Covarion structure in plastid genome evolution: a new statistical test

Covarion models of molecular evolution allow the rate of evolution of a site to vary through time. There are few simple and effective tests for covarion evolution, and consequently, little is known about the presence of covarion processes in molecular evolution. We describe two new tests for covarion evolution and demonstrate with simulations that they perform well under a wide range of conditions. A survey of covarion evolution in sequenced plastid genomes found evidence of covarion drift in at least 26 out of 57 genes. Covarion evolution is most evident in first and second codon positions of the plastid genes, and there is no evidence of covarion evolution in third codon positions. Therefore, the significant covarion tests are likely due to changes in the selective constraints of amino acids. The frequency of covarion evolution within the plastid genome suggests that covarion processes of evolution were important in generating the observed patterns of sequence variation among plastid genomes.     

发育重演律与生物进化

发育重演律是生物个体发育的一般规律,该规律认为生物个体的发育是类囊胚不断形成和演化的过程,并认为生物进化亦是类囊胚不断形成和演化的过程.因类囊胚层级不断增加而导致的生物体结构复杂程度提高的演化为纵向进化,而不能提高生物体复杂程度的演化为横向演化,生物的纵向进化具有周期性.生物种系进化与个体发育之间具有严格的对应关系,一个物种经历的纵向进化的周期数与该物种所属个体完成发育所经历的细胞分化的周期数相等.     

Relationships among Teachers’ Knowledge and Beliefs Regarding the Teaching of Evolution: A Case for Turkey

The research study investigated the possible associations among science and biology teachers?? knowledge and belief variables concerning teaching evolution in science and biology classes. Specifically, this study examined how a set of variables including teachers?? understanding of evolution and nature of science (NOS) is related to the set of variables including teachers?? acceptance of evolution and perceptions of teaching evolution (i.e., perceptions of the necessity of addressing evolution in their classrooms, perceptions of the factors that impede addressing evolution in their classrooms, and personal science teaching efficacy beliefs regarding evolution). Data were collected from science and biology teachers through administration of Evolution Content Knowledge Test, Measure of Acceptance of the Theory of Evolution, Nature of Science as Argument Questionnaire and Teachers?? Perceptions of Teaching Evolution Scale. Canonical correlation analysis findings suggested that teachers who had thorough understanding of evolution and NOS were likely to both accept the scientific validity of evolution and believe the necessity of addressing evolution in the classrooms. On the other hand, teachers with thorough understanding of evolution and NOS did not necessarily believe that they have a stronger sense of self-efficacy beliefs regarding teaching evolution and that there are fewer obstacles to addressing evolution in the classroom. The research is significant in that it provides empirical evidence clarifying the interactions between teachers?? understanding and beliefs in teaching evolution. Implications for science teacher education are discussed.     

Perspective: reverse evolution

For some time, the reversibility of evolution was primarily discussed in terms of comparative patterns. Only recently has this problem been studied using experimental evolution over shorter evolutionary time frames. This has raised questions of definition, experimental procedure, and the hypotheses being tested. Experimental evolution has provided evidence for multiple population genetic mechanisms in reverse evolution, including pleiotropy and mutation accumulation. It has also pointed to genetic factors that might prevent reverse evolution, such as a lack of genetic variability, epistasis, and differential genotype-by-environment interactions. The main focus of this perspective is on laboratory studies and their relevance to the genetics of reverse evolution. We discuss reverse evolution experiments with Drosophila, bacterial, and viral populations. Field studies of the reverse evolution of melanism in the peppered moth are also reviewed.     

A field guide for teaching evolution in the social sciences

The theory of evolution by natural selection has begun to revolutionize our understanding of perception, cognition, language, social behavior, and cultural practices. Despite the centrality of evolutionary theory to the social sciences, many students, teachers, and even scientists struggle to understand how natural selection works. Our goal is to provide a field guide for social scientists on teaching evolution, based on research in cognitive psychology, developmental psychology, and education. We synthesize what is known about the psychological obstacles to understanding evolution, methods for assessing evolution understanding, and pedagogical strategies for improving evolution understanding. We review what is known about teaching evolution about nonhuman species and then explore implications of these findings for the teaching of evolution about humans. By leveraging our knowledge of how to teach evolution in general, we hope to motivate and equip social scientists to begin teaching evolution in the context of their own field.     

体内连续进化技术的研究进展

实验室进化是遗传育种、提高微生物性能的重要方式。近几十年来,实验室进化的方法快速发展,应用也越来越广泛,但是常见的菌株进化策略以及针对特定蛋白的进化存在突变过程不连续,需要多轮操作、工作量大等缺点。微生物突变和筛选技术的进步促进了体内连续进化的发展,大大提高了实验室进化的效率。体内连续进化技术实现了体内突变,完美地把突变与筛选相结合,以最少的人工干预进化出特定表型。文中总结了近年来在微生物底盘中开发的基因组范围的体内连续进化技术,以及独立于基因组的针对特定蛋白的体内连续进化技术,主要对这些技术实现体内连续突变的原理及其相关应用进行了介绍。在此基础上,分析了现有技术的优缺点,并对体内连续进化技术的发展进行了展望。     

The evolution of plant development

There has been much recent interest in the evolution of plant development and especially in trying to understand the developmental genetic basis of morphological evolution. Significant progress has been made in understanding the evolution of floral organization and the mechanisms that might underlie the evolution of compound leaves and inflorescence morphology. These advances are reinforcing the idea that phenotypic evolution can proceed via changes at few loci of large effect and that promoter evolution may be an important and frequent mechanism.     

Thoughts on the cultural evolution of man. Developmental imprinting and transgenerational effect

The biological evolution of man stopped since it has been conveyed to the objects, created by man. This paper introduces the concept of "conveyed evolution". Being part of the cultural evolution, the conveyed evolution is a continuation of the biological one. There are several similarities between the laws of biological and conveyed evolution, albeit the differences are important as well. Some laws of the conveyed evolution are described here. The conveyed evolution has man-made repair mechanisms (medicine, protection of environment) which defend man from harm. Man's fragility limits the progress of conveyed evolution. However, artificial compounds or environmental pollutants which are provoked by the conveyed evolution induce chemical (hormonal) imprinting in the developmental critical periods, which is transmitted to the progeny generations (transgenerational effect). This could cause evolutionary alterations without mutation.     

We Know in Part: James McCosh on Evolution and Christian Faith

James McCosh (1811–1894), president of Princeton College from 1868 to 1888, played a significant role in the American reception of evolution in the late 1800s – he was one of the more prominent clergyman to assuage the public’s fears of evolution while incorporating evolution into a conservative Christian worldview. McCosh was a prolific writer, whose books document his intellectual journey from hostility to acceptance of evolution. Three things will stand out in this overview that have not been emphasized in detail in other works: (1) James McCosh’s perspective on evolution dramatically changed over time; (2) McCosh’s motivations for engaging in the evolution-religion debate serve to clear up confusion regarding McCosh’s final position on evolution; and (3) the theological and philosophical basis for McCosh’s acceptance of evolution was established while McCosh was still hostile to evolution. His theological background therefore ‘pre-adapted’ him for evolution, and he was able to preach theology and evolution without substantially altering his theology.     

Muslims and evolution: a study of Pakistani physicians in the United States

This study investigated the views of Pakistani-American medical doctors regarding biological evolution. We used a mixed-methods approach, chiefly consisting of a short interview that presented evolution in the contexts of microbial, animal, and human evolution; evolution's acceptability or unacceptability to Muslims; and evolution's relevance to medicine. The participants were 23 doctors attending a convention in the United States. Fourteen participants accepted evolution, three rejected evolution, and six held other views. While a majority of participants indicated that they accepted evolution, a slightly smaller plurality accepted human evolution. A majority of participants, including some who did not wholly accept or reject evolution, thought that one could mutually accept evolution and also believe in Allah. Nearly every participant, including two who rejected evolution, thought that evolution was relevant to medicine. We find that participants assigned a plurality of meanings to the theory that depended on interactions between a participant’s perception of religion, science, medicine, and a host of other cultural influences. This study is the first of a collection of studies carried out by the authors, who collected data with the same instrument in five other countries with significant populations of Muslim doctors and medical students.     

Experimental evolution: experimental evolution and evolvability

The suggestion that there are characteristics of living organisms that have evolved because they increase the rate of evolution is controversial and difficult to study. In this review, we examine the role that experimental evolution might play in resolving this issue. We focus on three areas in which experimental evolution has been used previously to examine questions of evolvability; the evolution of mutational supply, the evolution of genetic exchange and the evolution of genetic architecture. In each case, we summarize what studies of experimental evolution have told us so far and speculate on where progress might be made in the future. We show that, while experimental evolution has helped us to begin to understand the evolutionary dynamics of traits that affect evolvability, many interesting questions remain to be answered.     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

比较基因组学在哺乳动物进化研究中的应用

哺乳动物经过长期进化,使其基因组在结构和功能上存在着明显的差异,构成了表型进化的基础。随着人类、部分哺乳动物基因组测序的完成,以比较基因组学为主要研究手段的哺乳动物进化研究应运而生,从而为在基因组水平上深入认识哺乳动物进化关系、揭示生命的起源和进化提供依据。对比较基因组学的主要研究方法进行了综述,进而探讨其在哺乳动物进化研究中的应用,并对哺乳动物比较基因组学的发展进行了展望。     

On some aspects of parallel evolution in Chelicerata

A study is made of some aspects of parallel evolution in Chelicerata. Definitions are given of parallel evolution, convergence, homology and analogy. It is pointed out that the concept of parallel evolution (parallelism) is initially formed in an empirical way, and that a judgment must be based on formal criteria. Particular attention is paid to the rôle of gene regulation in parallel evolution, to the special case of convergence as a result of heterologous regulatory mechanisms, to parallel evolution in homonomous structures (and the superposition of parallelisms and divergences), and to parallelism in the evolution of characters used in higher classification.     

Influence of evolution on the stability of ecological communities

In randomly assembled communities, diversity is known to have a destabilizing effect. Evolution may affect this result, but our theoretical knowledge of its role is mostly limited to models of small food webs. In the present article, I introduce evolution in a two-species Lotka-Volterra model in which I vary the interaction type and the cost constraining evolution. Regardless of the cost type, evolution tends to stabilize the dynamics more often in trophic interactions than for mutualism or competition. I then use simulations to study the effect of evolution in larger communities that contain all interaction types. Results suggest that evolution usually stabilizes the dynamics. This stabilizing effect is stronger when evolution affects trophic interactions, but happens for all interaction types. Stabilization decreases with diversity and evolution becomes destabilizing in very diverse communities. This suggests that evolution may not counteract the destabilizing effect of diversity observed in random communities.     

Evolutionary histology and the theory of evolution (on the 100th anniversary of the birth of Academician A. A. Zavarzin

Darwin's theory did not touch upon the problem of evolution of tissues. An attempt made by Heckel to explain phylogeny of tissues, basing on principles of selection and divergence, failed. It was not at once understood that evolution of separate levels of organization possessed certain specificity. The theory of parallelism, suggested by A. A. Zavarzin, stated the notion on specific regularities in evolution of tissues. Having analysed the correlation between the theory of evolution and evolutional histology, A. A. Zavarzin demonstrated that darwinism developed predominantly at the theory of speciation. This approach is correct for the period of the new evolutionary synthesis, too. The synthetic theory of evolution does not take into consideration evolution of tissues. A. A. Zavarzin's theory contributed to reorganization of methodology of the evolutional biology. The historical method was enriched by a certain principle on specific regularities of evolution for each level of organization in the alive. Simultaneously, the genesis of the parallelism theory discovered that correct explanation of the regularities in evolution of tissues is possible only under conditions that the evolution of histostructures can be inserted into the evolution of ontogenesis and species.     

Cognitive Apartheid: On the Manner in Which High School Students Understand Evolution without Believing in Evolution

High school science students are often unwilling to learn about evolution due to a perceived conflict with their religious beliefs. Other students are able to understand evolution despite the fact that they do not believe in evolution. According to Cobern (Sci Educ 80:579?C610, 1996), students can wall off that which is believed from that which is not believed in a process he called cognitive apartheid. A mixed-methods study was conducted to determine the extent to which understanding of evolution differed among high school Advanced Placement science students who did and did not believe in evolution. Two students who demonstrate a sophisticated understanding of evolution despite their admonition that they do not believe in evolution were then interviewed. Eight themes emerged from the interview that provide insight into the views of students learning of evolution despite the fact that they do not believe in evolution. Based on these themes, several implications for the teaching of evolution are presented.     

Correlated evolution between male ejaculate allocation and female remating behaviour in seed beetles (Bruchidae)

Sperm competition theory suggests that female remating rate determines the selective regime that dictates the evolution of male ejaculate allocation. To test for correlated evolution between female remating behaviour and male ejaculate traits, we subjected detailed experimental data on female and male reproductive traits in seven-seed beetle species to phylogenetic comparative analyses. The evolution of a larger first ejaculate was positively correlated with the evolution of a more rapid decline in ejaculate size over successive matings. Further, as predicted by theory, an increase in female remating rate correlated with the evolution of larger male testes but smaller ejaculates. However, an increase in female remating was associated with the evolution of a less even allocation of ejaculate resources over successive matings, contrary to classic sperm competition theory. We failed to find any evidence for coevolution between the pattern of male ejaculate allocation and variation in female quality and we conclude that some patterns of correlated evolution are congruent with current theory, whereas some are not. We suggest that this may reflect the fact that much sperm competition theory does not fully incorporate other factors that may affect the evolution of male and female traits, such as trade-offs between ejaculate expenditure and other competing demands and the evolution of resource acquisition.     

Directed evolution of novel protein functions

Directed evolution has been successfully used to engineer proteins for basic and applied biological research. However, engineering of novel protein functions by directed evolution remains an overwhelming challenge. This challenge may come from the fact that multiple simultaneously or synergistic mutations are required for the creation of a novel protein function. Here we review the key developments in engineering of novel protein functions by using either directed evolution or a combined directed evolution and rational or computational design approach. Specific attention will be paid to a molecular evolution model for generation of novel proteins. The engineered novel proteins should not only broaden the range of applications of proteins but also provide new insights into protein structure-function relationship and protein evolution.