Independent Molecular Basis of Convergent Highland Adaptation in Maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.     

Adaptation of Rodents Living in a Highland: Combination of Mitochondrial Introgression and Convergent Molecular Evolution

Populations of four species of narrow-headed rats of the genus Stenocephalemys were examined for the presence of a mutation in the mitochondrial cytochrome b gene resulting in an amino acid substitution in the translated protein. This substitution was also found in hamsters of the subfamily Sigmodontinae inhabiting the highlands of the Andes. Simulation of three-dimensional structure of the protein showed that this substitution is located in the active site and may have a functional significance. We assumed an independent emergence of this substitution in the populations of two Afroalpine species of Stenocephalemys, which is the first known example of a combination of introgression and convergent molecular evolution.     

Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia

Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.     

Demographic History,Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia

Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.     

Adaptation to climate through flowering phenology: a case study in Medicago truncatula

Local climatic conditions likely constitute an important selective pressure on genes underlying important fitness‐related traits such as flowering time, and in many species, flowering phenology and climatic gradients strongly covary. To test whether climate shapes the genetic variation on flowering time genes and to identify candidate flowering genes involved in the adaptation to environmental heterogeneity, we used a large Medicago truncatula core collection to examine the association between nucleotide polymorphisms at 224 candidate genes and both climate variables and flowering phenotypes. Unlike genome‐wide studies, candidate gene approaches are expected to enrich for the number of meaningful trait associations because they specifically target genes that are known to affect the trait of interest. We found that flowering time mediates adaptation to climatic conditions mainly by variation at genes located upstream in the flowering pathways, close to the environmental stimuli. Variables related to the annual precipitation regime reflected selective constraints on flowering time genes better than the other variables tested (temperature, altitude, latitude or longitude). By comparing phenotype and climate associations, we identified 12 flowering genes as the most promising candidates responsible for phenological adaptation to climate. Four of these genes were located in the known flowering time QTL region on chromosome 7. However, climate and flowering associations also highlighted largely distinct gene sets, suggesting different genetic architectures for adaptation to climate and flowering onset.     

植物对荒漠生境的趋同适应

植物体的表型特征是其基因与生态因子二者共同作用的结果,生活在荒漠生境中的植物由于遭受相同的自然选择压力,在外部形态、内部结构、生活史特征、生理特性、次生代谢产物的合成以及大分子物质的诱导产生等诸多表型方面均表现出高度趋同的现象。随着研究手段的改善,对植物趋同适应的研究已逐渐深入到了分子水平。研究荒漠生境中植物的趋同适应对于人们深刻地认识和理解植物与环境间的相互关系及其分子基础,以及利用功能基因改良重要作物的抗逆性等将会产生深远的影响;对极端干旱环境下特殊次生代谢产物的定向发现及重要先导化合物的筛选等有着重大的指导意义;同时对我国的西部开发及干旱区的生态恢复亦有重要的参考价值。     

Convergent evolution of the mating behaviour of founder-flush populations of the housefly

Courtship bouts of six founder-flush populations (two-pair founder-flush) and two nonbottlenecked controls of the housefly were videotaped over the course of 26 generations in order to evaluate the stability of mating behaviour. Limited-choice mate preference tests were conducted periodically to assess levels of homogamic preference. Both founder-flush and control treatments showed significant evolutionary potential in courtship, along with homogamic and heterogamic preferences. The founder-flush populations were significantly differentiated from the controls in courtship repertoire, but all of the populations pursued convergent evolutionary trajectories in adapting to the laboratory, resulting in dissolution of homogamic preferences. The phenotypic shifts in courtship and mate preferences were unrelated to evolutionary trends in overall mating vigour; therefore, the convergence in courtship could not be attributed to either a fitness meltdown due to inbreeding or the purge of deleterious alleles. Only one founder-flush population showed some independence from the selectional pressures for convergence; therefore, the single two-pair founder-flush event was generally inadequate to stimulate stable incipient speciation. This study thus demonstrates how convergent evolution can dissolve founder-flush effects.     

Important role of genetic drift in rapid polygenic adaptation

We analyzed a model to determine the factors that facilitate or limit rapid polygenic adaptation. This model includes population genetic terms of mutation and both directional and stabilizing selection on a highly polygenic trait in a diploid population of finite size. First, we derived the equilibrium distribution of the allele frequencies of the multilocus model by diffusion approximation. This formula describing the equilibrium allele frequencies as a mutation‐selection‐drift balance was examined by computer simulation using parameter values inferred for human height, a well‐studied polygenic trait. Second, assuming that a sudden environmental shift of the fitness optimum occurs while the population is in equilibrium, we analyzed the adaptation of the trait to the new optimum. The speed at which the trait mean approaches the new optimum increases with the equilibrium genetic variance. Thus, large population size and/or large mutation rate may facilitate rapid adaptation. Third, the contribution of an individual locus i to polygenic adaptation depends on the compound parameter , where is the effect size, the equilibrium frequency of the trait‐increasing allele of this locus, and . Thus, only loci with large values of this parameter contribute coherently to polygenic adaptation. Given that mutation rates are relatively small, this is more likely in large populations, in which the effects of drift are limited.     

拟南芥开花时间调控的分子基础

在合适的时间开花对大多数植物的生存和成功繁衍极为重要。开花时间受错综复杂的环境因素和植物自身的遗传因子影响,由开花调控因子所构成的光周期、春化、温度、赤霉素、自主以及年龄等至少6条既相互独立又相互联系的遗传途径调控。该文综述了有关拟南芥(Arabidopsis thaliana)开花时间调控的分子机制的最新研究进展,并对今后的研究进行了展望。     

Dynamics of Adaptation During Three Years of Evolution Under Long-Term Stationary Phase

Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years, following exhaustion of external resources, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time, E. coli continuously adapts genetically through the accumulation of mutations. For nonmutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates through the acquisition of additional mutation rate–enhancing mutations. Different mutator and nonmutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to coexist within their populations for many years, under LTSP.     

The rhythmic expression of genes controlling flowering time in southern and northern populations of invasive Ambrosia artemisiifolia

Aims Flowering time has been suggested to be an important adaptive trait during the dispersal of invasive species, and identifying the molecular mechanisms underlying flowering time may provide insight into the local adaptation during the process of invasion. Here, we conducted a preliminary exploration on the genetic basis of the differentiation of flowering time in Ambrosia artemisiifolia .Methods Using relative real-time fluorescent quantitative polymerase chain reaction, we investigated the expression levels of eight flowering-related genes, including AP1, FT, SOC1, CRY2, FKF1, GI, CO2 and SPY, in leaves and flowers at different time points in individuals from northern Beijing and southern Wuhan populations that exhibit significant differences in flowering times to identify any rhythmic changes in gene expression and their association with differential flowering times.Important findings The differentiation of flowering time in the A. artemisiifolia populations was closely associated with five genes involved in flowering pathways. The floral pathway integrators FT and SOC1 and floral meristem identity gene AP1 exhibited increased expression during flowering. The photoreceptor CRY2 in the light-dependent pathway and the SPY gene in the gibberellin pathway displayed specific expression patterns over time. In earlier-flowering Beijing plants, CRY2 expression was lower and SPY expression was higher than in Wuhan plants. The expression patterns of these five genes suggest a molecular basis for the differentiation of flowering time in A. artemisiifolia .     

运动细胞自适应性过程中双相性现象的分子机制及动态数值模拟

盘基网柄菌细胞(Dictyostelium)和白细胞(leukocyte)等真核运动细胞受到外界信号刺激时,在最初的1～2 min内,胞内信号转导的首要成员PI(3,4,5)P3的浓度随时间变化呈现"双相性"(biphasic adaptation),即先后出现一大一小两个峰值,然后平息。为解释这一现象,特别是第二个峰值产生的原因,根据已有实验资料,分析了有关分子机制,建立了相应的数学模型。其中,PI(3,4,5)P3及其激活酶和抑制酶的浓度变化由一组耦合的非稳态反应-扩散方程描述,外界刺激及效应因子(如Rac和Scar/WAVE)的相互激励包含在源项中,并由蒙特-卡诺(Monte-Carlo)法处理,数值模拟结果与已有实验一致。研究发现,质膜上处于激活态的效应因子Scar/WAVE是影响PI(3,4,5)P3第二个峰值的关键,起正反馈作用。在受到胞外信号刺激后的前期,Scar/WAVE的激活态浓度受到小G蛋白Rac活性的抑制,后期反过来受到PI(3,4,5)P3的抑制,从而始终处于较低水平,这使得第二个峰值较小;当Scar/WAVE的总浓度低于0.005μmol/L后,PI(3,4,5)P3不会出现第二个峰值。由于Scar/WAVE是肌动蛋白结合蛋白,可以推测:许多经肌动蛋白合成抑制剂处理过的盘基网柄菌细胞在实验中仍然出现"双相性",应与此时的细胞骨架活性未被完全抑制有关。     

Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization

Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.     

谷胱甘肽还原酶和超氧化物歧化酶在玉米幼苗热激诱导的交叉适应中的作用

玉米幼苗经过热激处理后,在随后的高温、低温、干旱和盐胁迫环境中,其存活率明显高于未热激的幼苗,表明热激能提高植物的抗热性、抗冷性、抗旱性和抗盐性,证实了玉米幼苗交叉适应现象的存在;热激还可提高谷胱甘肽还原酶(GR)和超氧化物歧化酶(SOD)的活性,且在上述4种胁迫过程中GR、SOD活性水平与玉米幼苗的存活率呈正相关,表明GR和SOD参与玉米幼苗交叉适应的形成.     

光周期影响植物花时的分子机制

日长感知是植物所具有的重要的生物学功能,光周期是决定植物开花时间的关键环境因子之一。光周期的暗期长度是决定植物成花的决定因素。通过形态学和遗传学研究,揭示了光周期敏感的一些遗传特性,并确定了光敏感指数的标准。构建了光周期性状相关的分子标记连锁图谱,是进行基因定位、克隆和分子标记辅助选择的重要基础工作,也是进行光周期机理研究的有效途径。通过模式植物拟南芥的研究,建立了一个长日促进开花的遗传途径。它的机理可以综合为:光和感光信息体系结合产生信号并传导,CO表达被激活。在每日日长循环、光体系及遗传背景的变化基础上,如果CO的表达和日长状况协调,那么CO激活FT表达,随后开花。水稻、小麦、玉米等作物在光周期机理研究方面也取得了一些进展。     

Morphological Adaptation of Inflorescences in Plants that Develop at Low Temperatures in Early Spring: The Convergent Evolution of "Downy Plants"

Abstract: A new category of plants that exhibit convergent evolution, namely "downy plants", is described and discussed here on the bais of natural selection. So-called snowball plants can be represented by Saussurea gossypiphora D. Don (Compositae), which has extremely dense trichomes on well-developed bracts that are tightly packed around floral buds. Plants whose morphology is similar to that of S. gossypiphora are found at high elevations of alpine zones in the Nepalese Himalayas, where temperatures are low and precipitation is high (frequent rain) in summer. Nonetheless, we noticed that plants with a morphology similar to that of Himalaya snowball plants are commonly distributed from temperature to Arctic zones, and are even found in Alaska where precipitation is very limited. Willows ( Salix spp.: Salicaceae) and deciduous magnolias (Magnoliaceae) are typical examples of such plants. Measurements of temperature inside and outside the inflorescences of Salix (pussy willow or catkin) and of Magnolia suggested that the pubescent bracts might play a role in keeping the interior of buds warm, but that the effect depends on light intensity. Our examination of such species led us to extend the concept of "snowball plants" to a larger group of plants, namely "downy plants", that are characterized by very dense trichomes on tightly packed bracts of inflorescences. Downy plants are thereby considered to represent a convergent adaptation that allows blooming at low temperatures.     

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.     

寄主氮源胁迫下刺吸式昆虫的表现及其适应性对策

寄主氮源胁迫下刺吸式昆虫的表现及其适应性对策马巨法胡国文程家安（中国水稻研究所,杭州３１０００６）（浙江农业大学,杭州３１００２９）ＰｏｐｕｌａｔｉｏｎＰｅｒｆｏｒｍａｎｃｅｓｏｆｔｈｅＳａｐＦｅｅｄｅｒｓｕｎｄｅｒＬｏｗＮｉｔｒｏｇｅｎＳｔｒｅｓ...