EXPERIMENTAL EVOLUTION MEETS MARINE PHYTOPLANKTON

Our perspective highlights potentially important links between disparate fields—biological oceanography, climate change research, and experimental evolutionary biology. We focus on one important functional group—photoautotrophic microbes (phytoplankton), which are responsible for ～50% of global primary productivity. Global climate change currently results in the simultaneous change of several conditions such as warming, acidification, and nutrient supply. It thus has the potential to dramatically change phytoplankton physiology, community composition, and may result in adaptive evolution. Although their large population sizes, standing genetic variation, and rapid turnover time should promote swift evolutionary change, oceanographers have focussed on describing patterns of present day physiological differentiation rather than measure potential adaptation in evolution experiments, the only direct way to address whether and at which rate phytoplankton species will adapt to environmental change. Important open questions are (1) is adaptation limited by existing genetic variation or fundamental constraints? (2) Will complex ecological settings such as gradual versus abrupt environmental change influence adaptation processes? (3) How will increasing environmental variability affect the evolution of phenotypic plasticity patterns? Because marine phytoplankton species display rapid acclimation capacity (phenotypic buffering), a systematic study of reaction norms renders them particularly interesting to the evolutionary biology research community.     

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.     

Evolutionary morphology and Evo-devo: Hierarchy and novelty

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology.     

生物进化研究的回顾与展望

生物进化是自然科学的永恒之迷。随着历史的发展和科学的进步,生物进化思想从早期的萌芽,到自然选择学说、新达尔文主义,从现代综合理论,到分子进化的中性学说。再到新灾变论和点断平衡论等。当前,由于生物学各分支学科的飞速发展．它们就各自的研究对象在宏观和微观上不断地拓展和深入,并在不同的层次上形成了广泛的交叉、渗透和融合,现代的进化生物学研究从宏观的表型到微观的分子,从群体遗传改变的微进化到成种事件以及地史上生物类群谱系演化的宏进化,从直接的化石证据到基于形态性状、分子证据和环境变迁的综合推理,从基于遗传基础的比较基因组学到演化机理的进化发育生物学等。可以预见,在新的世纪里,在哲学和具体方法论(如系统论、控制论和信息论)的指导下,在生命科学、其他自然科学乃至社会科学工作者的通力合作下,综合遗传、发育和进化等研究领域的各种理论成果,生物进化理论即将出现也一定会出现的一个新的大综合和新的大统一。     

What has become of the refugia hypothesis to explain biological diversity in Amazonia?

The spatial distribution of biodiversity and related processes is the core of Biogeography. Amazonia is the world's most diverse rainforest and the primary source of diversity to several Neotropical regions. The origins of such diversity continue to be an unresolved question in evolutionary biology. Among many competing hypotheses to explain the evolution of the Amazonian biodiversity, one stands out as the most influential: the refugia hypothesis by Jürgen Haffer. Here, we provide a chronological overview on how the refugia hypothesis evolved over the decades and how the criticism from different fields affected its acceptance. We conclude that the refugia hypothesis alone cannot explain the diversification of the complex Amazonian diversity, and perhaps it was not the most important diversification mechanism. However, the debate provoked by refugia has produced a great amount of knowledge on Amazonian climatic, geological, and evolutionary processes, as well as on species distributions, movements, and history.     

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

Background  

Homology is a key concept in both evolutionary biology and genomics. Detection of homology is crucial in fields like the functional annotation of protein sequences and the identification of taxon specific genes. Basic homology searches are still frequently performed by pairwise search methods such as BLAST. Vast improvements have been made in the identification of homologous proteins by using more advanced methods that use sequence profiles. However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure.     

On the shape and fabric of human history

In this paper we outline two debates about the nature of human cultural history. The first focuses on the extent to which human history is tree-like (its shape), and the second on the unity of that history (its fabric). Proponents of cultural phylogenetics are often accused of assuming that human history has been both highly tree-like and consisting of tightly linked lineages. Critics have pointed out obvious exceptions to these assumptions. Instead of a priori dichotomous disputes about the validity of cultural phylogenetics, we suggest that the debate is better conceptualized as involving positions along continuous dimensions. The challenge for empirical research is, therefore, to determine where particular aspects of culture lie on these dimensions. We discuss the ability of current computational methods derived from evolutionary biology to address these questions. These methods are then used to compare the extent to which lexical evolution is tree-like in different parts of the world and to evaluate the coherence of cultural and linguistic lineages.     

The Geography of Evolution and the Evolution of Geography

Insights into the geography of life have played a fundamental role in motivating major developments in evolutionary biology. The focus here is on outlining some of these major developments, specifically in the context of paleontology, by emphasizing the significance of geographic isolation and allopatric speciation, punctuated equilibria, and the Turnover Pulse Hypothesis to evolutionary theory. One of the major debates in evolution concerns the relative contributions of abiotic and biotic factors to macroevolution, and each one of these developments increasingly suggested that it was climatic and geologic factors, rather than competition, that played the primary role in motivating macroevolution. New technical developments, including in the area of Geographic Information Systems, allow continued detailed testing of the relative roles that biotic as opposed to abiotic factors play in causing evolution, and some of the work in this area will also be described.     

Phenotypic Novelty in EvoDevo: The Distinction Between Continuous and Discontinuous Variation and Its Importance in Evolutionary Theory

The introduction of novel phenotypic structures is one of the most significant aspects of organismal evolution. Yet the concept of evolutionary novelty is used with drastically different connotations in various fields of research, and debate exists about whether novelties represent features that are distinct from standard forms of phenotypic variation. This article contrasts four separate uses for novelty in genetics, population genetics, morphology, and behavioral science, before establishing how novelties are used in evolutionary developmental biology (EvoDevo). In particular, it is detailed how an EvoDevo-specific research approach to novelty produces insight distinct from other fields, gives the concept explanatory power with predictive capacities, and brings new consequences to evolutionary theory. This includes the outlining of research strategies that draw attention to productive areas of inquiry, such as threshold dynamics in development. It is argued that an EvoDevo-based approach to novelty is inherently mechanistic, treats the phenotype as an agent with generative potential, and prompts a distinction between continuous and discontinuous variation in evolutionary theory.     

Toward an integration of evolutionary biology and ecosystem science

At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.     

鱼类线粒体DNA研究新进展

线粒体DNA是分子生物学研究中的一个热门领域,已成为鱼类进化生物学和群体遗传学研究的重要分子遗传标记。本文对鱼类线粒体DNA分子生物学的最新研究进展进行了较详细的阐述。重点介绍鱼类线粒体DNA全序列的研究进展、组成及特征,鱼类线粒体DNA非编码区结构研究进展,鱼类线粒体DNA多态性及其主要的检测方法;综述了最近有关鱼类线粒体DNA在鱼类系统学、种间杂交渐渗、种群识别、起源和进化、地理分化等研究中的应用情况。     

The morphogenesis of evolutionary developmental biology

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.     

Popper, falsifiability, and evolutionary biology

First, a brief history is provided of Popper's views on the status of evolutionary biology as a science. The views of some prominent biologists are then canvassed on the matter of falsifiability and its relation to evolutionary biology. Following that, I argue that Popper's programme of falsifiability does indeed exclude evolutionary biology from within the circumference of genuine science, that Popper's programme is fundamentally incoherent, and that the correction of this incoherence results in a greatly expanded and much more realistic concept of what is empirical, resulting in the inclusion of evolutionary biology. Finally, this expanded concept of empirical is applied to two particular problems in evolutionary biology — viz., the species problem and the debate over the theory of punctuated equilibria — and it is argued that both of them are still mainly metaphysical.     

Phylogeny,extinction and conservation: embracing uncertainties in a time of urgency

Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.     

Social insects: from selfish genes to self organisation and beyond

Selfish gene and self-organisation approaches have revolutionised the study of social insects and have provided unparalleled insights into the highly sophisticated nature of insect social evolution. Here, we briefly review the core programs and interfaces with communication and recognition studies that characterise these fields today, and offer an interdisciplinary future perspective for the study of social insect evolutionary biology.     

Alternative hypotheses linking the immune system and mate choice for good genes

Why do males often have extravagant morphological and behavioural traits, and why do females prefer to mate with such males? The answers have been the focus of considerable debate since Darwin''s The descent of man, and selection in relation to sex appeared in 1871. Recently the broadening of investigation to include fields outside evolutionary biology has shed new light on mate choice and sexual selection. Here, we focus on a specific set of hypotheses relating the biology of resisting disease-causing organisms with the production of condition-dependent sexual signals (advertisements). We present a framework that distinguishes three different hypotheses about trade-offs within the immune system that affect general condition. Hamilton and Zuk''s original hypothesis suggests that hosts fight off disease through resistance to particular pathogens, which consequently lowers resistance to other pathogens. Changes in pathogens over evolutionary time in turn favours changes in which genes confer the best resistance. Alternatively, the immunocompetence hypotheses suggests that the energetic costs of mounting a response to any pathogen compete for resources with other things, such as producing or maintaining advertisements. Finally, improving resistance to pathogens could increase the negative impacts of the immune system on the host, via immunopathologies such as allergies or autoimmune diseases. If both disease and immunopathology affect condition, then sexual advertisements could signal a balance between the two. Studies of hypothesized links between genes, condition, the immune system and advertisements likely will require careful consideration of which hypothesis is being considered, and may necessitate different measures of immune system responses and different experimental protocols.     

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.     

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony—the change in rate and timing of developmental events, (2) homeosis—the ontogenetic replacement of features, (3) heterometry—the change in quantity of a feature, (4) exaptation—the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty—the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.     

黏菌学的发展

黏菌是一类在陆地生态系统中广泛分布的真核生物,在其生活史的不同阶段,既有体现原生动物运动性的营养体,也具有高度特异化的繁殖体,其形态结构与生理特征,兼具了“菌物”与“动物”的特性,独特的进化地位以及与环境、人类健康的密切关系,使得以黏菌为模式生物的研究在生物学、遗传学、生理学、生态学、信息科学等学科均具有广泛的科学意义和重要的应用价值。自17世纪以来,黏菌研究者们从早期的经典分类学,逐步拓展到从生物学各分支学科领域系统全面地认识黏菌类群。在近几十年中,黏菌研究在系统学、生物学、生态学等方向取得了长足的进步。本文扼要介绍了黏菌学在各领域内的代表性研究进展和前沿性科学问题,同时对相关领域未来的发展进行了展望。     

On the co‐evolution of surface oxygen levels and animals

Few topics in geobiology have been as extensively debated as the role of Earth's oxygenation in controlling when and why animals emerged and diversified. All currently described animals require oxygen for at least a portion of their life cycle. Therefore, the transition to an oxygenated planet was a prerequisite for the emergence of animals. Yet, our understanding of Earth's oxygenation and the environmental requirements of animal habitability and ecological success is currently limited; estimates for the timing of the appearance of environments sufficiently oxygenated to support ecologically stable populations of animals span a wide range, from billions of years to only a few million years before animals appear in the fossil record. In this light, the extent to which oxygen played an important role in controlling when animals appeared remains a topic of debate. When animals originated and when they diversified are separate questions, meaning either one or both of these phenomena could have been decoupled from oxygenation. Here, we present views from across this interpretive spectrum—in a point–counterpoint format—regarding crucial aspects of the potential links between animals and surface oxygen levels. We highlight areas where the standard discourse on this topic requires a change of course and note that several traditional arguments in this “life versus environment” debate are poorly founded. We also identify a clear need for basic research across a range of fields to disentangle the relationships between oxygen availability and emergence and diversification of animal life.