Evolutionary Epistemology, Social Epistemology, and the Demic Structure of Science

One of the principal difficulties in assessing Science as aProcess (Hull 1988) is determining the relationship between the various elements of Hull's theory. In particular, it is hard to understand precisely how conceptual selection is related to Hull's account of the social dynamics of science. This essay aims to clarify the relation between these aspects of his theory by examining his discussion of the``demic structure' of science. I conclude that the social account cando significant explanatory work independently of the selectionistaccount. Further, I maintain that Hull's treatment of the demicstructure of science points us toward an important set of issues insocial epistemology. If my reading of Science as a Process iscorrect, then most of Hull's critics (e.g., those who focus solelyon his account of conceptual selection) have ignored promisingaspects of his theory.     

Etiological Theories of Function: A Geographical Survey

Formulations of the essential commitment of the etiological theory of functions have varied significantly, with some individual authors' formulations even varying from one place to another. The logical geography of these various formulations is different from what is standardly assumed; for they are not stylistic variants of the same essential commitment, but stylistic variants of two non-equivalent versions of the etiological theory. I distinguish these strong and weak versions of the etiological theory (which differ with respect to the role of selection in their definitions of function), draw out their respective implications, and argue that the weak version is to be preferred to the strong.     

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 dynamics in structured populations

Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.     

Evolutionary dynamics of n-player games played by relatives

One of the core concepts in social evolution theory is kin selection. Kin selection provides a perspective to understand how natural selection operates when genetically similar individuals are likely to interact. A family-structured population is an excellent example of this, where relatives are engaged in social interactions. Consequences of such social interactions are often described in game-theoretical frameworks, but there is a growing consensus that a naive inclusive fitness accounting with dyadic relatedness coefficients are of limited use when non-additive fitness effects are essential in those situations. Here, I provide a general framework to analyse multiplayer interactions among relatives. Two important results follow from my analysis. First, it is generally necessary to know the n-tuple genetic association of family members when n individuals are engaged in social interactions. However, as a second result, I found that, for a special class of games, we need only measures of lower-order genetic association to fully describe its evolutionary dynamics. I introduce the concept of degree of the game and show how this degree is related to the degree of genetic association.     

黑莓的实生选优

南京中山植物园于1986年从美国引入一批黑莓品种赫尔（Hull）种子,培育出实生苗350株,其中无刺苗232株。经过8年实生选优,从中选出钟山17－13优株,并通过组培无性繁殖。其果实大,平均果重5．98g,最大9．7g,不仅远高于其他实生单株,也高于原品种赫尔。萌枝粗壮,具有较好的栽培性状,值得扩繁种植。     

生态群落物种共存的进化机制

本文概述了目前对生态群落的物种共存研究中存在的若干问题及动、植物群落物种共存机制的研究进展。植物群落的物种共存主要介绍与环境、种子再迁移、生态位分化、竞争平衡理论、种库假设、再生生态位等有关的几种假设、生态学上相似种的共存及“原”群落概念等。动物群落的物种共存机制主要从以下几方面叙述：（1）异质环境中的资源分割,主要指动物斑状滋养的不同利用;（2）避免竞争排斥的行为机制,如边缘效应、聚群效应、扩散行为、相互作用和干扰;（3）特化者和泛化者的共存,包括：竞争是物种向多功能进化的作用力、最佳觅食理论与生态学特化及特化概念的发展。最后指出进一步研究的方向。     

Evolutionary genetics of maternal effects

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population.     

Evolutionary history and climate conditions constrain the flower colours of woody plants in China

进化历史和气候条件共同影响中国木本植物花色的分布 本研究以中国木本植物为研究对象,主要探讨两个问题：(1)不同生活型物种花色组成的差异;(2)生物地理区、进化年龄和气候条件对不同花色地理分布格局的影响。研究使用7673种木本植物的物种分布数据和花色信息(分为白色、红色、黄色、黄绿色、绿色和蓝紫色),并结合属级系统进化树来比较不同生活型(包括灌木、乔木和藤本)物种花色组成的差异,分析不同生物地理区、进化年龄和现代气候对花色地理格局的影响。研究结果表明,与乔木和藤本植物相比,灌木具有更高比例 的由花青素着色的红色花和蓝紫色花物种。中国木本植物的花色地理格局受到区域效应和现代气候(尤其是降水和UVB辐射)的共同影响。倾向于蜂媒传粉的黄色花和蓝紫色花物种和由花青素着色、耐环境胁迫的红色花和蓝紫色花物种比例在中国西北部地区更高。绿色花物种的进化起源更早,但进化时间对花色地理格局的解释力很弱。这些结果说明中国木本植物花色的地理格局受到进化历史和现代环境的共同影响。     

Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates

Cathepsin L family, an important cysteine protease found in lysosomes, is categorized into cathepsins B, F, H, K, L, S, and W in vertebrates. This categorization is based on their sequence alignment and traditional functional classification, but the evolutionary relationship of family members is unclear. This study determined the evolutionary relationship of cathepsin L family genes in vertebrates through phylogenetic construction. Results showed that cathepsins F, H, S and K, and L and V were chronologically diverged. Tandem-repeat duplication was found to occur in the evolutionary history of cathepsin L family. Cathepsin L in zebrafish, cathepsins S and K in xenopus, and cathepsin L in mice and rats underwent evident tandem-repeat events. Positive selection was detected in cathepsin L-like members in mice and rats, and amino acid sites under positive selection pressure were calculated. Most of these sites appeared at the connection of secondary structures, suggesting that the sites may slightly change spatial structure. Severe positive selection was also observed in cathepsin V (L2) of primates, indicating that this enzyme had some special functions. Our work provided a brief evolutionary history of cathepsin L family and differentiated cathepsins S and K from cathepsin L based on vertebrate appearance. Positive selection was the specific cause of differentiation of cathepsin L family genes, confirming that gene function variation after expansion events was related to interactions with the environment and adaptability.     

Deconstructing Darwin: Evolutionary theory in context

The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwins contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory.     

The semantic approach to evolutionary theory

Paul Thompson, John Beatty, and Elisabeth Lloyd argue that attempts to resolve certain conceptual issues within evolutionary biology have failed because of a general adherence to the received view of scientific theories. They maintain that such issues can be clarified and resolved when one adopts a semantic approach to theories. In this paper, I argue that such conceptual issues are just as problematic on a semantic approach. Such issues arise from the complexity involved in providing formal accounts of theoretical laws and scientific explanations. That complexity is due to empirical and pragmatic considerations, not one's adherence to a particular formal approach to theories. This analysis raises a broader question. How can any formal account properly represent the complex nature of empirical phenomena?     

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline

Histones and their posttranslational modifications facilitate diverse chromatin functions in eukaryotes. Core histones (H2A, H2B, H3, and H4) package genomes after DNA replication. In contrast, variant histones promote specialized chromatin functions, including DNA repair, genome stability, and epigenetic inheritance. Previous studies have identified only a few H2B variants in animals; their roles and evolutionary origins remain largely unknown. Here, using phylogenomic analyses, we reveal the presence of five H2B variants broadly present in mammalian genomes. Three of these variants have been previously described: H2B.1, H2B.L (also called subH2B), and H2B.W. In addition, we identify and describe two new variants: H2B.K and H2B.N. Four of these variants originated in mammals, whereas H2B.K arose prior to the last common ancestor of bony vertebrates. We find that though H2B variants are subject to high gene turnover, most are broadly retained in mammals, including humans. Despite an overall signature of purifying selection, H2B variants evolve more rapidly than core H2B with considerable divergence in sequence and length. All five H2B variants are expressed in the germline. H2B.K and H2B.N are predominantly expressed in oocytes, an atypical expression site for mammalian histone variants. Our findings suggest that H2B variants likely encode potentially redundant but vital functions via unusual chromatin packaging or nonchromatin functions in mammalian germline cells. Our discovery of novel histone variants highlights the advantages of comprehensive phylogenomic analyses and provides unique opportunities to study how innovations in chromatin function evolve.     

Evolutionary history of an adaptive radiation in species pairs of threespine sticklebacks (Gasterosteus): insights from mitochondrial DNA

Species pairs of threespine stickleback, Gasterosteus aculeatus, co-exist in several lakes in the Strait of Georgia, southwestern British Columbia. One species, ‘benthics’ is robust-bodied and is morphologically and behaviourally specialized for benthivory. The other species, ‘limnetics’ is specialized for planktivory in open-water habitats of the lakes. We examined mitochondrial DNA restriction site variation in benthic and limnetic sticklebacks as well as in solitary freshwater, anadromous (sea-run), and marine populations to test: (i) if benthic and limnetic pairs have evolved only once or multiple times (parallel evolution) and (ii) if the species have evolved sympatrically, or allopatrically from ‘double invasions’ of lakes by ancestral anadromous/marine sticklebacks. Stickleback mtDNA comprised a single clade with a low (mean = 0.40%) degree of sequence divergence among the 77 haplotypes resolved. Most nucleotide diversity (97%) was found within (rather than among) populations of anadromous/marine sticklebacks whereas most diversity (77%) was found among populations in freshwater sticklebacks. Significant differences in haplotype frequencies were found between benthics and limnetics in three of the four species pair lakes examined, but in all cases the pairs within lakes were characterized by unique assemblages of closely related haplotypes. Hierarchical clustering of divergence estimates suggested that comparable species from different lakes have originated independently in all lakes because in no case did comparable species from different lakes cluster together. Divergent species within lakes tended to be more closely related to one another than to species in other lakes and there were two cases were benthics and limnetics within a particular lake were monophyletic. In two of the four two-species lakes, limnetics were less divergent from putative ancestral anadromous/marine stickleback as predicted by the double invasion hypothesis, but in the two other lakes benthics were less divergent. Our data argue strongly that the species pairs have evolved independently in each lake were they now co-exist. Further, in two lakes our data are consistent with the species having evolved by sympatric divergence, but allopatric divergence followed by introgression of mtDNA that has obscured ancestral relationships cannot be discounted completely. Finally, despite remaining uncertainty about the geography of speciation, the species appear to have evolved in the face of gene flow arguing that natural selection acting on trophic ecology has been a major component of ecological speciation in sticklebacks.     

云南被子植物蔷薇分支的进化历史研究

本文以云南被子植物蔷薇分支为研究对象,基于物种间的演化关系,结合其地理分布,从进化历史的角度探讨了物种、特有种、受威胁物种的种类组成及系统发育组成的分布格局,并整合自然保护地的空间分布,对生物多样性的重点保护区域进行识别。结果显示：云南被子植物蔷薇分支的物种密度与系统发育多样性、特有种密度、受威胁物种密度均呈显著正相关,云南南部和西北部是物种丰富度与系统发育多样性最为丰富的区域;就云南整体而言,蔷薇分支的标准化系统发育多样性较低;云南南部、东南部、西北部是蔷薇分支的重点保护区域。     

Evolutionary Dynamics of Seed Size and Seedling Competitive Ability

We present a model for the evolutionary dynamics of seed size when there is a trade-off between seed size and seed number, and seedlings from large seeds are better competitors and have a higher precompetitive survival than seedlings from small seeds. We find that strong competitive asymmetry, high resource levels, and intermediate harshness of the precompetitive environment favor coexistence of plants with different seed sizes. If the evolution of seed size is mutation-limited and single mutations have only a small phenotypic effect, then an initially monomorphic population reaches the final evolutionarily stable polymorphic state through one or more discrete evolutionary branching events. At each such branching event, a given lineage already present in the population divides into two phenotypically diverging daughter lines, each with its own seed size. If the precompetitive survival of seeds and seedlings is high for small and large seeds alike, however, evolutionary branching may be followed by the extinction of one or more lineages. Various results presented here are model-independent and point the way to a more general evolutionary bifurcation theory describing how the number and stability properties of evolutionary equilibria may change as a consequence of changes in model parameters.     

Evolutionary analyses of the avirulence effector AvrStb6 in global populations of Zymoseptoria tritici identify candidate amino acids involved in recognition

We analysed the population genetic diversity of AvrStb6, the first avirulence gene cloned from the wheat pathogen Zymoseptoria tritici, using 142 Z. tritici strains sampled from four wheat fields growing on three continents. Although AvrStb6 was located in a recombination hotspot, it was found in every strain, with 71 polymorphic sites that produced 41 distinct DNA haplotypes encoding 30 AvrStb6 protein isoforms. An AvrStb6 homologue was found in the closest known relative, Z. pseudotritici, but not in three other closely related Zymoseptoria species, indicating that this gene has emerged in Zymoseptoria quite recently. Two AvrStb6 homologues with nucleotide similarities greater than 70% were identified on chromosome 10 in all Z. tritici isolates, suggesting that AvrStb6 belongs to a multigene family of candidate effectors that has expanded recently through gene duplication. The AvrStb6 sequences exhibited strong evidence for non‐neutral evolution, including a large number of non‐synonymous mutations, with significant positive diversifying selection operating on nine of the 82 codons. It appears that balancing selection is operating across the entire gene in natural field populations. There was also evidence for co‐evolving codons within the gene that may reflect compensatory mutations associated with the evasion of recognition by Stb6. Intragenic recombination also appears to have affected the diversity of AvrStb6.     

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.     

Evolutionary quantitative genetics of nonlinear developmental systems

In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium‐term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time‐steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances.