Genetic diversity of Andean Polylepis (Rosaceae) woodlands and inferences regarding their fragmentation history

There is a long‐standing debate on whether the occurrence of the iconic high‐Andes Polylepis woodlands as small and isolated fragments is of natural or anthropogenic origin. We make inferences regarding the fragmentation history based on both a new population genetic study on P. besseri and a synthesis of available studies on the population genetics of Polylepis woodlands. We infer the timing of the main woodland fragmentation event by analysing: (1) the remaining levels of population genetic diversity and the relation to population size; (2) among‐population genetic differentiation; and (3) the difference in genetic diversity between the offspring and adult generation. We retrieved seven publications on the population genetics of five Polylepis spp. We did not find a relationship between population size and genetic diversity, and genetic differentiation was low compared with that reported for similar plant species. These findings do not support a history of long‐term fragmentation. The offspring showed a loss of genetic diversity and increasing differentiation compared with adults, suggesting that the main habitat fragmentation event is of relatively recent origin. For P. besseri, no significant differences were found between the adult and offspring genetic variation. We discuss the conservation and restoration consequences for this important high‐Andean genus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 544–554.     

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis‐regulatory, rather than the coding, regions of developmental genes. This “cis‐regulatory hypothesis” has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis‐regulatory hypothesis. We then test the empirical support for the cis‐regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis‐regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis‐regulatory changes published annually is rapidly increasing. Above the species level, cis‐regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis‐regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question “Do coding or cis‐regulatory mutations cause more phenotypic evolution?” hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.     

Forward from the crossroads of ecology and evolution

Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.     

UNVEILing connections between genotype,phenotype, and fitness in natural populations

Understanding the links between genetic variation and fitness in natural populations is a central goal of evolutionary genetics. This monumental task spans the fields of classical and molecular genetics, population genetics, biochemistry, physiology, developmental biology, and ecology. Advances to our molecular and developmental toolkits are facilitating integrative approaches across these traditionally separate fields, providing a more complete picture of the genotype‐phenotype map in natural and non‐model systems. Here, we summarize research presented at the first annual symposium of the UNVEIL Network, an NSF‐funded collaboration between the University of Montana and the University of Nebraska, Lincoln, which took place from the 1st to the 3rd of June, 2018. We discuss how this body of work advances basic evolutionary science, what it implies for our ability to predict evolutionary change, and how it might inform novel conservation strategies.     

合成生物学与微生物遗传物质的重构

作为一门新兴学科的合成生物学已经展现出巨大的科学价值和应用前景。近年来已经发表了多篇综述文章,从不同角度对合成生物学进行了总结和论述。文章首次对合成生物学和微生物遗传学之间的关系进行了阐述,同时介绍了合成生物学在微生物遗传物质的重构方面最近的研究进展,包括微生物遗传物质的合成、设计和精简,遗传元件的标准化和遗传线路的模块化。也探讨了合成生物学与微生物遗传工程的关系。     

基于高密度SNP数据的东亚人群遗传结构研究

目的 东亚疆域辽阔,民族众多,有着广泛多样的语言。中国34个省级行政区可划分为7个地理分区,人群主要分属世界七大语系。已有研究主要集中在东亚人群的起源、迁徙、融合等遗传历史。本文基于5 147份世界人群个体的高密度单核苷酸多态性（SNP）数据,从地域及语言两个角度研究东亚人群尤其是中国人群与世界其他人群的遗传关系,研究中国人群的遗传关系和遗传结构。方法 收集了5 147份世界人群个体的高密度SNP数据,并对其进行质控、合并。通过频率差异分析方法对最终获得的32 789个SNP进行统计学检验,并进一步使用主成分分析、系统发育树、祖先成分分析和D检验统计等方法,对东亚人群与世界其他人群的遗传关系,以及中国人群的遗传关系和遗传结构进行研究。结果 研究发现东亚人群与非洲、美洲和欧洲人群存在显著差异。中国人群可分为7个亚群,不同人群间的遗传聚类与其地理分布、语系语族和族源历史有很强的相关性。结论 本文研究了中国人群与世界人群的遗传关系和差异,并系统研究了中国人群的遗传亚结构。这将丰富东亚人群的群体遗传学、法医遗传学等研究基础,为个体化医疗等工作提供数据支撑。     

雪豹保护遗传学和基因组学研究进展

雪豹(Panthera uncia)隶属于食肉目猫科豹属,是生活在青藏高原及其周边地区的旗舰物种。随着分子生物学和高通量测序技术的发展,雪豹保护遗传学和保护基因组学研究得到快速的发展,其中非损伤性遗传取样法显著推动了雪豹保护遗传学研究。本文综述了非损伤性遗传取样法在雪豹物种鉴定、个体识别和性别鉴定等研究中的应用,雪豹的系统发生地位、系统地理格局和种群遗传结构及其亚种争议、演化历史、适应性演化和基因组特征等保护遗传学和基因组学方面的研究现状和进展,并对雪豹保护遗传学和基因组学未来发展趋势进行了展望,以期促进雪豹保护生物学研究和保护对策的科学制定。     

An ecologist's guide to the animal model

1. Efforts to understand the links between evolutionary and ecological dynamics hinge on our ability to measure and understand how genes influence phenotypes, fitness and population dynamics. Quantitative genetics provides a range of theoretical and empirical tools with which to achieve this when the relatedness between individuals within a population is known.
2. A number of recent studies have used a type of mixed-effects model, known as the animal model, to estimate the genetic component of phenotypic variation using data collected in the field. Here, we provide a practical guide for ecologists interested in exploring the potential to apply this quantitative genetic method in their research.
3. We begin by outlining, in simple terms, key concepts in quantitative genetics and how an animal model estimates relevant quantitative genetic parameters, such as heritabilities or genetic correlations.
4. We then provide three detailed example tutorials, for implementation in a variety of software packages, for some basic applications of the animal model. We discuss several important statistical issues relating to best practice when fitting different kinds of mixed models.
5. We conclude by briefly summarizing more complex applications of the animal model, and by highlighting key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.     

Cladodes,leaf-like organs in Asparagus,show the significance of co-option of pre-existing genetic regulatory circuit for morphological diversity of plants

Plants in the genus Asparagus have determinate leaf-like organs called cladodes in the position of leaf axils. Because of their leaf-like morphology, axillary position, and morphological variation, it has been unclear how this unusual organ has evolved and diversified. In the previous study, we have shown that cladodes in the genus Asparagus are modified axillary shoots and proposed a model that cladodes have arisen by co-option and deployment of genetic regulatory circuit (GRC) involved in leaf development. Moreover, we proposed that the alteration of the expression pattern of genes involved in establishment of adaxial/abaxial polarity has led to the morphological diversification from leaf-like to rod-like form of cladodes in the genus. Thus, these results indicated that the co-option and alteration of pre-existing GRC play an important role in acquisition and subsequent morphological diversification.Here, we present data of further expression analysis of A. asparagoides. The results suggested that only a part of the GRC involved in leaf development appears to have been co-opted into cladode development. Based on our study and several examples of the morphological diversification, we briefly discuss the importance of co-option of pre-existing GRC and its genetic modularity in the morphological diversity of plants during evolution.     

Advancing ecological understandings through technological transformations in noninvasive genetics

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics.     

植物景观遗传学研究进展

植物景观遗传学是新兴的景观遗传学交叉学科的一个重要研究方向。目前植物景观遗传学的研究虽落后于动物,但其在生物多样性保护方面具有的巨大潜力不可忽视。从景观特征对遗传结构、环境因素对适应性遗传变异影响两个方面,系统综述了近十年来国际上植物景观遗传学的研究焦点和研究进展,比较了植物景观遗传学与动物景观遗传学研究在研究设计和研究方法上的异同,并基于将来植物景观遗传学由对空间遗传结构的描述发展为对景观遗传效应的量化分析及预测的发展框架,具体针对目前景观特征与遗传结构研究设计的系统性差、遗传结构与景观格局在时间上的误配、适应性位点与环境变量的模糊匹配、中性遗传变异与适应性遗传变异研究的分隔、景观与遗传关系分析方法的局限等五个方面提出了研究对策。     

天敌瓢虫种群遗传学及其在生物防治中的应用

天敌瓢虫常在农业生产的生物防治中被广泛引进和使用。这种使用过程往往会导致天敌瓢虫在遗传水平的改变,并最终影响到其生物防治的使用效果和本地生态多样性。对天敌瓢虫种群遗传学的研究,有助于我们认识甚至预测这种遗传改变的规律和生态机制,从而为生物防治计划的优化提供理论基础。本文介绍了种群遗传学的研究方法,分析在生物防治中促进天敌瓢虫遗传改变的因素,以及几种常见的天敌瓢虫种群演变情况,并讨论种群遗传学在天敌瓢虫研究的未来方向。     

Evolutionary change in the functional specificity of genes.

Species throughout the animal kingdom share not only housekeeping but also many key regulatory genes. Nonetheless, species differ from one another developmentally and thus, also morphologically. One of the general aims of comparative developmental genetics is to understand how similar molecules can generate the known diversity of biological form. Here, we argue that gene function can change in different ways during the evolution of developmental processes. Genes can be recruited to serve completely new functions in a new regulatory linkage (co-option), they can change their molecular specificity while remaining in the original (homologous) developmental program and can, at the same time, retain other functions. We describe evidence for such evolutionary patterns based on the comparison of loss-of-function mutations of homologous genes of the two free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Ultimately, it is the interplay of conservation and change of the specificity of genes and genetic networks that generates developmental novelty over evolutionary time.     

新编人类群体遗传学实验一组

本文介绍了一组新编的人群嗅阈测量实验。该实验既兼顾了培养学生进行人类群体遗传调查的基本方法与技能和调查当地人群的嗅觉相关基因频率与分布两方面,又兼顾了课堂实验与课外研究两方面,是实验教学改革中比较成功的一种类型。 Abstract:This paper presents a group of new experiments on human olfactory threshold measurement.It is a successful educational reform in teaching of genetic experiment.It considered not only training students' skills in the research on population genetics and investigating local population's olfactory allelic frequency,but also class experiments and research out of the class.     

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.     

植物分子群体遗传学研究动态

分子群体遗传学是当代进化生物学研究的支柱学科, 也是遗传育种和关于遗传关联作图和连锁分析的基础理论学科。分子群体遗传学是在经典群体遗传的基础上发展起来的, 它利用大分子主要是DNA序列的变异式样来研究群体的遗传结构及引起群体遗传变化的因素与群体遗传结构的关系, 从而使得遗传学家能够从数量上精确地推知群体的进化演变, 不仅克服了经典的群体遗传学通常只能研究群体遗传结构短期变化的局限性, 而且可检验以往关于长期进化或遗传系统稳定性推论的可靠程度。同时, 对群体中分子序列变异式样的研究也使人们开始重新审视达尔文的以“自然选择”为核心的进化学说。到目前为止, 分子群体遗传学已经取得长足的发展, 阐明了许多重要的科学问题, 如一些重要农作物的DNA多态性式样、连锁不平衡水平及其影响因素、种群的变迁历史、基因进化的遗传学动力等, 更为重要的是, 在分子群体遗传学基础上建立起来的新兴的学科如分子系统地理学等也得到了迅速的发展。文中综述了植物分子群体遗传研究的内容及最新成果。     

寄生蠕虫的群体遗传学研究

寄生蠕虫群体遗传学研究常用的遗传标记有等位酶、线粒体DNA、随机扩增多态性DNA或扩增性片段长度多态性和微卫星DNA等。应用这些遗传标记的研究表明,大多数寄生蠕虫群体遗传结构有不同水平的变异,这些变异的产生主要与寄生虫的生活史和群体生态、宿主的地理分布和环境等因素有关,并因此提出了有关遗传变异的一些假说。本文对寄生蠕虫群体遗传学的研究作一综述。 Abstract:Genetic markers including allozyme,mtDNA,RAPD/RFLP and micro DNA have been used in the research of helminth population genetics.Available data on helminth genetic variability have shown that most helminth populations exhibit different levels of genetic variation resulting mainly from the pattern of life cycle,geographical distribution and parasite-host interaction,and several hypotheses have been proposed to explain the genetic variation.     

以发育模块重复征用和整合为基础的进化创新机制

进化新征的起源和分化是进化发育生物学研究的核心问题。通过对多细胞生物早期发育调控机制的比较分析,发现亲缘关系较远的生物所共有的一些形态特征受保守的发育调控程序调节（深同源性）。许多创新性状的发生是基于对预先存在的基因或发育调控模块的重复利用和整合。发育基因调控网络在结构和功能上高度模块化,因此不仅可以通过模块拆分和重复征用改变发育程式,而且也增强了调控网络自身的进化力。研究基因调控网络和发育系统的进化动态将有助于更深入地认识生物演化过程中创新性状发生和表型进化的分子机制。