Beyond the evolutionary theory of ageing, from functional genomics to evo-gero

By the mid 1970s, the mechanisms by which ageing can evolve had a secure theoretical basis in population genetics. Here, we discuss how subsequent evolutionary work has focussed on testing and extending this theory, and on attempting to integrate it with other emerging facets of the biology of ageing, such as genetic studies of long-lived mutants and of phenotypic plasticity in ageing, such as in response to nutritional status. We also describe how functional genomic studies are providing new insights into the evolutionary forces shaping genome evolution and lifespan control. Future challenges include understanding the biochemistry of longevity and how its failure generates ageing and associated diseases, and the determination of the genetic basis of lifespan evolution and the great plasticity that it displays.     

Comparative analysis of essential genes and nonessential genes in Escherichia coli K12

Genes can be classified as essential or nonessential based on their indispensability for a living organism. Previous researches have suggested that essential genes evolve more slowly than nonessential genes and the impact of gene dispensability on a gene’s evolutionary rate is not as strong as expected. However, findings have not been consistent and evidence is controversial regarding the relationship between the gene indispensability and the rate of gene evolution. Understanding how different classes of genes evolve is essential for a full understanding of evolutionary biology, and may have medical relevance in the design of new antibacterial agents. We therefore performed an investigation into the properties of essential and nonessential genes. Analysis of evolutionary conservation, protein length distribution and amino acid usage between essential and nonessential genes in Escherichia coli K12 demonstrated that essential genes are relatively preserved throughout the bacterial kingdom when compared to nonessential genes. Furthermore, results show that essential genes, compared to nonessential genes, have a significantly higher proportion of large (>534 amino acids) and small proteins (<139 amino acids) relative to medium-sized proteins. The pattern of amino acids usage shows a similar trend for essential and nonessential genes, although some notable exceptions are observed. These findings help to clarify our understanding of the evolutionary mechanisms of essential and nonessential genes, relevant to the study of mutagenesis and possibly allowing prediction of gene properties in other poorly understood organisms.     

Does the Segregation of Evolution in Biology Textbooks and Introductory Courses Reinforce Students’ Faulty Mental Models of Biology and Evolution?

The well-established finding that substantial confusion and misconceptions about evolution and natural selection persist after college instruction suggests that these courses neither foster accurate mental models of evolution’s mechanisms nor instill an appreciation of evolution’s centrality to an understanding of the living world. Our essay explores the roles that introductory biology courses and textbooks may play in reinforcing undergraduates’ pre-existing, faulty mental models of the place of evolution in the biological sciences. Our content analyses of the three best-selling introductory biology textbooks for majors revealed the conceptual segregation of evolutionary information. The vast majority of the evolutionary terms and concepts in each book were isolated in sections about evolution and diversity, while remarkably few were employed in other sections of the books. Standardizing the data by number of pages per unit did not alter this pattern. Students may fail to grasp that evolution is the unifying theme of biology because introductory courses and textbooks reinforce such isolation. Two goals are central to resolving this problem: the desegregation of evolution as separate “units” or chapters and the active integration of evolutionary concepts at all levels and across all domains of introductory biology.     

How developmental is evolutionary developmental biology?

Evolutionary developmental biology (evo-devo) offers both an account of developmental processes and also new integrative frameworks for analyzing interactions between development and evolution. Biologists and philosophers are keen on evo-devo in part because it appears to offer a comfort zone between, on the one hand, what some take to be the relative inability of mainstream evolutionary biology to integrate a developmental perspective; and, on the other hand, what some take to be more intractable syntheses of development and evolution. In this article, I outline core concerns of evo-devo, distinguish theoretical and practical variants, and counter Sterelny's recent argument that evo-devo's attention to development, while important, offers no significant challenge to evolutionary theory as we know it. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.     

Mouse models and the evolutionary developmental biology of the skull

Understanding development is relevant to understanding evolutionbecause developmental processes structure the expression ofphenotypic variation upon which natural selection acts. Advancesin developmental biology are fueling a new synthesis of developmentaland evolutionary biology, but it remains unclear how to usedevelopmental information that largely derives from a few modelorganisms to test hypotheses about the evolutionary developmentalbiology of taxa such as humans and other primates that havenot been or are not amenable to direct study through experimentaldevelopmental biology. In this article, we discuss how and whenmodel organisms like mice are useful for studying the evolutionarydevelopmental biology of even rather distantly related and morphologicallydifferent groups like primates. A productive approach is tofocus on processes that are likely to play key roles in producingevolutionarily significant phenotypic variation across a largephylogenetic range. We illustrate this approach by applyingthe analysis of craniofacial variation in mouse mutant modelsto primate and human evolution.     

Evolution of evolutionary physiology

In 19th century and at the beginning 20th century, reports appeared in the field of comparative and ontogenetic physiology and the value of these methods for understanding of evolution of functions. The term "evolutionary physiology" was suggested by A. N. Severtsov in 1914. In the beginning of 30s, in the USSR, laboratories for researches in problems of evolutionary physiology were created, the results of these researches having been published. In 1956 in Leningrad, the Institute of Evolutionary Physiology was founded by L. A. Orbeli. He formulates the goals and methods of evolutionary physiology. In the following half a century, the evolutionary physiology was actively developed. The evolutionary physiology solves problems of evolution of function of functions evolution, often involving methods of adjacent sciences, including biochemistry, morphology, molecular biology.     

The interface of protein structure, protein biophysics, and molecular evolution

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.     

Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons

Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.     

Complexity: the organizing principle at the interface of biological (dis)order

The term complexity means several things to biologists. When qualifying morphological phenotype, on the one hand, it is used to signify the sheer complicatedness of living systems, especially as a result of the multicomponent aspect of biological form. On the other hand, it has been used to represent the intricate nature of the connections between constituents that make up form: a more process-based explanation. In the context of evolutionary arguments, complexity has been defined, in a quantifiable fashion, as the amount of information, an informatic template such as a sequence of nucleotides or amino acids stores about its environment. In this perspective, we begin with a brief review of the history of complexity theory. We then introduce a developmental and an evolutionary understanding of what it means for biological systems to be complex. We propose that the complexity of living systems can be understood through two interdependent structural properties: multiscalarity of interconstituent mechanisms and excitability of the biological materials. The answer to whether a system becomes more or less complex over time depends on the potential for its constituents to interact in novel ways and combinations to give rise to new structures and functions, as well as on the evolution of excitable properties that would facilitate the exploration of interconstituent organization in the context of their microenvironments and macroenvironments.     

Evolutionary and developmental studies of unifacial leaves in monocots: Juncus as a model system

An important objective in evolutionary developmental biology is to understand the molecular genetic mechanisms that have given rise to morphological diversity. Leaves in angiosperms generally develop as a flattened structure with clear adaxial–abaxial polarity. In monocots, however, a unifacial leaf has evolved in a number of divergent species, in which leaf blades consist of only the abaxial identity. The mechanism of unifacial leaf development has long been a matter of debate for comparative morphologists. However, the underlying molecular genetic mechanism remains unknown. Unifacial leaves would be useful materials for developmental studies of leaf-polarity specification. Moreover, these leaves offer unique opportunities to investigate important phenomena in evolutionary biology, such as repeated evolution or convergent evolution of similar morphological traits. Here we describe the potential of unifacial leaves for evolutionary developmental studies and present our recent approaches to understanding the mechanisms of unifacial leaf development and evolution using Juncus as a model system.     

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Eyes provide a rich narrative for understanding evolution, having attracted the attention of preeminent scientists and communicators alike. Until recently, this narrative has focused primarily on the evolution of eye structure and far less on biochemistry or genetics. Although eye biochemistry was once likened to an unknown “black box;” the flood of discoveries in biochemistry is now allowing an increasingly detailed understanding of the processes involved in vision. As a result, evolutionary comparative (“tree-thinking”) analyses that use these data currently allow a new and still unfolding narrative, both richer in detail and more comprehensive in scope. Rather than toppling evolutionary theory by finding irreducibly complex molecular machines, eye evolution provides detailed accounts of how natural processes tinker with existing genetic components, duplicating and recombining them, to yield complex, intricate, and highly functional eyes. Understanding the new biochemical narrative is critical for researchers and teachers alike, in order to answer anti-evolutionist claims, and to provide an up-to-date account of the state of knowledge on the subject of eye evolution.     

Unresolved boundaries of evolutionary theory and the question of how inheritance systems evolve: 75 years of debate on the evolution of dominance

One of the key issues in the evolution of life is the evolution of inheritance systems. In population genetics, the earliest attempt at addressing the latter problem revolved around Fisher's theory on the evolution of dominance. Fisher's hypothesis was that inheritance systems could be modified during the evolutionary process in such a way that wild-type phenotypes could become dominant with respect to mutant phenotypes. This would result in the buffering of a population against the deleterious effects of mutations. The debate that ensued on this topic has been one of the most longstanding in evolutionary theory. At present, the prevalent view is that dominance cannot evolve as a direct result of selection. Furthermore, it has been argued that due to inherent constraints in biochemical systems, the manifestation of dominance is a default expectation and hence evolutionary explanations are not necessary. This has led to the position that the subject is generally resolved and no further debate is necessary. However, there are also several studies indicating that dominance levels can be modified as a result of changes in the genetic background. Furthermore, other studies have indicated that dominance selection is possible in certain circumstances. To a large degree, conclusions from both of the latter types of studies have been ignored. In this article, the history of several intellectual and methodological traditions that have contributed to this debate are traced, including experimental genetics, theoretical population genetics and theoretical biochemistry. In the light of both old and contemporary works on this topic, it is argued that contrary to the prevalent view, the evolution of dominance is not a resolved issue. A re-examination of this issue is essential, given that dominance evolution is likely to be an important stepping stone towards understanding the evolution of inheritance systems.     

The proper place of hopeful monsters in evolutionary biology

Hopeful monsters are organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage. The Synthetic Theory of evolutionary biology has rejected the evolutionary relevance of hopeful monsters, but could not fully explain the mechanism and mode of macroevolution. On the other hand, several lines of evidence suggest that hopeful monsters played an important role during the origin of key innovations and novel body plans by saltational rather than gradual evolution. Homeotic mutants are identified as an especially promising class of hopeful monsters. Examples for animal and plant lineages that may have originated as hopeful monsters are given. Nevertheless, a brief review of the history of the concept of hopeful monsters reveals that it needs refinements and empirical tests if it is to be a useful addition to evolutionary biology. While evolutionary biology is traditionally zoocentric, hopeful monsters might be more relevant for plant than for animal evolution. Even though during recent years developmental genetics has provided detailed knowledge about how hopeful monsters can originate in the first place, we know almost nothing about their performance in natural populations and thus the ultimate difference between hopeful and hopeless. Studying the fitness of candidate hopeful monsters (suitable mutants with profound phenotype) in natural habitats thus remains a considerable challenge for the future.     

Evolutionary physiology at 30+: Has the promise been fulfilled?

Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evidence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology.     

Evolution Education: Seeing the Forest for the Trees and Focusing Our Efforts on the Teaching of Evolution

Evolution is the underlying framework upon which all biology is based; however, when it comes to learning evolutionary concepts, many students encounter obstacles. There are many reasons as to why these obstacles occur. These reasons deal with evolution being treated as a discrete topic among many within a biology curriculum, misunderstanding the nature of science, and personal difficulties with understanding due to evolution’s seemingly abstract nature. In this article, we propose a different way of thinking about and teaching evolution in grades K-12, and it surrounds four core areas essential to the understanding of evolution: variation, selection, inheritance, and deep time. Possibilities for how these areas can affect learning are described and implications for assessment are also discussed.     

Paleobotany: Recent developments and future research directions

The current state of research in the field of paleobotany is reviewed, with emphasis on those areas that deal with more biological approaches to paleobotany. These would include such subjects as the reproductive biology of fossil plants, pollination biology in selected groups, paleobiochemistry, and information on the interaction of plants with other organisms (plant/animal interactions) and their environment (paleoecology). Also discussed are some of the more recent contributions to our understanding of Precambrian paleobiology and early angiosperm reproduction and evolution. Finally, we offer some speculation on the contributions that various areas of paleobotany may provide in the future.     

Thermodynamics and the conceptual structure of evolutionary theory

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.     

Examining the Interaction of Acceptance and Understanding: How Does the Relationship Change with a Focus on Macroevolution?

The goal of this research was to illuminate the relationship between students’ acceptance and understanding of macroevolution. Our research questions were: (1) Is there a relationship between knowledge of macroevolution and acceptance of the theory of evolution?; (2) Is there a relationship between the amount of college level biology course work and acceptance of evolutionary theory and knowledge of macroevolution?; and (3) Can college student acceptance of the theory of evolution and knowledge of macroevolution change over the course of a semester? The research participants included 667 students from a first-semester biology course and 74 students from the evolutionary biology course. Data were collected using both the MATE (a measure of the acceptance of evolutionary theory) and the MUM (a measure of understanding of macroevolution). Pre-instruction data were obtained for the introductory biology course, and pre- and post-data were obtained for the evolutionary biology course. Analysis revealed acceptance of evolution (as measured by the MATE) was correlated to understanding of macroevolution, and the number of biology courses was significantly correlated to acceptance and knowledge of macroevolution. Finally, there was a statistically significant change in students’ understanding of macroevolution and acceptance of evolution after the one-semester evolutionary biology course. Significance of these findings is discussed.     

How to Identify and Interpret Evolutionary Tree Diagrams

Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly defined nor conveyed to students. To help biology teachers and students learn how to more deeply interpret, understand and gain knowledge from diagrams that represent ancestor–descendant relationships and evolutionary lineages, we describe the different rooted and unrooted evolutionary tree visualisations and explain how they are best read. Examples from a study of tree-shaped diagrams in the journal Science are used to illustrate how to distinguish evolutionary trees from other tree-shaped representations that are easily misunderstood as visualising evolutionary relationships. We end by making recommendations for how our findings may be implemented in teaching practice in this important area of biology education.