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.     

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.     

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。     

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.     

Evolution and Religion: Attitudes of Scottish Bioscience Students to the Teaching of Evolutionary Biology

In a questionnaire-based survey, the proportion of Glasgow University first year biology students who rejected evolution in 2009–2011 was about 7%, similar to the previously reported average figure for 1987–1999. However, by final year, evolution rejection was absent in students who studied evolution beyond first year and 4% among those who did not. Evolution rejection was closely related to accepting a religion-based alternative, whereas acceptance was related to finding the evidence convincing. Although many religious students accepted evolution, 50% of Islamic students were rejecters, compared to 25% of Christians. A question testing acceptance of several scientific propositions showed no evidence that evolution rejecters were generally more skeptical of science than accepters. Rejecters were overall less secure than accepters in their identification of the correct definition for terms related to evolution and creationism, but, surprisingly, more than 10% of final year students chose a Lamarckian definition for Darwinian evolution. Accepters and rejecters responded equally poorly to a question on Darwin’s history, but level 4 was much better. A breakdown of evolution into three components (human origins, macroevolution, and microevolution) found that some evolution rejecters accepted some components, with microevolution having the highest acceptance and human origins the lowest. These findings are discussed in terms of strategies for evolution education and the phenomenon of evolution rejection worldwide.     

Evolution of precopulatory and post‐copulatory strategies of inbreeding avoidance and associated polyandry

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post‐copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post‐copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post‐copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post‐copulatory inbreeding avoidance might cause functional redundancy (i.e. ‘degeneracy’) potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual‐based modelling to quantify evolution of interacting precopulatory and post‐copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post‐copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower‐cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post‐copulatory inbreeding avoidance, but fixed post‐copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post‐copulatory inbreeding avoidance is precluded or costly, and evolution of post‐copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry.     

Advances in ultrahigh-throughput screening technologies for protein evolution

Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.     

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.     

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.     

Preservice Teacher Understanding and Vision of how to Teach Biological Evolution

The learning and teaching of biological evolution is conceptually challenging. To fully comprehend evolution, it is posited that individuals also need to understand the roles that the nature of science and situations of chance play in the process. The consistent detection of misconceptions of evolution suggests that new approaches to increasing understanding need to be explored. I predicted that preservice teachers’ ideas for teaching biological evolution could be influenced by three brief web-based interventions, one focused on the common misconceptions of evolution, one on the nature of science, and one on situations of uncertainty in the context of evolution. An experimental group received a combination of the three web-based tutorials while a control group received the misconceptions and nature of science instruction and a time on task filler tutorial. Participants were directed to develop a lesson idea applying the knowledge they learned from the tutorials. The lesson ideas were examined for evidence of the influence of the web-based instruction, participant understanding and misconceptions of concepts, and their ideas about teaching evolution. The results of this study revealed that the participating preservice teachers held a wide range of conception and misconception of evolution, were somewhat influenced by the tutorials, and had an array of visions for teaching evolution. The outcomes support the need for further investigation into the multifaceted nature of preparing preservice teachers to teach evolution.     

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.     

蛋白质突变体基因库构建方法的研究进展

体外定向进化是蛋白质工程中一个非常有效的设计策略。最近几年,在过去常用的寡核苷酸介导的随机突变、易错PCR和DNA改组等方法的基础上又出现了一些新的定向进化方法。本文对这些方法及其特点加以总结,为解决特定问题选取何种方法提供一定依据。最近研究表明：定向进化和理性设计相结合、定向进化和以结构为基础的计算设计方法相结合正成为蛋白质工程中两个新的发展方向。     

The evolution of female genitalia

Female genitalia have been largely neglected in studies of genital evolution, perhaps due to the long‐standing belief that they are relatively invariable and therefore taxonomically and evolutionarily uninformative in comparison with male genitalia. Contemporary studies of genital evolution have begun to dispute this view, and to demonstrate that female genitalia can be highly diverse and covary with the genitalia of males. Here, we examine evidence for three mechanisms of genital evolution in females: species isolating ‘lock‐and‐key’ evolution, cryptic female choice and sexual conflict. Lock‐and‐key genital evolution has been thought to be relatively unimportant; however, we present cases that show how species isolation may well play a role in the evolution of female genitalia. Much support for female genital evolution via sexual conflict comes from studies of both invertebrate and vertebrate species; however, the effects of sexual conflict can be difficult to distinguish from models of cryptic female choice that focus on putative benefits of choice for females. We offer potential solutions to alleviate this issue. Finally, we offer directions for future studies in order to expand and refine our knowledge surrounding female genital evolution.     

Interactive analysis of phylogeny and character evolution using the computer program MacClade

Computer programs for phylogenetic analysis have been important tools in systematics and evolutionary biology, but most have been designed primarily for the reconstruction of phylogenetic trees and not the interpretation of patterns of character evolution. Described here is the computer program MacClade, designed for interactive analysis of character evolution and phylogeny. For a given tree and a matrix of character data, MacClade displays its reconstruction of character evolution by shading the branches of the tree to indicate ancestral states. Trees can be manipulated for instance by picking up and moving branches. Assumptions underlying the reconstruction of character evolution can be varied extensively. With these manipulations and MacClade's graphical feedback, one can explore the relationships among phylogenetic trees, character data, assumptions and interpretations of character evolution. MacClade has extensive facilities for editing data, displaying various summaries of character evolution in charts and diagrams, and printing.     

Mainstreaming Caenorhabditis elegans in experimental evolution

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host–pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.     

Maximum entropy production and general trends in biospheric evolution

The biosphere has greatly shaped the past evolution of the Earth system. Here I argue that life evolved to maximize planetary entropy production. The evolution of the Earth system through time has thus evolved as far away from thermodynamic equilibrium as possible. I describe the implications of this hypothesis for the evolution of the global cycles of water and carbon and the implied consequences for biospheric evolution. This thermodynamic perspective of Earth’s biospheric evolution extends the views of Vernadski and Lovelock and puts it on a quantitative foundation.     

The probability of parallel genetic evolution from standing genetic variation

Parallel evolution is often assumed to result from repeated adaptation to novel, yet ecologically similar, environments. Here, we develop and analyse a mathematical model that predicts the probability of parallel genetic evolution from standing genetic variation as a function of the strength of phenotypic selection and constraints imposed by genetic architecture. Our results show that the probability of parallel genetic evolution increases with the strength of natural selection and effective population size and is particularly likely to occur for genes with large phenotypic effects. Building on these results, we develop a Bayesian framework for estimating the strength of parallel phenotypic selection from genetic data. Using extensive individual‐based simulations, we show that our estimator is robust across a wide range of genetic and evolutionary scenarios and provides a useful tool for rigorously testing the hypothesis that parallel genetic evolution is the result of adaptive evolution. An important result that emerges from our analyses is that existing studies of parallel genetic evolution frequently rely on data that is insufficient for distinguishing between adaptive evolution and neutral evolution driven by random genetic drift. Overcoming this challenge will require sampling more populations and the inclusion of larger numbers of loci.     

Sex against virulence: the coevolution of parasitic diseases

Reciprocal selection is the underlying mechanism for host-parasite coevolutionary arms races. Its driving force is the reduction of host lifespan or fecundity that is caused by a parasite. Parasites evolve to optimize host exploitation, while hosts evolve to minimize the 'parasite-induced' loss of fitness (virulence). Research on the evolution of virulence has mostly emphasized the role of parasite evolution in determining virulence. However, host evolution, accelerated by sexual recombination, contributes to the evolution and expression of virulence as well. The Red Queen hypothesis predicts that genetic variation among host offspring facilitates selection for reduced virulence. Here, we outline a synthesis between current thinking about the evolution of virulence and the evolution of sex.     

The causes of repeated genetic evolution

A general understanding of the evolutionary process is limited by the contingency of each evolutionary event, making it difficult, even retrospectively, to explain why things have unfolded the way they have. The repeated evolution of similar traits in organisms facing similar environmental conditions is a pervasive phenomenon, including for animal morphology, and is considered a strong evidence for adaptive evolution. Examples of repeated evolution of particular traits offer a unique opportunity to ask whether evolution has followed similar or different genetic paths. Case studies reveal that although multiple genetic paths were often possible to evolve a morphological trait, similar evolutionary trajectories have been followed repeatedly in independent lineages, suggesting that biases influence the course of genetic evolution. In the light of these examples we examine several factors influencing the genetic paths of adaptive evolution and in particular how the interplay between natural selection and genetic variations carves out predictable genetic trajectories of morphological evolution.