Eco-evolution from deep time to contemporary dynamics: The role of timescales and rate modulators

Eco-evolutionary dynamics, or eco-evolution for short, are often thought to involve rapid demography (ecology) and equally rapid heritable phenotypic changes (evolution) leading to novel, emergent system behaviours. We argue that this focus on contemporary dynamics is too narrow: Eco-evolution should be extended, first, beyond pure demography to include all environmental dimensions and, second, to include slow eco-evolution which unfolds over thousands or millions of years. This extension allows us to conceptualise biological systems as occupying a two-dimensional time space along axes that capture the speed of ecology and evolution. Using Hutchinson's analogy: Time is the ‘theatre’ in which ecology and evolution are two interacting ‘players’. Eco-evolutionary systems are therefore dynamic: We identify modulators of ecological and evolutionary rates, like temperature or sensitivity to mutation, which can change the speed of ecology and evolution, and hence impact eco-evolution. Environmental change may synchronise the speed of ecology and evolution via these rate modulators, increasing the occurrence of eco-evolution and emergent system behaviours. This represents substantial challenges for prediction, especially in the context of global change. Our perspective attempts to integrate ecology and evolution across disciplines, from gene-regulatory networks to geomorphology and across timescales, from today to deep time.     

The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Zanthoxylum armatum and Zanthoxylum bungeanum, known as ‘Chinese pepper’, are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.     

Innovation in wild chimpanzees (Pan troglodytes)

Innovations of behavior have major implications for the concept of culture in animals. Innovation has rarefy been documented in wild animal populations. The chimpanzees of the Ta? National Park, C?te d’Ivoire, spontaneously included new patterns of behavior in their repertoire during our study. Some innovations were incorporated into a minority of the group members’ repertoire, whereas others, such as building day nests in trees and on the ground more frequently, became general behaviors. Similarly, new contexts for use of leaf- clipping behavior and novel ways of feeding on some leaves appeared and rapidly became part of the behavior of most group members. The environmental parameters were too stable to explain these new forms of behavior, as most of them took place within 1 month during the same dry season. In a similar way, leaf- grooming acquired a new function in Gombe chimpanzees. A process similar to social conventions could explain the emergence of these new functions for an existing behavior in a way rather similar to human “fashion. ” Three major characteristics of human culture — the absence of individual variations in the performance of the behavior, the general use of the behavior by group members, and the ability to modify the function of a behavior — characterize leaf-clipping in Ta? chimpanzees and leaf- grooming in Gombe chimpanzees.     

User−Producer Interaction in Housing Energy Innovations

Von Hippel and colleagues have highlighted the crucial role of users in innovation in different industries and types of products. They describe the innovation process in terms of the distinct domains of knowledge that producers and users possess. Producers have knowledge about technical solutions and users about their needs, the context of use, and their own capabilities as users. Both sets of knowledge are characterized by "stickiness": They move relatively freely within their own domain but are difficult to transfer outside of it.
In the case of radical innovations for sustainable consumption, the problem of "sticky information" is compounded. Both producers and consumers need to reach out of their conventional competencies and search for new solutions. "Societal actors," such as government bodies or environmental experts, can show the way to such solutions, but this new knowledge needs to be integrated with the "sticky" knowledge about everyday practices in production and consumption.
In the present article we attempt to conceptualize the role and interaction of user and producer knowledge with the knowledge of environmental experts in housing energy innovations. We do so by applying the user−producer interaction framework to a case study on the introduction of low-energy housing concepts in Finland. On the basis of this analysis, we draw conclusions on the potential and limitations of today's practices in the field. For example, we suggest that user involvement can help to enhance the acceptance of low-energy solutions but that the methods for involving users need to be adapted to the particular circumstances in each industry.     

新工科背景下生物反应工程课程的多元化教学模式 改革与探索

生物反应工程作为一门理论性与应用性都很强的专业课程,在生物工程等相关专业的课程设置中处于桥梁和纽带地位,对新型应用型工科人才的培养发挥着重要的作用。但由于该课程中公式等抽象理论知识过多,导致学生学习效率十分低下。因此,为了适应新工科教育背景下对创新型人才培养的需求,提高学生的学习兴趣和积极性,并培养学生的自主学习等创新能力,教学团队在课程教学中通过引入虚拟仿真技术、开展微课教学、采用案例式教学模式、利用科研平台等多元化方式,对该课程的教学模式、方法和手段尝试改革和探索,取得了一定的教学效果,并就此进行了一些探讨,以期能为相关课程的教学改革提供一些思路和启示。     

Cisgenics as emerging bio-objects: bio-objectification and bio-identification in agrobiotech innovation

Cisgenesis is a genetic modification of a recipient organism with genetic material from a crossable organism. Trying to free cisgenics from the regulatory guidelines of genetically modified organisms (GMOs), some scientists have suggested to classify the genetically modified products by the origin of transferred genes. Aiming at exploring how scientists frame cisgenics in relation to current legal frameworks, we have sent an extensive survey to the totality of researchers working on cisgenics. Trying to provide cisgenics with a new, uncontroversial identity, the respondents present cisgenics as a method of obtaining “natural,” environmentally friendly and economically sustainable crops. However, such strategy is challenged by GMO corporations opposing a segmentation of the sector, and by the opponents of GMOs, who fear that deregulation on cisgenics leads to the deregulation of GMOs. Drawing from the concepts of bio-objectification and bio-identification, we show how the status of this bio-object is likely to remain contested and contestable.     

Governing synthetic biology for global health through responsible research and innovation

Synthetic biology (SynBio) is a global endeavour with research and development programs in many countries, and due (in part) to its multi-use characteristics it has potential to improve global health in the area of vaccine development, diagnostics, drug synthesis, and the detection and remediation of environmental toxins. However, SynBio will also concurrently require global governance. Here we present what we have learnt from the articles in this Special Issue, and the workshop we hosted in The Hague in February of 2012 on SynBio, global health, and global governance that generated many of the papers appearing here. Importantly we take the notion of ‘responsible research and innovation’ as a guiding perspective. In doing so our understanding of governance is one that shifts its focus from preventing risks and other potential negative implications, and instead is concerned with institutions and practices involved in the inclusive steering of science and technology towards socially desirable outcomes. We first provide a brief overview of the notion of global health, and SynBio’s relation to global health issues. The core of the paper explores some of the dynamics involved in fostering SynBio’s global health pursuits; paying particular attention to of intellectual property, incentives, and commercialization regimes. We then examines how DIYbio, Interactive Learning and Action, and road-mapping activities can be seen as positive and productive forms of governance that can lead to more inclusive SynBio global health research programs.     

STEME系统:一种助力体内定向进化的新工具

通过定向进化(directed evolution)可以快速进行蛋白工程改良及重要基因功能研究,以获得新型农艺性状突变体。近期,中国科学院遗传与发育生物学研究所高彩霞团队和李家洋团队合作构建了新型的饱和靶向内源诱变编辑器(saturated targeted endogenous mutagenesis editors, STEMEs),并在植物中实现了基因的定向进化和功能筛选。该系统融合了现有的2种单碱基编辑技术,成功实现在植物体内同时诱导C:G>T:A、A:T>G:C双碱基编辑,通过靶向OsACC羧基转移酶结构域编码序列定向进化出水稻除草剂抗性植株。这种在体内进行基因定向进化的新方法,对于今后农作物重要农艺性状的筛选和功能基因研究具有重要作用。本文对STEME系统的组成、编辑效率和应用原理进行介绍,并与已有的定向进化方法进行比较,为加速作物种质资源创新研究提供参考。     

Diversity and evolution of a trait mediating ant–plant interactions: insights from extrafloral nectaries in Senna (Leguminosae)

Background and Aims

Plants display a wide range of traits that allow them to use animals for vital tasks. To attract and reward aggressive ants that protect developing leaves and flowers from consumers, many plants bear extrafloral nectaries (EFNs). EFNs are exceptionally diverse in morphology and locations on a plant. In this study the evolution of EFN diversity is explored by focusing on the legume genus Senna, in which EFNs underwent remarkable morphological diversification and occur in over 80 % of the approx. 350 species.

Methods

EFN diversity in location, morphology and plant ontogeny was characterized in wild and cultivated plants, using scanning electron microscopy and microtome sectioning. From these data EFN evolution was reconstructed in a phylogenetic framework comprising 83 Senna species.

Key Results

Two distinct kinds of EFNs exist in two unrelated clades within Senna. ‘Individualized’ EFNs (iEFNs), located on the compound leaves and sometimes at the base of pedicels, display a conspicuous, gland-like nectary structure, are highly diverse in shape and characterize the species-rich EFN clade. Previously overlooked ‘non-individualized’ EFNs (non-iEFNs) embedded within stipules, bracts, and sepals are cryptic and may represent a new synapomorphy for clade II. Leaves bear EFNs consistently throughout plant ontogeny. In one species, however, early seedlings develop iEFNs between the first pair of leaflets, but later leaves produce them at the leaf base. This ontogenetic shift reflects our inferred diversification history of iEFN location: ancestral leaves bore EFNs between the first pair of leaflets, while leaves derived from them bore EFNs either between multiple pairs of leaflets or at the leaf base.

Conclusions

EFNs are more diverse than previously thought. EFN-bearing plant parts provide different opportunities for EFN presentation (i.e. location) and individualization (i.e. morphology), with implications for EFN morphological evolution, EFN–ant protective mutualisms and the evolutionary role of EFNs in plant diversification.