Curiously the same: swapping tools between linguistics and evolutionary biology

One of the major benefits of interdisciplinary research is the chance to swap tools between fields, to save having to reinvent the wheel. The fields of language evolution and evolutionary biology have been swapping tools for centuries to the enrichment of both. Here I will discuss three categories of tool swapping: (1) conceptual tools, where analogies are drawn between hypotheses, patterns or processes, so that one field can take advantage of the path cut through the intellectual jungle by the other; (2) theoretical tools, where the machinery developed to process the data in one field is adapted to be applied to the data of the other; and (3) analytical tools, where common problems encountered in both fields can be solved using useful tricks developed by one or the other. I will argue that conceptual tools borrowed from linguistics contributed to the Darwinian revolution in biology; that theoretical tools of evolutionary change can in some cases be applied to both genetic and linguistic data without having to assume the underlying evolutionary processes are exactly the same; and that there are practical problems that have long been recognised in historical linguistics that may be solved by borrowing some useful analytical tools from evolutionary biology.     

The genetic toolbox for Leishmania parasites

Leishmania parasites cause a variety of devastating diseases in tropical areas around the world. Due to the lack of vaccines and limited availability of drugs, new therapeutic targets are urgently needed. A variety of genetic tools have been developed to investigate the complex biology of this parasite and its interactions with the host. One of the main techniques is the generation of knock-out parasites via targeted gene replacement, a process that takes advantage of the parasites ability to undergo homologous recombination. Studying the effect of gene deletions in vitro and in infectivity models in vivo allows understanding the function of a target gene and its potential as a therapeutic target. Other genetic manipulations available include episomal and chromosomal complementation and the generation of overproducer strains. However, there are also limitations, such as the lack of RNA interference machinery in most Leishmania species and limited options for inducible expression systems. The genomes of several Leishmania species have now been sequenced and will provide powerful resources in combination with the genetic tools that are available. The increasing knowledge of parasite biology and host parasite interactions derived from these studies will raise the number of potential therapeutic targets, which are sorely needed to combat leishmaniasis.     

Symbiotic microorganisms: untapped resources for insect pest control

Symbiotic microorganisms offer one route to meet the anticipated heightened demand for novel insect pest management strategies created by growing human populations and global climate change. Two approaches have particular potential: the disruption of microbial symbionts required by insect pests, and manipulation of microorganisms with major impacts on insect traits contributing to their pest status (e.g. capacity to vector diseases, natural enemy resistance). Specific research priorities addressed in this article include identification of molecular targets against which highly specific antagonists can be designed or discovered, and management strategies to manipulate the incidence and properties of facultative microorganisms that influence insect pest traits. Collaboration with practitioners in pest management will ensure that the research agenda is married to agricultural and public health needs.     

Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

Simulation of Genomes: A Review

There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are increasing in size, with genome-wide data becoming a common place in many empirical studies. As far as more information is available, it becomes clear that simplest hypotheses are not consistent with data. Simulations will provide the key tool to contrast complex hypotheses on real data by generating simulated data under the hypothetical historical and evolutionary conditions that we want to contrast. Undoubtedly, developing tools for simulating large sequences that at the same time allow simulate natural selection, recombination and complex demography patterns will be of great interest in order to better understanding the trace left on the DNA by different interacting evolutionary forces. Simulation tools will be also essential to evaluate the sampling properties of any statistics used on genome-wide association studies and to compare performance of methods applied at genome-wide scales. Several recent simulation tools have been developed. Here, we review some of the currently existing simulators which allow for efficient simulation of large sequences on complex evolutionary scenarios. In addition, we will point out future directions in this field which are already a key part of the current research in evolutionary biology and it seems that it will be a primary tool in the future research of genome and post-genomic biology.     

Myths, models and mitigation of resistance to pesticides

Resistance to pesticides in arthropod pests is a significant economic, ecological and public health problem. Although extensive research has been conducted on diverse aspects of pesticide resistance and we have learned a great deal during the past 50 years, to some degree the discussion about ''resistance management'' has been based on ''myths''. One myth involves the belief that we can manage resistance. I will maintain that we can only attempt to mitigate resistance because resistance is a natural evolutionary response to environmental stresses. As such, resistance will remain an ongoing dilemma in pest management and we can only delay the onset of resistance to pesticides. ''Resistance management'' models and tactics have been much discussed but have been tested and deployed in practical pest management programmes with only limited success. Yet the myth persists that better models will provide a ''solution'' to the problem. The reality is that success in using mitigation models is limited because these models are applied to inappropriate situations in which the critical genetic, ecological, biological or logistic assumptions cannot be met. It is difficult to predict in advance which model is appropriate to a particular situation; if the model assumptions cannot be met, applying the model sometimes can increase the rate of resistance development rather than slow it down. Are there any solutions? I believe we already have one. Unfortunately, it is not a simple or easy one to deploy. It involves employing effective agronomic practices to develop and maintain a healthy crop, monitoring pest densities, evaluating economic injury levels so that pesticides are applied only when necessary, deploying and conserving biological control agents, using host-plant resistance, cultural controls of the pest, biorational pest controls, and genetic control methods. As a part of a truly multi-tactic strategy, it is crucial to evaluate the effect of pesticides on natural enemies in order to preserve them in the cropping system. Sometimes, pesticide-resistant natural enemies are effective components of this resistance mitigation programme. Another name for this resistance mitigation model is integrated pest management (IPM). This complex model was outlined in some detail nearly 40 years ago by V. M. Stern and colleagues. To deploy the IPM resistance mitigation model, we must admit that pest management and resistance mitigation programmes are not sustainable if based on a single-tactic strategy. Delaying resistance, whether to traditional pesticides or to transgenic plants containing toxin genes from Bacillus thuringiensis, will require that we develop multi-tactic pest management programmes that incorporate all appropriate pest management approaches. Because pesticides are limited resources, and their loss can result in significant social and economic costs, they should be reserved for situations where they are truly needed--as tools to subdue an unexpected pest population outbreak. Effective multi-tactic IPM programmes delay resistance (= mitigation) because the number and rates of pesticide applications will be reduced.     

Innovations: applications of insect transgenesis

The recent establishment of broadly applicable genetic transformation systems will allow the analysis of gene function in diverse insect species. This will increase our understanding of developmental and evolutionary biology. Furthermore, insect transgenesis will provide new strategies for insect pest management and methods to impair the transmission of pathogens by human disease vectors. However, these powerful techniques must be applied with great care to avoid harm to our environment.     

Exploiting volatile organic compounds in crop protection: A systematic review of 1-octen-3-ol and 3-octanone

The 21st century has brought new challenges to the agri-food industry due to population growth, global warming, and greater public awareness of environmental issues. Ensuring global food security for future generations is crucial. However, pests, weeds, and diseases still significantly contribute to crop losses, and the availability of effective conventional synthetic pesticides is decreasing. To address this, new and diverse pest management tools are needed. One pest management tool showing potential for invertebrate pest management is the exploitation of volatile organic compounds (VOCs)—in particular, the compounds 1-octen-3-ol and 3-octanone. This review aims to explore the extent to which 1-octen-3-ol and 3-octanone show potential in the future management of invertebrate crop and animal pests. A significant increase in the rate of publication of literature on the use of 1-octen-3-ol and 3-octanone in crop protection since 2018 is identified by this review, therefore, showing the potential importance of these compounds for use in future pest management. This review also identifies key interactions between naturally occurring biosynthesised 1-octen-3-ol and 3-octanone, and a range of invertebrate targets. Many of these interactions with key crop pests are sourced from the taxonomic families Lamiaceae, Fabaceae, and Trichomaceae. However, analysis of the practical application of these sources in an integrated pest management programme identifies clear limitations with the use of naturally occurring biosynthesised 1-octen-3-ol and 3-octanone. Rather, future focus should be placed on the development and exploitation of synthesised nature identical 1-octen-3-ol and 3-octanone for use as a biopesticide product. Overall, 1-octen-3-ol and 3-octanone show potential for exploitation in future crop protection, being abundant in source and diversity of invertebrate interactions. However, their use as a naturally occurring biosynthesised chemical is likely not practical for direct implementation in crop protection. Rather, focus should be placed on the development and exploitation of synthesised nature identical variants of these compounds for use as a biopesticide.     

基因工程生物的生态影响及其评价

随着基因工程技术的迅速发展,基因工程产生的生物将被广泛地应用于非受控的自然环境中,这将带来诸多的环境和生态方面的问题。本文概述了基因工程生物在非受控环境下可能产生的生态影响,提出了“基因工程生态学”这一新的应用生态学分支领域,探讨了该分支学科的概念、主要研究内容和目标,以及当前应采取的研究策略,并就发展基因工程生态学的有关问题提出了建议。     

植物病原物的群体遗传学

品种单一化、生产密集型和一年多茬的现代农业特点导致病原物呈现出进化速度加快、致病力增强及流行风险增大趋势。深入研究病原物群体遗传学对认识病害的流行、有效选育和使用抗性品种乃至控制病害具有重要意义。文章阐述了植物病原物群体遗传学的研究目标和内容、突变、基因迁移、基因重组、随机遗传漂变和自然选择5大遗传机制在植物病原物进化过程中的作用, 以及目前植物病原物群体遗传学研究的现状。     

植物病原物的群体遗传学

品种单一化、生产密集型和一年多茬的现代农业特点导致病原物呈现出进化速度加快、致病力增强及流行风险增大趋势。深入研究病原物群体遗传学对认识病害的流行、有效选育和使用抗性品种乃至控制病害具有重要意义。文章阐述了植物病原物群体遗传学的研究目标和内容、突变、基因迁移、基因重组、随机遗传漂变和自然选择5大遗传机制在植物病原物进化过程中的作用,以及目前植物病原物群体遗传学研究的现状。     

Regulatory impact on insect biotechnology and pest management

The application of insect biotechnology is promising for the development of environmentally compatible pest management solutions. As we have refined and enhanced genetic engineering techniques in several insect species that cause significant economic loss and public health injury, it has become clear that insect biotechnology will move forward as one of the key tools of pest management in agriculture and in the human environment. Well characterized genetic elements can be manipulated toward specific aims and maintain a viable insect, albeit one with diminished capacity to exchange genetic material, vector a virus or bacterium, or complete its life cycle. Despite this degree of knowledge and precision, there remain unanswered questions regarding environmental fate, release and public acceptance of this technology. The uncertainty surrounding any novel technology inevitably increases the level of regulatory scrutiny associated with its use. Although the term “insect biotechnology” has many connotations, it certainly includes the genetic modification of symbiotic or commensally associated microbes as a means of delivering a trait (e.g. a toxin) to manage plant and human diseases and insect pests. The distinction between this paratransgenic approach and direct genetic modification of insect pests is an important one biologically as well as from a regulatory standpoint. The regulatory framework for microbial applications to agriculture is in many instances in place; however, we must strive to forge the development of guidelines and regulations that will foster deployment of insect biotechnologies.     

Genome editing in Bombyx mori: New opportunities for silkworm functional genomics and the sericulture industry

In recent years, research in life sciences has been remarkably revolutionized owing to the establishment, development and application of genome editing technologies. Genome editing has not only accelerated fundamental research but has also shown promising applications in agricultural breeding and therapy. In particular, the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology has become an indispensable tool in molecular biology owing to its high efficacy and simplicity. Genome editing tools have also been established in silkworm (Bombyx mori), a model organism of Lepidoptera insects with high economic importance. This has remarkably improved the level and scope of silkworm research and could reveal new mechanisms or targets in basic entomology and pest management studies. In this review, we summarize the progress and potential of genome editing in silkworm and its applications in functional genomic studies for generating novel genetic materials.     

浅谈害虫成虫防治技术

目前害虫防治中的一系列问题如害虫幼虫抗药性上升、害虫天敌被大量杀伤、人畜中毒、环境污染与土壤农药残毒日趋严重 ,使以成虫为目标虫态或防治对象而开展的成虫防治策略被广为接受并广泛应用。本文对目前使用的各种成虫防治技术体系进行了概括 ,并列举了成虫防治技术的特点和优点 ,以及进行成虫防治的许多实例。其中信息化合物防治和遗传防治的飞速发展为成虫防治的应用提供了多种途径。     

State‐of‐the‐art CRISPR/Cas9 Technology for Genome Editing in Trypanosomatids

CRISPR/Cas9 technology has revolutionized biology. This prokaryotic defense system against foreign DNA has been repurposed for genome editing in a broad range of cell tissues and organisms. Trypanosomatids are flagellated protozoa belonging to the order Kinetoplastida. Some of its most representative members cause important human diseases affecting millions of people worldwide, such as Chagas disease, sleeping sickness and different forms of leishmaniases. Trypanosomatid infections represent an enormous burden for public health and there are no effective treatments for most of the diseases they cause. Since the emergence of the CRISPR/Cas9 technology, the genetic manipulation of these parasites has notably improved. As a consequence, genome editing is now playing a key role in the functional study of proteins, in the characterization of metabolic pathways, in the validation of alternative targets for antiparasitic interventions, and in the study of parasite biology and pathogenesis. In this work we review the different strategies that have been used to adapt the CRISPR/Cas9 system to Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., as well as the research progress achieved using these approaches. Thereby, we will present the state‐of‐the‐art molecular tools available for genome editing in trypanosomatids to finally point out the future perspectives in the field.     

对我国分子生态学研究近期发展战略的一些思考

分子生态学是多学科交叉的整合性研究领域, 是运用进化生物学理论解决宏观生物学问题的科学。经过半个多世纪的发展, 本学科已日趋成熟, 它不仅已经广泛渗透到宏观生物学的众多学科领域, 而且已经成为连接和融合很多不同学科的桥梁, 是目前最具活力的研究领域之一。其研究的范畴, 从最基础的理论和方法技术, 到格局和模式的发现和描述, 到对过程和机制的深入探讨, 再到付诸于实践的行动和规划指导等各个层次。分子生态学的兴起给宏观生物学带来了若干飞跃性的变化, 使宏观生物学由传统的以观察、测量和推理为主的描述性研究转变为以从生物和种群的遗传构成的变化和历史演化背景上检验、证明科学假设及揭示机制和规律为主的机制性/解释性研究, 因而使得对具有普遍意义的科学规律、生态和进化过程及机制的探索成为可能。分子生态学已经进入组学研究时代, 这使得阐明复杂生态过程、生物地理过程和适应性演化过程的机制性研究由原来难以企及的梦想变成完全可以实现的探求; 它也带来了全新的挑战, 其中最有深远影响的将是对分子生态学研究至关重要的进化生物学基础理论方面的突破, 例如遗传变异理论、种群分化理论、表观遗传因素的作用, 乃至进化生物学的基本知识构架等等。这些方面的进展必将使宏观生物学迎来一场空前的革命, 并对生态学的所有分支学科产生重大影响, 甚至催生诸如生态表观组学这样的新分支学科。对于中国科学家来说, 分子生态学组学时代的开启, 更是一个千载难逢的机遇, 为提出和建立生命科学的新方法、新假说、新思想和新理论提供了莫大的探索空间——此前我们对宏观生物学方法、理论和思想的发展贡献很小。然而, 限制组学时代重大突破的关键因素是理论、概念、理念、实验方法或分析方法方面的创新和突破, 这正是我国分子生态学研究最薄弱的环节。我国教育部门应尽快调整生命科学本科生培养的理念和方法, 以培养具备突出创新潜力的年轻一代后备人才; 同时, 科研项目资助部门和研究人员不仅应清醒地认识本学科领域的发展态势, 更要及时调整思路, 树立新的项目管理理念和治学 理念。     

Naturally occurring and synthetic constitutive-active cytokine receptors in disease and therapy

Cytokines control immune related events and are critically involved in a plethora of patho-physiological processes including autoimmunity and cancer development. Mutations which cause ligand-independent, constitutive activation of cytokine receptors are quite frequently found in diseases. Many constitutive-active cytokine receptor variants have been directly connected to disease development and mechanistically analyzed. Nature’s solutions to generate constitutive cytokine receptors has been recently adopted by synthetic cytokine receptor biology, with the goal to optimize immune therapeutics. Here, CAR T cell immmunotherapy represents the first example to combine synthetic biology with genetic engineering during therapy. Hence, constitutive-active cytokine receptors are therapeutic targets, but also emerging tools to improve or modulate immunotherapeutic strategies. This review gives a comprehensive insight into the field of naturally occurring and synthetic constitutive-active cytokine receptors.     

Engineering plant immune circuit: walking to the bright future with a novel toolbox

Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.     

THE EVOLUTION OF LANDSCAPE GENETICS

The main objective of this special section is not to review the broad field of landscape genetics, but to provide a glimpse of how the developing landscape genetics perspective has the potential to change the way we study evolution. Evolutionary landscape genetics is the study of how migration and population structure affects evolutionary processes. As a field it dates back to Sewall Wright and the origin of theoretical population genetics, but empirical tests of adaptive processes of evolution in natural landscapes have been rare. Now, with recent developments in technology, methodology, and modeling tools, we are poised to trace adaptive genetic variation across space and through time. Not only will we see more empirical tests of classical theory, we can expect to see new phenomena emerging, as we reveal complex interactions among evolutionary processes as they unfold in natural landscapes.     

Tsetse--A haven for microorganisms

Arthropods are involved in the transmission of parasitic and viral agents that cause devastating diseases in animals and plants. Effective control strategies for many of these diseases still rely on the elimination or reduction of vector insect populations. In addition to these pathogenic organisms, arthropods are rich in microbes that are symbiotic in their associations and are often necessary for the fecundity and viability of their hosts. Because the viability of the host often depends on these obligate symbionts, and because these organisms often live in close proximity to disease-causing pathogens, they have been of interest to applied biologists as a potential means to genetically manipulate populations of pest species. As knowledge on these symbiotic associations accumulates from distantly related insect taxa, conserved mechanisms for their transmission and evolutionary histories are beginning to emerge. Here, Serap Aksoy summarizes current knowledge on the functional and evolutionary biology of the multiple symbionts harbored in the medically and agriculturally important insect group, tsetse, and their potential role in the control of trypanosomiasis.