An integrated approach to Physcomitrella patens transcriptomics reveals importantclues of the evolutionary development of plant organs and sexual reproduction

Land plant evolution required the generation of a new body plan that could resist the harsher and fluctuating environmental conditions found outside of aquatic environments. Unraveling the genetic basis of plant developmental innovations is not only revealing in terms of an evolutionary point of view, but it is also important for understanding the emergence of agronomically important traits. Comparative genetic studies between basal and modern land plants, both at the genome and trancriptome levels, can help in the generation of hypotheses related to the genetic basis of plant evolutionary development.(...)

植物N;P计量化学：中国高等之外的分异规律与野外试验初步验证

元素化学计量学指从化学计量学的角度出发，通过分析比较生命物质不同结构层次（分子、细胞、器官、机体、种群、群落等）或生态系统中元素的相对比值，来研究各层次相互之间以及生态学过程中元素之间的关系。生态化学计量学研究可以把生态实体的各个层次存元素水平上统一起来，足近年来新兴的一个生态学研究领域，广泛应用于生态学研究中。C，N，P是生物地球化学循环中的重要元素，在生态系统中占有重要地位，许多环境问题都与它们有关，由此这三种元素的化学计量学受到生态学家们的普遍关注。C:N:P化学计量学在水生生态系统中研究较为深入，目前已发展到染色体水平，而在陆地生态系统中的研究较为匮乏近年来由于人类活动的强烈影响，这三种元素的循环在速度和规模上都发生了前所未有的改变，导致一系列环境问题的出现，因此C：N:P化学计量学在陆地生态系统中的研究就显得尤为重要。作为地球生命存在基础的绿色植物，在地球上已有数亿年的演化历史，研究陆地植物的元素化学计量学不仅有助于深入了解植物存在于地球上的内在机制，而且可以为许多环境问题的解决提供理论依据。本文首先建立中国不同地区植物氮磷含量数据库，通过数据分析找出一般规律，并进一步揭示植物不同进化阶段N:P化学计量比的变化规律。在此基础上，通过在内蒙古羊草草原设立不同施肥样地来模拟自然界不同氮磷环境，从试验水平上研究不同施肥处理及施肥梯度下生态系统中氮、磷、有机质的变化规律，并从化学计量学角度研究其内在机制。 利州新建成的中国维管植物数据库（包含1603种植物）研究了不同进化水平以及不同功能群（生活型）间植物N:P比的变化规律，并沿胡焕庸线（胡线）把中团分为为东西两部分，从总体水平上对比了东、西部间叫植物氮磷含量以及N：P的异同。结果表明：l）从演化水平来看，尽管氮磷含量表现出极大的差异，除豆科植物外，植物N：P基本保持稳定水平;2）木本植物与草本植物的N：P比差异．显著，木本植物之间（常绿乔木，常绿灌木，落叶乔木，落叶灌木）N：P不具有显著差异;3）中国东西部植物养分含量和N：P比表现出极显著差异，东部的养分含量低于西部，而N:P显著高于西部。 在内蒙古羊草草原两块永久实验样地（样地A：1980年围封样地和样地B：1999年田封样地）进行了为期两年的N素和P素添加试验。氮素添加梯度为0，5，15，30，50，80 g NHN03.m.2.yr-1。P素添加梯度为0，2，4，8，16，and 32 g P2Osm-2 yr-1（仪分析了羊草器官的结果）。分别从植物器官、物种、功能群水平研究了N素添加对N:P化学计量学的影响，此外还研究了土壤和凋落物C：N:P化学计量学对N素添加的响应。结合生物量的变化趋势，探讨了元素化学计量学对养分状况的指示作用。 1．羊草器官对施肥的响应结果表明，添加N素可以显著提高羊草器官中的含N量，p素可以显著提高器官中的含P量：除2001年样地A中的根茎外，根茎中的含P量基本不受N素添加的影响;茎中的含P量同样表现出不受N素添加影响的趋势（2000年B区茎除外）：N素添加可以显著增大羊草叶片中的含P量(B区2000年叶片除外)。P素添加对羊草器官的含N量没有影响;羊草器官中的氮磷含量施肥处理下表现出显著的正相关关系（N素添加下B区叶片除外）。N素添加对羊草器官的N:P比没有显著影响（A区茎2000年和B区叶片2000年除外）：P素添加显著降低了羊草器官中的N:P比。 2．四种优势植物（羊草、羽茅、针茅和苔草）地上生物量和N:P化学计量学对氮肥的响应研究发现，四个物种的氮磷含量均具有极显著相关关系;氮肥可以显著提高样地A中的羽茅生物量，降低苔草的生物量，而使样地B中的羊草生物量增大;两块样地中，四个物种的氮磷含量及N：P比均随N素水平的增高而增大（样地A中的羽茅N:P比除外）。 3．基于生活型划分的功能群（多年生根茎禾草，多年生丛生禾草，豆科植物，多年生杂类草，一二年生植物，灌木和半灌木）对N素添加的响应研究表明：施N可以提高样地A中的多年生丛生禾草的生物量，而使样地B中的多年生根苇禾草增加;多年生杂类草的相对多度在两个样地中均随施氨水平的增加而显著 降低：在样地B中，施氮可以显著提高不同功能群的氮磷含量;在样地A中，功能群N、P含量对施肥的响应并没有一致的变化规律，添加N素可以显著提高不同功能群的含N量（豆科植物除外），多年生根茎禾草和多年生杂类草的P含量有显著增大的趋势（P < 0.005），而其它功能群（豆科植物、灌木和小半灌木、多年生杂类草和～二年生杂类草）的P含量基本恒定（P>0.05）;在样地A中，多年生丛生禾草，多年生杂类草，一二年生植物，灌木和半灌木的N：P比随施氨水平的增加而显著增大，多年生根茎禾草和豆科植物的N:P比基本不变;在样地B中，多年生丛生禾草的N:P比随施氨水平的增加而显著增大，多年生根茎禾草、多年生杂类草和…二年生杂类草不受施氨水平的影响。 4．添加N素对根实验结果表明：两块样地中，上层根(0-10 cm)的生物量仅在施N后第一年显著增加，而下层根(10-20 cm)的地下生物量在两年的施N处理下均不受施肥梯度的影响i在样地A中，施肥后第一年对根的N、P含量影响不显著，施肥后第二年可以显著增大上层根的N、P含量;在样地B中，添加N素后第一年可以显著增大根的含P量; 在两个样地中，两年的N肥处理对根的N：P比没有显著影响：在施氨处理中，根的N、P含量及N:P比在施肥第一年的响应要高于第二年。 5．所有处理中，上层土壤(O-lO cm)养分含量（有机碳，全氮，全磷）均高于下层土壤（10-20 cm）;在样地A中，氮素添加对r十壤有机碳没有显著性作用，在施肥第一年可以显著增加上层土壤的N、P含量，而在施肥后第二年对土壤N、P含量没有显著影响;在样地B中，添加N素对两年的土壤养分均没有显著影响：养分添加两个样地土壤中的元素比值（C:N比，C:P比，N:P比）没有显著影响;土壤养分对施N一年后的响应要高于第二年。 6．养分添加对凋落物化学特征及化学计量学特征的影响研究结果表明：凋落物现存量不受施肥的影响;2001年凋落物现存量与2000年和2001年的地上生物量相关关系不显著;添加N素可以显著提高凋落物的N含量，而对有机碳含量和P含量没有显著影响;凋落物C：N比随施肥梯度的增大而显著降低，N:P比显著增高，而C:P比没有明显变化。 以上研究结果表明，不同植物功能群的N:P比存在差异，人类活动强烈影响自然植被中的植物N：P比;但植物的N：P比不受植物进化的影响（豆科植物除外）;由于植物已有数亿年的演化历史，同时N与P在植物的结构和功能上具有密切的联系，在生物地球化学循环中办存在耦合作用。因此植物N：P比值恒定可能是一普适性规律。 N素添加试验表明，在植物根、地上器官、物种和功能群水平上N与P均呈显著正相关关系，反映了植物体内的氮磷含量具有协同作用。共存种对N肥的响应不同，表明物种受不同元素的制约。因此除非把生态系统中所有物种对施肥的响应刻画清楚，笼统的认定生态系统缺乏某种元素是不适当的。 施肥试验表明，两种围封时间样地的主要限制性元素不同。极度退化(样地B)植物生长主要缺N，而在保护较好样地(样地A)，P也逐步成为一种限制因素。反映了随着保护时间的增加，植物生长逐渐由N限制型向N、P共同限制型过渡。添加的养分要么被植物吸收，挥发到大气中，或以凋落物的形式返还到土壤表层。但是对养分的预算有待于进一步研究。土壤中的养分含量对N素添加有…个滞后效应，而植物响应较为迅速。功能群N:P比在施肥实验中不能保持恒定，可能是由于实验时间较短的缘故;化学计量学的研究表明羊草草原分解凋落物的微生物受P素的制约，可能是由于植物体内具有高的P素再转运机制。这一结论有待于进一步的验证。氮肥降低了凋落物的C:N比，因此凋落物的分解速率可能将要发生改变。这需要进一步开展C循环的研究。

Gene genealogies and population variation in plants

Early in the development of plant evolutionary biology, genetic drift, fluctuations in population size, and isolation were identified as critical processes that affect the course of evolution in plant species. Attempts to assess these processes in natural populations became possible only with the development of neutral genetic markers in the 1960s. More recently, the application of historically ordered neutral molecular variation (within the conceptual framework of coalescent theory) has allowed a reevaluation of these microevolutionary processes. Gene genealogies trace the evolutionary relationships among haplotypes (alleles) with populations. Processes such as selection, fluctuation in population size, and population substructuring affect the geographical and genealogical relationships among these alleles. Therefore, examination of these genealogical data can provide insights into the evolutionary history of a species. For example, studies of Arabidopsis thaliana have suggested that this species underwent rapid expansion, with populations showing little genetic differentiation. The new discipline of phylogeography examines the distribution of allele genealogies in an explicit geographical context. Phylogeographic studies of plants have documented the recolonization of European tree species from refugia subsequent to Pleistocene glaciation, and such studies have been instructive in understanding the origin and domestication of the crop cassava. Currently, several technical limitations hinder the widespread application of a genealogical approach to plant evolutionary studies. However, as these technical issues are solved, a genealogical approach holds great promise for understanding these previously elusive processes in plant evolution.

Plant rhizosphere specificity and variability in the insect and plant adhesins, Madl and Mad2, within the genus Metarhizium suggest plant adaptation as an evolutionary force

Metarhizium is a soil-inhabiting fungus currently used as a biological control agent against various insect species, and research efforts are typically focused on its ability to kill insects. In section 1, we tested the hypothesis that species of Metarhizium are not randomly distributed in soils but show plant rhizosphere-specific associations. Results indicated an association of three Metarhizium species (Metarhizium robertsii, M. brunneum and M. guizhouense) with the rhizosphere of certain types of plant species. M. robertsii was the only species that was found associated with grass roots, suggesting a possible exclusion of M. brunneum and M. guizhouense, which was supported by in vitro experiments with grass root exudate. M. guizhouense and M. brunneum only associated with wildflower rhizosphere when co-occurring with M. robertsii. With the exception of these co-occurrences, M. guizhouense was found to associate exclusively with the rhizosphere of tree species, while M. brunneum was found to associate exclusively with the rhizosphere of shrubs and trees. These associations demonstrate that different species of Metarhizium associate with specific plant types. In section 2, we explored the variation in the insect adhesin, Madl, and the plant adhesin, Mad2, in fourteen isolates of Metarhizium representing seven different species. Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions. Phylogenetic analysis of 5' EF-Ia, which is used for species identification, as well as Madl and Mad2 sequences demonstrated that the Mad2 phylogeny is more congruent with 5' EF-1a than Madl. This suggests Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation. While other abiotic and biotic factors cannot be excluded in contributing to divergence, it appears that plant associations have been the driving factor causing divergence among Metarhizium species.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Functional traits determine plant co-occurrence more than environment or evolutionary relatedness in global drylands

Plant-plant interactions are driven by environmental conditions, evolutionary relationships (ER) and the functional traits of the plants involved. However, studies addressing the relative importance of these drivers are rare, but crucial to improve our predictions of the effects of plant-plant interactions on plant communities and of how they respond to differing environmental conditions. To analyze the relative importance of - and interrelationships among - these factors as drivers of plant-plant interactions, we analyzed perennial plant co-occurrence at 106 dryland plant communities established across rainfall gradients in nine countries. We used structural equation modelling to disentangle the relationships between environmental conditions (aridity and soil fertility), functional traits extracted from the literature, and ER, and to assess their relative importance as drivers of the 929 pairwise plant-plant co-occurrence levels measured. Functional traits, specifically facilitated plants' height and nurse growth form, were of primary importance, and modulated the effect of the environment and ER on plant-plant interactions. Environmental conditions and ER were important mainly for those interactions involving woody and graminoid nurses, respectively. The relative importance of different plant-plant interaction drivers (ER, functional traits, and the environment) varied depending on the region considered, illustrating the difficulty of predicting the outcome of plant-plant interactions at broader spatial scales. In our global-scale study on drylands, plant-plant interactions were more strongly related to functional traits of the species involved than to the environmental variables considered. Thus, moving to a trait-based facilitation/competition approach help to predict that: (1) positive plant-plant interactions are more likely to occur for taller facilitated species in drylands, and (2) plant-plant interactions within woody-dominated ecosystems might be more sensitive to changing environmental conditions than those within grasslands. By providing insights on which species are likely to better perform beneath a given neighbour, our results will also help to succeed in restoration practices involving the use of nurse plants. (C) 2014 Geobotanisches Institut ETH, Stiftung Ruebel. Published by Elsevier GmbH. All rights reserved.

Rapid plant diversification: Planning for an evolutionary future

Systematic conservation planning is a branch of conservation biology that seeks to identify spatially explicit options for the preservation of biodiversity. Alternative systems of conservation areas are predictions about effective ways of promoting the persistence of biodiversity; therefore, they should consider not only biodiversity pattern but also the ecological and evolutionary processes that maintain and generate species. Most research and application, however, has focused on pattern representation only. This paper outlines the development of a conservation system designed to preserve biodiversity pattern and process in the context of a rapidly changing environment. The study area is the Cape Floristic Region (CFR), a biodiversity hotspot of global significance, located in southwestern Africa. This region has experienced rapid (post-Pliocene) ecological diversification of many plant lineages; there are numerous genera with large clusters of closely related species (flocks) that have subdivided habitats at a very fine scale. The challenge is to design conservation systems that will preserve both the pattern of large numbers of species and various natural processes, including the potential for lineage turnover. We outline an approach for designing a system of conservation areas to incorporate the spatial components of the evolutionary processes that maintain and generate biodiversity in the CFR. We discuss the difficulty of assessing the requirements for pattern versus process representation in the face of ongoing threats to biodiversity, the difficulty of testing the predictions of alternative conservation systems, and the widespread need in conservation planning to incorporate and set targets for the spatial components (or surrogates) of processes.

Sexual selection in a tropical fruit fly : role of a plant derived chemical in mate choice

The specific mechanisms by which selective pressures affect individuals are often difficult to resolve. In tephritid fruit flies, males respond strongly and positively to certain plant derived chemicals. Sexual selection by female choice has been hypothesized as the mechanism driving this behaviour in certain species, as females preferentially mate with males that have fed on these chemicals. This hypothesis is, to date, based on studies of only very few species and its generality is largely untested. We tested the hypothesis on different spatial scales (small cage and seminatural field-cage) using the monophagous fruit fly, Bactrocera cacuminata. This species is known to respond to methyl eugenol (ME), a chemical found in many plant species and one upon which previous studies have focused. Contrary to expectation, no obvious female choice was apparent in selecting ME-fed males over unfed males as measured by the number of matings achieved over time, copulation duration, or time of copulation initiation. However, the number of matings achieved by ME-fed males was significantly greater than unfed males 16 and 32 days after exposure to ME in small cages (but not in a field-cage). This delayed advantage suggests that ME may not influence the pheromone system of B. cacuminata but may have other consequences, acting on some other fitness consequence (e.g., enhancement of physiology or survival) of male exposure to these chemicals. We discuss the ecological and evolutionary implications of our findings to explore alternate hypotheses to explain the patterns of response of dacine fruit flies to specific plant-derived chemicals.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

The evolutionary value of recombination is constrained by genome modularity

Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV), we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general.

Managed livestock grazing is compatible with the maintenance of plant diversity in semidesert grasslands

Even when no baseline data are available, the impacts of 150 years of livestock grazing on natural grasslands can be assessed using a combined approach of grazing manipulation and regional-scale assessment of the flora. Here, we demonstrate the efficacy of this method across 18 sites in the semidesert Mitchell grasslands of northeastern Australia. Fifteen-year-old exclosures (ungrazed and macropod grazed) revealed that the dominant perennial grasses in the genus Astrebla do not respond negatively to grazing disturbance typical of commercial pastoralism. Neutral, positive, intermediate, and negative responses to grazing disturbance were recorded amongst plant species with no single life-form group associated with any response type. Only one exotic species, Cenchrus ciliaris, was recorded at low frequency. The strongest negative response was from a native annual grass, Chionachne hubbardiana, an example of a species that is highly sensitive to grazing disturbance. Herbarium records revealed only scant evidence that species with a negative response to grazing have declined through the period of commercial pastoralism. A regional analysis identified 14 from a total of 433 plant species in the regional flora that may be rare and potentially threatened by grazing disturbance. However, a targeted survey precluded grazing as a cause of decline for seven of these based on low palatability and positive responses to grazing and other disturbance. Our findings suggest that livestock grazing of semidesert grasslands with a short evolutionary history of ungulate grazing has altered plant composition, but has not caused declines in the dominant perennial grasses or in species richness as predicted by the preceding literature. The biggest impact of commercial pastoralism is the spread of woody leguminous trees that can transform grassland to thorny shrubland. The conservation of plant biodiversity is largely compatible with commercial pastoralism provided these woody weeds are controlled, but reserves strategically positioned within water remote areas are necessary to protect grazing-sensitive species. This study demonstrates that a combination of experimental studies and regional surveys can be used to understand anthropogenic impacts on natural ecosystems where reference habitat is not available.