Real‐time observation of flexible domain movements in CRISPR–Cas9

The CRISPR‐associated protein Cas9 is widely used for genome editing because it cleaves target DNA through the assistance of a single‐guide RNA (sgRNA). Structural studies have revealed the multi‐domain architecture of Cas9 and suggested sequential domain movements of Cas9 upon binding to the sgRNA and the target DNA. These studies also hinted at the flexibility between domains; however, it remains unclear whether these flexible movements occur in solution. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single‐molecule FRET. We found that the flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures. Importantly, the HNH nuclease domain only accessed the DNA cleavage position during such flexible movements, suggesting the importance of this flexibility in the DNA cleavage process. Our FRET data also revealed the conformational flexibility of apo‐Cas9, which may play a role in the assembly with the sgRNA. Collectively, our results highlight the potential role of domain fluctuations in driving Cas9‐catalyzed DNA cleavage.     

种群密度对大果虫实形态特征与异速生长的影响

为揭示种群密度与植物形态特征、器官生物量间的异速生长关系,阐明植物在退化土地恢复过程中的适应策略,以大果虫实为材料,通过异速生长分析方法,研究种群密度对其形态特征、生物量分配与异速生长的影响。结果表明,种群密度对大果虫实的株型构建产生了显著地影响。随着密度增大,大果虫实株高呈减小趋势,其分枝数及分枝长度明显减小。大果虫实各器官生物量随密度增大而显著减小。随密度增大,茎和繁殖器官生物量分配呈减小趋势,根和叶片生物量分配呈增大趋势。这与最优化分配理论中水分、营养物质及光资源受限时的情况一致。密度对大果虫实株高:根生物量间异速生长具有显著影响,且对株高与器官生物量间异速指数和个体大小产生了极显著影响。密度对根:地上部分、叶片:根、繁殖器官:根生物量间的影响属于表观可塑性,而对根:茎、茎:地上部分、叶:其他器官及繁殖器官:其他器官生物量间的影响属于真正可塑性,说明密度改变了大果虫实的株型发育系统,并影响各器官间的异速生长,进而权衡器官生物量分配以完成生活史。     

川西林线交错带岷江冷杉幼苗异龄叶形态对长期模拟增温的响应

全球气候变暖对高纬度、高海拔地区的植物形态产生强烈影响。川西林线交错带是青藏高原东部高寒生态系统的重要组成部分,对全球变化极度敏感。以川西林线交错带岷江冷杉(Abies faxoniana)幼苗异龄叶为对象,采用原位开顶式生长室(Open-top chamber,OTCs)模拟增温,研究了长期模拟增温下岷江冷杉幼苗异龄叶片叶长、叶厚等叶形态的响应,采用表型可塑性指数和变异系数对叶形态的可塑性进行分析。结果表明:增温限制岷江冷杉幼苗叶片的增长、增宽和叶面积、体积的扩大,使叶长、叶宽、叶面积、叶体积分别较对照减小12.77%、11.86%、17.76%、11.49%;增温促进叶片厚度的增加,较对照增加7.27%;除叶长宽比外,增温对其余叶形态均产生显著影响(P0.05)。叶形态对模拟增温的响应具有显著的年龄差异(P0.05)。温度、叶龄的交互效应对叶长和叶面积影响显著(P0.05),对叶宽和叶厚影响不显著(P0.05)。两种表型可塑性分析结果表明,除1 a叶叶长外,增温不同程度增大各叶形态可塑性。长期增温使冷杉幼苗叶片有旱生倾向且形态值更发散。研究提供了岷江冷杉幼苗叶片对长期增温的差异性响应证据,为评估青藏高原东缘优势植物对响应气候变暖提供了基础数据和理论参考。     

Direct Control of SPEECHLESS by PIF4 in the High-Temperature Response of Stomatal Development

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Spatiotemporal dynamics and genome‐wide association analysis of desiccation tolerance in Drosophila melanogaster

Water availability is a major environmental challenge to a variety of terrestrial organisms. In insects, desiccation tolerance varies predictably over spatial and temporal scales and is an important physiological determinant of fitness in natural populations. Here, we examine the dynamics of desiccation tolerance in North American populations of Drosophila melanogaster using: (a) natural populations sampled across latitudes and seasons; (b) experimental evolution in field mesocosms over seasonal time; (c) genome‐wide associations to identify SNPs/genes associated with variation for desiccation tolerance; and (d) subsequent analysis of patterns of clinal/seasonal enrichment in existing pooled sequencing data of populations sampled in both North America and Australia. A cline in desiccation tolerance was observed, for which tolerance exhibited a positive association with latitude; tolerance also varied predictably with culture temperature, demonstrating a significant degree of thermal plasticity. Desiccation tolerance evolved rapidly in field mesocosms, although only males showed differences in desiccation tolerance between spring and autumn collections from natural populations. Water loss rates did not vary significantly among latitudinal or seasonal populations; however, changes in metabolic rates during prolonged exposure to dry conditions are consistent with increased tolerance in higher latitude populations. Genome‐wide associations in a panel of inbred lines identified twenty‐five SNPs in twenty‐one loci associated with sex‐averaged desiccation tolerance, but there is no robust signal of spatially varying selection on genes associated with desiccation tolerance. Together, our results suggest that desiccation tolerance is a complex and important fitness component that evolves rapidly and predictably in natural populations.     

紫耳箭竹克隆形态可塑性对典型冠层结构及光环境的响应

在重庆金佛山国家自然保护内,选择了3种典型群落类型(落叶阔叶林、常绿落叶阔叶混交林和常绿阔叶林),使用Hemiview数字植物冠层分析系统量化群落冠层结构和光环境特征,并对林下紫耳箭竹(Fargesia decurvata)的形态可塑性特征进行调查,分析冠层结构和光环境特征改变下紫耳箭竹形态可塑性的差异,并探讨它们之间的相互关系。结果表明:(1)随着落叶阔叶林"常绿落叶阔叶混交林"常绿阔叶林演替的进行,群落的冠层开度降低,叶面积指数增加,平均叶倾角变小,趋于水平化,冠层对光的截获能力提高,林下光照的强度降低(P0.05)。(2)随着光照强度的降低,紫耳箭竹分株矮小化,叶片变窄,生物量积累降低,但通过增大比茎长、叶面积率和比叶面积提高对光的利用效率,并增大分枝角度和比隔长有效适应弱光环境。(3)在光照条件差的常绿阔叶林下,紫耳箭竹降低对地下茎的投资,将较多的生物量用于秆的增高增长和叶片的生长;而在光照条件好的落叶阔叶林环境下,紫耳箭竹降低对枝、叶生物量的分配,则加大对地下茎的投资,可认为是克隆植物对水分资源所表现的一种觅食行为。研究表明,紫耳箭竹种群随着冠层结构的改变发生了明显的可塑性变化,这些可塑性变化是种群对冠层结构和光环境差异的适应性反应的结果,有利于增强种群对异质生境中光资源的获取和利用;群落内部可以通过调控冠层结构的改变协调和控制小径竹种群的发展。     

The influence of developmental environment on courtship song in cactophilic Drosophila

Closely related species often differ in the signals involved in sexual communication and mate recognition. Determining the factors influencing signal quality (i.e. signal's content and conspicuousness) provides an important insight into the potential pathways by which these interspecific differences evolve. Host specificity could bias the direction of the evolution of sexual communication and the mate recognition system, favouring sensory channels that work best in the different host conditions. In this study, we focus on the cactophilic sibling species Drosophila buzzatii and D. koepferae that have diverged not only in the sensory channel used for sexual communication and mate recognition but also in the cactus species that use as primary hosts. We evaluate the role of the developmental environment in generating courtship song variation using an isofemale line design. Our results show that host environment during development induces changes in the courtship song of D. koepferae males, but not in D. buzzatii males. Moreover, we report for the first time that host rearing environment affects the conspicuousness of courtship song (i.e. song volume). Our results are mainly discussed in the context of the sensory drive hypothesis.     

Gene flow does not prevent personality and morphological differentiation between two blue tit populations

Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to 5 years. We then compared adult phenotypes between the two populations, as well as trait‐specific Q_st and F_st. Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Q_st–F_st comparisons revealed that the trait divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Q_st–F_st comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits.     

Coherent synthesis of genomic associations with phenotypes and home environments

Local adaptation is often studied via (i) multiple common garden experiments comparing performance of genotypes in different environments and (ii) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome‐wide association model of genotype interactions with continuous environmental gradients (G × E), that is reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome–environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness trade‐offs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting G × E associations with fitness were enriched in genic regions, putative partial selective sweeps and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point towards the loci underlying G × E and local adaptation; coherent models of diverse data provide a principled basis for synthesis.