Evolutionary roots of catalysis by nicotinamide and flavins in C-H oxidoreductases and in photosynthesis

The evolutionary information obtained from sequencing proteins and RNA's fades out completely for early periods in evolution. Information for tracing evolution even further could stem from the analysis of coenzyme mechanisms. Likewise, placing cofactors in their proper evolutionary context gives new hints concerning their actual mechanisms of catalysis.     

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life‐history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life‐history and dispersal evolution during range shift. In roughly equal parts, life‐history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion.     

Evolutionary developmental biology and genomics

Reciprocal questions often frame studies of the evolution of developmental mechanisms. How can species share similar developmental genetic toolkits but still generate diverse life forms? Conversely, how can similar forms develop from different toolkits? Genomics bridges the gap between evolutionary and developmental biology, and can help answer these evo-devo questions in several ways. First, it informs us about historical relationships, thus orienting the direction of evolutionary diversification. Second, genomics lists all toolkit components, thereby revealing contraction and expansion of the genome and suggesting mechanisms for evolution of both developmental functions and genome architecture. Finally, comparative genomics helps us to identify conserved non-coding elements and their relationship to genome architecture and development.     

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data

Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for functional divergence and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts in gene expression or leverage advances in contemporary statistical learning for performing classification, nor is it capable of predicting the parameters driving duplicate gene evolution. Thus, here we develop CLOUD, a multi-layer neural network built on a model of gene expression evolution that can both classify duplicate gene retention mechanisms and predict their underlying evolutionary parameters. We show that not only is the CLOUD classifier substantially more powerful and accurate than CDROM, but that it also yields accurate parameter predictions, enabling a better understanding of the specific forces driving the evolution and long-term retention of duplicate genes. Further, application of the CLOUD classifier and predictor to empirical data from Drosophila recapitulates many previous findings about gene duplication in this lineage, showing that new functions often emerge rapidly and asymmetrically in younger duplicate gene copies, and that functional divergence is driven by strong natural selection. Hence, CLOUD represents a major advancement in classifying retention mechanisms and predicting evolutionary parameters of duplicate genes, thereby highlighting the utility of incorporating sophisticated statistical learning techniques to address long-standing questions about evolution after gene duplication.     

Divergent outcomes of reinforcement speciation: the relative importance of assortative mating and migration modification

Most studies of reinforcement speciation focus on the evolution of assortative mating, but R. A. Fisher argued that migration modification is likely to be a common alternative mechanism. Despite previous models showing that assortative mating and migration modification may both be involved in reinforcement, no one has determined their relative evolutionary importance. This is surprising because understanding the biological conditions favoring these mechanisms may explain why certain pairs of species exhibit abutting, nonoverlapping geographical ranges with habitat fidelity while other pairs coexist in sympatry with sexual isolation. In this article, we explicitly model the evolution of both mechanisms simultaneously. First, we explore how these mechanisms differ in their evolutionary dynamics. Second, we ask how they affect each other's evolution and whether the interaction alters their relative importance in reinforcement. Our results reveal that assortative mating may evolve faster and under a broader range of biological conditions than migration modification. However, direct evolutionary interactions favor migration modification when populations experience strong divergent selection. Depending on the nature of postmating isolation, these mechanisms may either interfere with each other's evolution or coevolve in the same system. These results illustrate the importance of studying multiple mechanisms of speciation simultaneously in future speciation models.     

Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization

Multilevel selection has been indicated as an essential factor for the evolution of complexity in interacting RNA-like replicator systems. There are two types of multilevel selection mechanisms: implicit and explicit. For implicit multilevel selection, spatial self-organization of replicator populations has been suggested, which leads to higher level selection among emergent mesoscopic spatial patterns (traveling waves). For explicit multilevel selection, compartmentalization of replicators by vesicles has been suggested, which leads to higher level evolutionary dynamics among explicitly imposed mesoscopic entities (protocells). Historically, these mechanisms have been given separate consideration for the interests on its own. Here, we make a direct comparison between spatial self-organization and compartmentalization in simulated RNA-like replicator systems. Firstly, we show that both mechanisms achieve the macroscopic stability of a replicator system through the evolutionary dynamics on mesoscopic entities that counteract that of microscopic entities. Secondly, we show that a striking difference exists between the two mechanisms regarding their possible influence on the long-term evolutionary dynamics, which happens under an emergent trade-off situation arising from the multilevel selection. The difference is explained in terms of the difference in the stability between self-organized mesoscopic entities and externally imposed mesoscopic entities. Thirdly, we show that a sharp transition happens in the long-term evolutionary dynamics of the compartmentalized system as a function of replicator mutation rate. Fourthly, the results imply that spatial self-organization can allow the evolution of stable folding in parasitic replicators without any specific functionality in the folding itself. Finally, the results are discussed in relation to the experimental synthesis of chemical Darwinian systems and to the multilevel selection theory of evolutionary biology in general. To conclude, novel evolutionary directions can emerge through interactions between the evolutionary dynamics on multiple levels of organization. Different multilevel selection mechanisms can produce a difference in the long-term evolutionary trend of identical microscopic entities.     

Causal mechanisms of evolution and the capacity for niche construction

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved.     

Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo,Evo-Eco and Evolutionary Transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions.     

Evolutionary Medicine: A Key to Introducing Evolution

Science teachers can use examples and concepts from evolutionary medicine to teach the three concepts central to evolution: common descent, the processes or mechanisms of evolution, and the patterns produced by descent with modification. To integrate medicine into common ancestry, consider how the evolutionary past of our (or any) species affects disease susceptibility. That humans are bipedal has produced substantial changes in our musculoskeletal system, as well as causing problems for childbirth. Mechanisms such as natural selection are well exemplified in evolutionary medicine, as both disease-causing organism and their targets adapt to one another. Teachers often use examples such as antibiotic resistance to teach natural selection: it takes little alteration of the lesson plan to make explicit that evolution is key to understanding the principles involved. Finally, the pattern of evolution can be illustrated through evolutionary medicine because organisms sharing closer ancestry also share greater susceptibility to the same disease-causing organisms. Teaching evolution using examples from evolutionary medicine can make evolution more interesting and relevant to students, and quite probably, more acceptable as a valid science.     

The end of regressive evolution: examining and interpreting the evidence from cave fishes

The evolution of hypogean fauna in general and hypogean fishes in particular has been controversial. Explanations regarding the reduction or loss of phenotypic characters such as eyes and pigmentation range from neo‐Lamarckism to neutral mutations, with 'regressive evolution' being a catch‐all characterization for such processes. The assumptions required for special evolutionary mechanisms underlying the evolution of cave dwellers have been based on generalizations about the animals and their environments drawn from relatively few observations. The evidence offered for notions such as pre‐adaptation of colonizing fauna and the purported impoverished nutrients in all caves is examined and it appears that the generalizations cannot be supported. Some major accomplishments in field and laboratory studies of hypogean fishes are summarized, including work highlighting developmental phenotypic plasticity. At the end, it is argued that evolution of hypogean fauna can be explained by well‐known mechanisms within the current context of evolutionary biology.     

The active evolutionary lives of echinoderm larvae

Echinoderms represent a researchable subset of a dynamic larval evolutionary cosmos. Evolution of echinoderm larvae has taken place over widely varying time scales from the origins of larvae of living classes in the early Palaeozoic, approximately 500 million years ago, to recent, rapid and large-scale changes that have occurred within living genera within a span of less than a million years to a few million years. It is these recent evolutionary events that offer a window into processes of larval evolution operating at a micro-evolutionary level of evolution of discrete developmental mechanisms. We review the evolution of the diverse larval forms of living echinoderms to outline the origins of echinoderm larval forms, their diversity among living echinoderms, molecular clocks and rates of larval evolution, and finally current studies on the roles of developmental regulatory mechanisms in the rapid and radical evolutionary changes observed between closely related congeneric species.     

Investigating the evolution and development of biological complexity under the framework of epigenetics

Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore the link between complexity and adaptation. Although recently developed metrics allow for a unified framework, they omit developmental mechanisms. We argue that a better approach to the empirical study of complexity and its evolution includes developmental mechanisms. We then consider epigenetic mechanisms and their role in shaping developmental and evolutionary trajectories, as well as the development and organization of complexity. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Finally, we explore hybridization complexes and hybrid organisms as potential models for studying the association between epigenetics and complexity. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Adaptive evolution in ecological communities

Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.     

Evolutionary innovation and diversification of carotenoid‐based pigmentation in finches

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary “innovation” that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes—where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved—supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification.     

Crossing the line: selection and evolution of virulence traits

The evolution of pathogens presents a paradox. Pathogenic species are often absolutely dependent on their host species for their propagation through evolutionary time, yet the pathogenic lifestyle requires that the host be damaged during this dependence. It is clear that pathogenic strategies are successful in evolutionary terms because a diverse array of pathogens exists in nature. Pathogens also evolve using a broad range of molecular mechanisms to acquire and modulate existing virulence traits in order to achieve this success. Detailing the benefit of enhanced selection derived through virulence and understanding the mechanisms through which virulence evolves are important to understanding the natural world and both have implications for human health.     

基因组水平的插入和缺失变异研究进展

插入和缺失(insertion and deletion)是DNA和蛋白质在进化过程中发生的序列长度上的改变,由于缺乏祖先序列的信息,不能肯定其到底是插入事件还是缺失事件,故统称之为增减(indel)。indel是分子水平进化变异的主要来源之一,近年来对这种进化事件的研究已经涵盖了其发生频率、大小、分布模式、序列进化模型及应用等各个方面。该文总结了基因组水平上插入和缺失的研究进展和发生机制;介绍了已经提出的插入和缺失进化模型,包括TKF91、TKF92、"Long Indel"模型和序列环境模型;讨论了插入和缺失作为分子标记在分子进化、基因分型和药物设计等方面的应用。     

The role of behavior in evolution: a search for mechanism

Behavior has been viewed as a pacemaker of evolutionary change because changes in behavior are thought to expose organisms to novel selection pressures and result in rapid evolution of morphological, life history and physiological traits. However, the idea that behavior primarily drives evolutionary change has been challenged by an alternative view of behavior as an inhibitor of evolution. According to this view, a high level of behavioral plasticity shields organisms from strong directional selection by allowing individuals to exploit new resources or move to a less stressful environment. Here, I suggest that absence of clear mechanisms underlying these hypotheses impedes empirical evaluation of behavior’s role in evolution in two ways. First, both hypotheses focus on behavioral shifts as a key step in the evolutionary process but ignore the developmental mechanisms underlying these shifts and this has fostered unwarranted assumptions about the specific types of behavioral shifts that are important for evolutionary change. Second, neither hypothesis provides a means of connecting within-individual changes in behavior to population-level processes that lead to evolutionary diversification or stasis. To resolve these issues, I incorporate developmental and evolutionary mechanisms into a conceptual framework that generates predictions about the types of behavior and types of behavioral shifts that should affect both micro and macroevolutionary processes.     

Opsins and cell fate in the Drosophila Bolwig organ: tricky lessons in homology inference

The Drosophila Bolwig organs are small photoreceptor bundles that facilitate the phototactic behavior of the larva. Comparative literature suggests that these highly reduced visual organs share evolutionary ancestry with the adult compound eye. A recent molecular genetic study produced the first detailed account of the mechanisms controlling differential opsin expression and photoreceptor subtype determination in these enigmatic eyes of the Drosophila larva. Here, the evolutionary implications are examined, taking into account the dynamic diversification of opsin genes and the spatial regulation of opsin homolog expression in other insects. It is concluded that, consistent with their common evolutionary roots, the Drosophila larval and adult eyes use the same mechanisms for the regulation of opsin expression and photoreceptor cell fate specification. Strikingly, the structurally highly derived Bolwig organs retained a more ancestral state of opsin expression and regulation. Inconspicuous in size, the Drosophila larval eyes deliver useful lessons in the reconstruction of homology between neuronal cell types with gene expression data, and on the conservative nature of gene regulatory network evolution during the emergence of novel organs from ancestral templates.