Proportions of different habitat types are critical to the fate of a resistance allele

We describe a simple deterministic theoretical framework for analysing the gene frequency evolution of two alternative alleles at a single genetic locus in a habitat comprising two environments in which the genotypes have different relative fitnesses. We illustrate this for adaptation of pest insects, where one allele (resistance to toxins expressed in transgenic crops) is favoured in one environment (transgenic plants) and the other allele (susceptibility to toxins) is favoured in the other environment (‘refuges’ of non-transgenic plants). The evolution of allele frequencies depends on selection pressure because of relative sizes of the environments and relative fitnesses of the genotypes in each environment. We demonstrate that there are critical threshold proportions for habitat division that determine equilibrium allele frequencies. The stability of the system depends on relationships between the relative genotype fitnesses. In some cases, the division of the habitat in exactly the threshold proportions removes selection pressure and maintains polymorphism at all allele frequencies.     

Partial bivoltinism in a gregarious endoparasitoid: larval diapause as influenced by season and sharing a host

The yearly timing of the life cycle of a parasitoid is a key element of its life‐history strategy. I examine here factors influencing the expression of partial bivoltinism in Tetrastichus julis Walker (Hymenoptera: Eulophidae), a specialist parasitoid introduced to North America to attack its univoltine host, the cereal leaf beetle, Oulema melanopus (L.) (Coleoptera: Chrysomelidae). The varying tendency was assessed of individuals of this gregarious larval parasitoid to either emerge as adults in the same summer they mature, or to enter diapause to emerge the following year. Parasitized hosts were obtained by rearing cereal leaf beetles collected as mature larvae from grain fields in northern Utah (western USA) throughout the growing seasons in 2013 and 2014. Cocoons spun by these beetles were held to determine patterns over the spring and summer in the tendency of the parasitoid to forgo larval diapause. A high percentage (nearly 90% in 2013) of parasitoid individuals were found to forgo diapause and emerge in the same summer from earliest maturing hosts. This percentage rapidly declined to 20% or less of individuals forgoing diapause and emerging from cocoons as the summer advanced. The percentage of parasitoid individuals forgoing diapause increased significantly at a given time of season (early or late) as the number of conspecifics with which an individual shared a host larva increased. These results may reflect a trade‐off for individual parasitoids in which greater success in finding – and ovipositing in – host larvae the following spring vs. in summer, is countered by reduced survivorship in diapausing over the winter vs. emerging in the same summer in which the parasitoid matures. Expression of partial bivoltinism of T. julis, as affected strongly by both season and within‐host density, results in high rates of parasitism of cereal leaf beetles both early and late in the season.     

Hyposensitive canopy conductance renders ecosystems vulnerable to meteorological droughts

Increased meteorological drought intensity with rising atmospheric demand for water (hereafter vapor pressure deficit [VPD]) increases the risk of tree mortality and ecosystem dysfunction worldwide. Ecosystem-scale water-use strategy is increasingly recognized as a key factor in regulating drought-related ecosystem responses. However, the link between water-use strategy and ecosystem vulnerability to meteorological droughts is poorly established. Using the global flux observations, historic hydroclimatic data, remote-sensing products, and plant functional-trait archive, we identified potentially vulnerable ecosystems, examining how ecosystem water-use strategy, quantified by the percentage bias (δ) of the empirical canopy conductance sensitivity to VPD relative to the theoretical value, mediated ecosystem responses to droughts. We found that prevailing soil water availability substantially impacted δ in dryland regions where ecosystems with insufficient soil moisture usually showed conservative water-use strategy, while ecosystems in humid regions exhibited more pronounced climatic adaptability. Hyposensitive and hypersensitive ecosystems, classified based on δ falling below or above the theoretical sensitivity, respectively, achieved similar net ecosystem productivity during droughts, employing different structural and functional strategies. However, hyposensitive ecosystems, risking their hydraulic system with a permissive water-use strategy, were unable to recover from droughts as quickly as hypersensitive ones. Our findings highlight that processed-based models predicting current functions and future performance of vegetation should account for the greater vulnerability of hyposensitive ecosystems to intensifying atmospheric and soil droughts.     

低温对蝶蛹金小蜂卵成熟及其数量动态的影响

寄生蜂卵成熟动态影响其产卵决策行为,因而对于认识寄生蜂搜寻行为生态学机理具有重要意义。以蝶蛹金小蜂(Pteromalus puparum)-菜粉蝶(Pieris rapae)为模式生物,首先连续3周每隔24 h详细观察子代蜂幼期不同发育阶段的体型、卵巢管以及寄主蛹的外部形态,以此为基础观察了低温处理(模拟越冬温度)被寄生蛹对子代蜂成熟卵数量动态的影响。蝶蛹金小蜂胚后发育历时约2周,其中卵期1 d;幼虫历期约7 d。初孵幼虫体透明;胚后第3—6天体积快速增大,然后减缓,体色由绿变黄;胚后第8天进入预蛹,第9—12天蛹淡色,复眼由淡黄变为深红,第13—14天蛹暗黑色,并逐渐带有金属光泽。卵巢管在羽化当天即开始沉积卵黄,并在羽化后1—4 d连续增加直到出现卵吸收;羽化后5—6 d成熟卵数量增速不明显甚至略有减小。寄主蛹随子代蜂从卵发育至幼虫再到蛹体色从绿色变为灰褐色再到土黄色。低温处理被寄生的寄主蛹(寄生蜂处于老熟幼虫或蛹期)后,羽化成虫的卵巢管略细,成熟卵数量较少。成熟卵数量的变化不仅受低温处理的影响,而且受雌蜂体型大小和日龄的影响;低温处理明显减缓卵成熟速率,各日龄期成熟卵数量均明显减少;适温下成熟卵数量于羽化后第4天达到峰值,而低温处理下成熟卵数量达到峰值的时间延迟至第7天。研究表明,越冬低温对来年羽化的蝶蛹金小蜂卵成熟动态具有不良影响。     

长链非编码RNA的功能与疾病治疗的潜力

人类基因组转录本长度>200 nt（核苷酸）、不编码蛋白质的RNA分子为长链非编码RNA（long non-coding RNA,lncRNA)。lncRNA可在多个层面调节基因表达,其功能失调与包括肿瘤在内的很多人类疾病密切相关。本文概述lncRNA的种类、功能与疾病的关系,讨论基于lncRNA基因编辑、干细胞修饰及其与miRNA、蛋白质相互作用等的治疗潜能。     

基于功能性状的水杉原生母树种群生境适应策略

植物的功能性状变异和表型可塑性是其应对异质生境的主要机制, 对植物的生长和分布有重要贡献。本文以湖北星斗山国家级自然保护区的水杉(Metasequoia glyptostroboides)原生母树为研究对象, 分析了母树种群功能性状对树木形态、地形因子及人为干扰的响应机制。结果表明: 水杉原生母树叶面积、叶干重和比叶面积的变异幅度大, 可塑性较强, 而枝和叶的干物质含量稳定性最高。人为干扰和4个地形因子均对每个功能性状变异方差有5%-20%的解释度, 冠幅对枝、叶干物质含量的变异方差有高达38%和76%的解释度。5个功能性状主要受海拔、坡位和人为干扰影响, 其中, 比叶面积对环境因子和干扰的响应规律不明显, 叶面积和叶干重在强烈人为干扰的环境中普遍增大, 枝和叶的干物质含量对坡向的变化最敏感。总之, 水杉原生母树种群通过功能性状变异对环境能产生一定的可塑性响应, 但人为干扰对母树生长影响较大, 建议人工辅助更新, 并适度减少农业和建筑对现存母树的影响。     

Sampling strategy optimization to increase statistical power in landscape genomics: A simulation‐based approach

An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographical representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites (20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.     

高寒地区植食性小哺乳动物的越冬对策

利用多年工作积累的观察资料 ,讨论几种植食性小哺乳动物的越冬对策。其中 ,高原鼢鼠、甘肃鼠兔和根田鼠均贮存食物 ,以减少寒冷条件下的取食暴露。高原鼢鼠以个体为单位贮存和利用贮存食物 ,相互之间不协作 ;而两种地面活动的种类则可能以家庭为单位贮存和分享越冬食物。喜马拉雅旱獭体型较大 ,不贮存食物 ,它以冬眠方式越冬 ,这是一种对食物依赖最小的方式。高原鼠兔 ,既不贮存食物 ,也不进入冬眠 ,而是主要靠增加身体产热能力来保持体温 ,抵御严寒。作者认为 ,动物自身的生理限制、生活方式、环境条件以及捕食风险等诸多因素的综合作用决定动物的越冬对策。     

Neutral space analysis for a Boolean network model of the fission yeast cell cycle network

Background

Interactions between genes and their products give rise to complex circuits known as gene regulatory networks (GRN) that enable cells to process information and respond to external stimuli. Several important processes for life, depend of an accurate and context-specific regulation of gene expression, such as the cell cycle, which can be analyzed through its GRN, where deregulation can lead to cancer in animals or a directed regulation could be applied for biotechnological processes using yeast. An approach to study the robustness of GRN is through the neutral space. In this paper, we explore the neutral space of a Schizosaccharomyces pombe (fission yeast) cell cycle network through an evolution strategy to generate a neutral graph, composed of Boolean regulatory networks that share the same state sequences of the fission yeast cell cycle.

Results

Through simulations it was found that in the generated neutral graph, the functional networks that are not in the wildtype connected component have in general a Hamming distance more than 3 with the wildtype, and more than 10 between the other disconnected functional networks. Significant differences were found between the functional networks in the connected component of the wildtype network and the rest of the network, not only at a topological level, but also at the state space level, where significant differences in the distribution of the basin of attraction for the G₁ fixed point was found for deterministic updating schemes.

Conclusions

In general, functional networks in the wildtype network connected component, can mutate up to no more than 3 times, then they reach a point of no return where the networks leave the connected component of the wildtype. The proposed method to construct a neutral graph is general and can be used to explore the neutral space of other biologically interesting networks, and also formulate new biological hypotheses studying the functional networks in the wildtype network connected component.     

Historical and contemporary gene dispersal in wild carrot (Daucus carota ssp. carota) populations

Background and Aims

Wild carrot is the ancestor of cultivated carrot and is the most important gene pool for carrot breeding. Transgenic carrot may be released into the environment in the future. The aim of the present study was to determine how far a gene can disperse in wild carrot populations, facilitating risk assessment and management of transgene introgression from cultivated to wild carrots and helping to design sampling strategies for germplasm collections.

Methods

Wild carrots were sampled from Meijendel and Alkmaar in The Netherlands and genotyped with 12 microsatellite markers. Spatial autocorrelation analyses were used to detect spatial genetic structures (SGSs). Historical gene dispersal estimates were based on an isolation by distance model. Mating system and contemporary pollen dispersal were estimated using 437 offspring of 20 mothers with different spatial distances and a correlated paternity analysis in the Meijendel population.

Key Results

Significant SGSs are found in both populations and they are not significantly different from each other. Combined SGS analysis indicated significant positive genetic correlations up to 27 m. Historical gene dispersal σ_g and neighbourhood size N_b were estimated to be 4–12 m [95 % confidence interval (CI): 3–25] and 42–73 plants (95 % CI: 28–322) in Meijendel and 10–31 m (95 % CI: 7–∞) and 57–198 plants (95 % CI: 28–∞) in Alkmaar with longer gene dispersal in lower density populations. Contemporary pollen dispersal follows a fat-tailed exponential-power distribution, implying pollen of wild carrots could be dispersed by insects over long distance. The estimated outcrossing rate was 96 %.

Conclusions

SGSs in wild carrots may be the result of high outcrossing, restricted seed dispersal and long-distance pollen dispersal. High outcrossing and long-distance pollen dispersal suggest high frequency of transgene flow might occur from cultivated to wild carrots and that they could easily spread within and between populations.