matrix reflects the number of independent variational dimensions of the phenotype. Covariance matrices with less than full rank indicate lack of variation in some directions of the phenotype space and thus are an indication of absolute evolutionary constraints. Because selection acts upon phenotypic variation, the rank of P represents the upper limit of the dimensionality in G, relevant for selection response. The limitations of current methods to estimate matrix rank motivated us to analyze and adjust a bootstrap method and evaluate its performance by simulation. The results show that the modified bootstrap method (ABRE) gives reliable and rather conservative rank estimates when the sample size is sufficient for the number of variables studied (the sample size is at least five-fold the number of variables). Applying the method to various datasets suggests high phenotypic dimensionality in all cases. The analysis thus provides no evidence for absolute evolutionary constraints. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolutionary escape from the prisoner's dilemma

The classic prisoner's dilemma model of game theory is modified by introducing occasional variations on the options available to players. Mutation and selection of game options reliably change the game matrix, gradually, from a prisoner's dilemma game into a byproduct mutualism one, in which cooperation is stable, and "temptation to defect" is replaced by temptation to cooperate. This result suggests that when there are many different potential ways of interacting, exploring those possibilities may make escape from prisoner's dilemmas a common outcome in the world. A consequence is that persistent prisoner's dilemma structures may be less common than one might otherwise expect.     

Evolutionary stability of egg trading and parceling in simultaneous hermaphrodites: the chalk bass revisited

Several species of simultaneously hermaphroditic seabasses living on coral reefs mate by alternating male and female roles with a partner. This is known as egg trading, one of the classic and most widely cited examples of social reciprocity among animals. Some of the egg-trading seabass species, including the chalk bass, Serranus tortugarum, switch mating roles repeatedly, having subdivided their clutch of eggs into parcels offered to the partner for fertilization. Here we attempt to understand these dynamics as a pair of evolutionary games, modifying some previous approaches to better reflect the biological system. We find that the trading of egg clutches is evolutionarily stable via byproduct mutualism and resistant to invasion by rare individuals that take the male role exclusively. We note why and how parceling may reflect sexual conflict between individuals in the mating pair. We estimate evolutionarily stable parcel numbers and show how they depend on parameter values. Typically, two or more sequential parcel numbers are evolutionarily stable, though the lowest of these yields the highest fitness. Assuming that parcel numbers are adjusted to local conditions, we predict that parcel numbers in nature are inversely related both to mating group density (except at low density) and predation risk.     

Palaeontology and Evolutionary Developmental Biology: A Science of the Nineteenth and Twenty–first Centuries

A wind of change has swept through palaeontology in the past few decades. Contrast Sir Peter Medawar’s dismissive: ‘palaeontology is a particularly undemanding branch of science’ (as recalled by John Maynard Smith in Sabbagh 1999, p. 158) with ‘Palaeontology: grasping the opportunities in the science of the twenty–first century’, the title of a contribution to a special issue of Geobios by the Cambridge palaeontologist, Simon Conway Morris (1998a). The winds of change have come partly from palaeontologists seeking to broaden the impact of their studies and partly from biologists (neontologists) realizing the contributions that palaeontology can make to their disciplines. Consequently, impressions of past life preserved in stone are coming alive. Fossils are being described and analyzed using new tools and languages as the static fossil record becomes a record of transitions in patterns that can be explained and related to biological, ecological, climatic and tectonic changes. The latest addition is evolutionary developmental biology, or ‘evo–devo’, whose language provides a new basis upon which to interpret anatomical change, both materially and mechanistically. In this review I examine the major contributions made by palaeontology, how palaeontology has been linked to evolution and to embryology in the past, and how links with evo–devo have enlivened and will continue to enliven both palaeontology and evo–devo. Closer links between the two fields should illuminate important unresolved issues related to the origin of the metazoans (e.g. Why is there a conflict between molecular clocks and the fossil record in timing the metazoan radiation; were Precambrian metazoan ancestors similar to extant larvae or to miniature adults?) and to diversification of the metazoans (e.g. How do developmental constraints bias the direction of evolution; how do microevolutionary developmental processes relate to macroevolutionary changes?).     

Network properties, species abundance and evolution in a model of evolutionary ecology

We study the evolution of the network properties of a populated network embedded in a genotype space characterized by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution produces two distinct types of network. When a specific genotype is only able to influence a few other genotypes, the ecosystem consists of separate non-interacting clusters (i.e. isolated compartments) in genotype space. When different types may influence a large number of other sites, the network becomes one large interconnected cluster. The distribution of interaction strengths--but not the number of connections--changes significantly with time. We find that the species abundance is only realistic for a high level of species connectivity. This suggests that real ecosystems form one interconnected whole in which selection leads to stronger interactions between the different types. Analogies with niche and neutral theory and assembly models are also considered.