Phylogeographic studies in plants: problems and prospects

Genetic structuring of plant populations is strongly influenced by both common ancestry and current patterns of interpopulation genetic exchange. The interaction of these two forces is particularly confounding and hence interesting in plants. This complexity of plant genetic structures is due in part to a diversity of reproductive ecologies affecting genetic exchange and the fact that reproductive barriers are often weak between otherwise morphologically well-defined species. Phylogeographic methods provide a means of examining the history of genetic exchange among populations, with the potential to distinguish biogeographic patterns of genetic variation caused by gene flow from those caused by common ancestry. With regard to plants, phylogeography will be most useful when applied broadly across the entire spectrum of potential genetic exchange. Although current phylogeographic studies of plants show promise, widespread application of this approach has been hindered by a lack of appropriate molecular variation; this problem is discussed and possible solutions considered.     

中国亚热带地区阔叶林植物的谱系地理历史

中国亚热带地区因丰富的植物物种多样性备受生物地理学研究关注,丰富的多样性与中新世以来的地质气候变化密切相关。谱系地理学已成为探讨植物分布模式和遗传格局受地质气候变化影响的主要手段。总结了该地区阔叶林植物对中新世以来地质气候变化的响应模式和种群分化的历史成因。在中新世和上新世时,由于全球变冷、青藏高原抬升和亚洲内陆干旱,阔叶林植物被迫向南退缩,形成不同的谱系。同时,亚洲季风的增强为遗传多样性的增加提供了良好的环境。在更新世冰期和间冰期时,大部分落叶阔叶林和常绿阔叶林植物在多个避难所间存在长期隔离,不同的避难所种群各自经历局部地区的收缩和扩张。长期的隔离使不同谱系间进一步分化,形成高水平的遗传多样性和遗传分化。少部分植物在冰期时向南退缩,并在间冰期时明显向北扩张。最后,就分化时间的准确估计和探究遗传格局背后的机制两方面展望了未来的研究趋势。     

食虫植物研究的现状和趋势

综述了食虫植物的研究概况 ,包括研究历史、食虫植物的捕虫与消化机制 ,食虫的效果以及食虫植物与环境的生态关系 ,旨在促进我国关于食虫植物的研究     

Phylogeographic Studies Depict the Role of Space and Time Scales of Plant Speciation in a Highly Diverse Neotropical Region

Phylogeographic studies have merged different disciplines to explain speciation processes at both spatial and time scales. Although the number of phylogeographic extant studies has increased almost exponentially, few have been conducted in tropical countries, especially using plants. Plants are interesting models for such studies because their responses to different habitat conditions are reflected directly in the size and distribution of populations, enabling direct tests of alternative demographic scenarios. Here, we review phylogeographic studies using plant species occurring in different vegetation domains within Brazil, which has the greatest number of plant species in the world. Based on a detailed examination of 41 published articles, we synthesized the current knowledge and discussed the main processes driving the high levels of plant diversity within Brazilian domains. General patterns of diversification could be inferred due to the number of species studied, especially in the Cerrado and Atlantic Forest, the most intensively studied domains (34.1% and 17.1% of the studies, respectively). Distinct vegetation types within both biomes were affected differently by the Pleistocene climatic oscillations. Edaphic conditions and geographical barriers (rivers and mountains) have also influenced the phylogeographical patterns of plants species from Amazonia and the Atlantic Forest. Other Brazilian domains, such as the Caatinga, Pantanal, and Pampas, have been studied to a lesser extent and no common phylogeographic pattern across species could be inferred. Issues regarding past connections between distinct domains also remain unclear, including those affecting the two main forest domains in South America. Future research on plant species will fill these information gaps, improving our understanding of the complex diversification processes affecting the South American biota.     

Wildlife population assessment: past developments and future directions

We review the major developments in wildlife population assessment in the past century. Three major areas are considered: mark-recapture, distance sampling, and harvest models. We speculate on how these fields will develop in the next century. Topics for which we expect to see methodological advances include integration of modeling with Geographic Information Systems, automated survey design algorithms, advances in model-based inference from sample survey data, a common inferential framework for wildlife population assessment methods, improved methods for estimating population trends, the embedding of biological process models into inference, substantially improved models for conservation management, advanced spatiotemporal models of ecosystems, and greater emphasis on incorporating model selection uncertainty into inference. We discuss the kind of developments that might be anticipated in these topics.     

利用植物生产异源蛋白的研究进展

植物作为生产异源蛋白的生物反应器,近年来颇受关注,与复杂,昂贵的以细胞培养为基础的表达系统相比,具有安全、廉价及规模化生等特点。作者简述了利用植物生产外源蛋白的主要策略及异源基因在植物中表达的研究进展。     

Neurotransmitters: past, present, and future directions

As originally conceived, central neurotransmitters operated uniformly, exciting or inhibiting postsynaptic targets by receptors that activated passive ionic conductances. As the list of transmitter substances and their actions expanded, concepts of transmitter actions have broadened and grown more complex to include a variety of intramembranous and intracytoplasmic second messengers that can regulate both active and passive ionic conductances. Present-day research directions center on further expansion of the lists of identified transmitter candidates, and on the more precise characterization of their sites and mechanisms of receptor regulation and transduction. Current research is also illuminating the means by which neurotransmitters act in a coordinated fashion to regulate common synaptic targets. Future directions will likely include new forms of interneuronal, intraneuronal, and glial signals, including lipids, steroids, and as-yet-undiscovered superfamilies of peptides and receptors. Although recent advances in understanding specific transmitters have been achieved largely through in vitro electrophysiological analyses, it is hoped that future research will recast these events in the context of the intact functioning brain. Neurotransmitters are likely to remain a productive focus of future research.     

Radiation-induced bystander effects: past history and future directions

There has been a recent upsurge of interest in the phenomenon now known as radiation-induced bystander effects. This is largely due to the increased awareness of the contribution of indirect and delayed effects, such as genomic instability, to cellular outcomes after low-dose exposures. It is also due to the availability of tools such as the microbeam and advanced cell culture systems and to the ability to study end points such as gene or protein expression at low doses which were previously difficult to study. This review looks at the history of bystander effects in the earlier literature, in which the clastogenic effect of plasma from irradiated patients was well known. The effect was known to persist for several years and to cause transgenerational effects, making it similar to what we now call genomic instability. The review then examines the current data and controversies which are now beginning to resolve the questions concerning the mechanisms underlying the induction and transmission of both bystander effects and genomic instability. Finally, the possible impact of data concerning radiation-induced bystander effects on radiotherapy and radiation protection is discussed.     

Phylogeographic structure and past history of the circum-Mediterranean species Tomicus destruens Woll. (Coleoptera: Scolytinae)

Phylogeographic studies are often focused on temperate European species with relict footholds in the Mediterranean region. Past climatic oscillations usually induced range contractions and expansions from refugial areas located in southern Europe, and spatial distribution of genetic diversity show that northward expansions were usually pioneer-like. Actually, few studies have focused on circum-Mediterranean species, which probably were not influenced in the same way by climatic oscillations. We present the phylogeography of the bark beetle Tomicus destruens, which is restricted to the whole Mediterranean basin and the Atlantic coasts of North Africa and Portugal. We systematically sequenced 617 bp of the mitochondrial genes COI and COII for 42 populations (N = 219). Analysis revealed 53 haplotypes geographically structured in two clades, namely eastern and western clades, that diverged during the Pleistocene. A contact zone was identified along the Adriatic coast of Italy. Interestingly, we found contrasting levels of genetic structure within each clade. The eastern group was characterized by a significant phylogeographic pattern and low levels of gene flow, whereas the western group barely showed a spatial structure in haplotype distribution. Moreover, the main pine hosts were different between groups, with the Aleppo-brutia complex in the east and the maritime pine in the west. Potential roles of host species, climatic parameters and geographical barriers are discussed and the phylogeographic patterns are compared to classical models of postglacial recolonization in Europe.     

Invasive alien plants in China: role of clonality and geographical origin

Biological invasions have become a significant threat to the global environment. Unfortunately, to date there is no consensus on invasion mechanisms and predictive models. Controversies range from whether we can reliably predict which species may become invasive to which species characteristics (e.g., life history, taxonomic groups, or geographic origin) contribute to the invasion processes. We examined 126 invasive alien plant species in China to understand the role of clonality and geographical origin in their invasion success. These species were categorized into three groups (I, II, III) based on their invasiveness in terms of current spatial occupation and the degree of damage to invaded habitats. Clonal plants consisted of almost half (44%) of the 126 invasive species studied, and consisted of 66% of 32 the most invasive alien plant species (Group I). There was a significant positive relationship between clonality and species invasiveness. A 68% of the 126 species studied originated in the continent of America (North and/or South America). These preliminary findings support that America is the primary geographical origin of invasive alien plant species in China and that clonality of the invasive plant species contributed significantly to the their invasiveness. The results suggest an urgent need at the global scale to investigate the mechanisms whereby plant clonal growth influences plant invasions, and the need for a focus at regional scale to examine factors affecting the exchange of invasive plant species between America and China.     

植物亲缘地理学的研究现状与发展趋势

新生代以来剧烈的地质和气候变化,特别是第四纪冰期和间冰期的反复交错对温带植物类群的地理分布格局、种群结构和物种分化造成了深刻影响。近20年来,随着分子标记技术的发展和分析方法的成熟,植物亲缘地理学利用基因谱系关系和在种群中的时空分布来追溯种群的进化历史,在探讨植物类群对地质气候变迁的响应以及种群分化的历史成因等方面开展了大量工作,取得了一些重要进展。在取得这些成绩的同时,作者也注意到了被研究者所忽略的一些问题。试图对这些问题进行初步的总结,着重于分析方法和几个常用软件的使用,并对今后的发展趋势进行了展望。     

Phylogeographic concordance factors quantify phylogeographic congruence among co‐distributed species in the Sarracenia alata pitcher plant system

Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co‐distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long‐standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co‐diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research.     

Survival analysis in clinical trials: past developments and future directions

The field of survival analysis emerged in the 20th century and experienced tremendous growth during the latter half of the century. The developments in this field that have had the most profound impact on clinical trials are the Kaplan-Meier (1958, Journal of the American Statistical Association 53, 457-481) method for estimating the survival function, the log-rank statistic (Mantel, 1966, Cancer Chemotherapy Report 50, 163-170) for comparing two survival distributions, and the Cox (1972, Journal of the Royal Statistical Society, Series B 34, 187-220) proportional hazards model for quantifying the effects of covariates on the survival time. The counting-process martingale theory pioneered by Aalen (1975, Statistical inference for a family of counting processes, Ph.D. dissertation, University of California, Berkeley) provides a unified framework for studying the small- and large-sample properties of survival analysis statistics. Significant progress has been achieved and further developments are expected in many other areas, including the accelerated failure time model, multivariate failure time data, interval-censored data, dependent censoring, dynamic treatment regimes and causal inference, joint modeling of failure time and longitudinal data, and Baysian methods.     

鸟类学研究:过去二十年的回顾和对中国未来发展的建议

为了解中国鸟类学研究的状况和发展趋势,我们利用在线文献数据库(Web of Science)检索了1991-2010年间发表的与鸟类有关的文献,对中国和其他国家的鸟类学研究论文、研究领域、研究机构等进行了分析和比较。结果发现,中国鸟类学研究发展很快,专业研究人员数量在1991-2010年间增长了近四倍,在国际上发表的研究论文的数量近几年年均增长25%;论文数量占世界的比例已经由1991-2000年的0.46%上升到了2001-2010年期间的1.53%,世界排名由第27位上升至第16位,并且研究领域更加多元化,论文水平不断提高。在鸟类系统发育与演化、合作繁殖和婚配、禽流感、巢寄生等领域的许多成果开始在国际相关领域的高水平刊物上发表,在古鸟类以及雉类和鹤类等濒危鸟类的保护研究方面位居世界前列。但从整体而言,中国鸟类学研究与世界上一些发达国家相比还有很大差距。为此我们对中国鸟类学未来的发展提出了一些建议,包括需要更加关注鸟类的生活史对策、气候变化和城市化对鸟类的影响、鸟类迁徙、濒危物种保护生物学等领域的研究,进一步加强国际交流与合作,规范鸟类研究及数据保存和处理的方法,采取更有效措施加大对青年研究人员的支持力度等。     

Aerobic MTBE biodegradation: an examination of past studies, current challenges and future research directions

With the current practice of amending gasoline with up to 15% by volume MTBE, the contamination of groundwater by MTBE has become widespread. As a result, the bioremediation of MTBE-impacted aquifers has become an active area of research. A review of the current literature on the aerobic biodegradation of MTBE reveals that a number of cultures from diverse environments can either partially degrade or completely mineralize MTBE. MTBE is either utilized as a sole carbon and energy source or is degraded cometabolically by cultures grown on alkanes. Reported degradation rates range from 0.3 to 50 mg MTBE/g cells/h while growth rates (0.01–0.05 g MTBE/g cells/d) and cellular yields (0.1–0.2 g cells/g MTBE) are generally low. Studies on the mechanisms of MTBE degradation indicate that a monooxygenase enzyme cleaves the ether bond yielding tert-butyl alcohol (TBA) and formaldehyde as the dominant detectable intermediates. TBA is further degraded to 2-methyl-2-hydroxy-1-propanol, 2-hydroxyisobutyric acid, 2-propanol, acetone, hydroxyacteone and eventually, carbon dioxide. The majority of these intermediates are also common to mammalian MTBE metabolism. Laboratory studies on the degradation of MTBE in the presence of gasoline aromatics reveal that while degradation rates of other gasoline components are generally not inhibited by MTBE, MTBE degradation could be inhibited in the presence of more easily biodegradable compounds. Controlled field studies are clearly needed to elucidate MTBE degradation potential in co-contaminant plumes. Based on the reviewed studies, it is likely that a bioremediation strategy involving direct metabolism, cometabolism, bioaugmentation, or some combination thereof, could be applied as a feasible and cost-effective treatment method for MTBE contamination.     

中国近海浮游动物多样性研究的过去和未来

中国是世界上南北纬度跨度最大的国家之一.复杂的气候、水文和地形因素形成了我国海洋环境的多样性,也造就了浮游动物多样性的格局.我国浮游动物多样性的研究经历了分类、分布为主、环境变化对浮游动物的影响和浮游动物环境适应研究等阶段.在我国,地形、季风和水团是形成海洋环境格局的三大驱动力,因此不同环境对浮游动物的影响是较为活跃的研究方面.无论在我国还足在世界上,浮游动物对环境适应的研究是薄弱环节,研究方法的缺乏是重要的原因.近年来,已经解决了利用现场调查获得的多学科观测数据和资料(field data)结合统计方法求得种类最适温度、最适温度区间等生态学参数的技术难点.yield-density函数模型,麦夸特(Marquardt)法曲线拟合,中值定理,龙贝格(Romberg)积分法计算等数学方法得到应用.这些研究方法应用在生态类群划分是一项创新,对于浮游动物多样性成因分析有重大意义,未来浮游动物多样性应从不同生境、不同时空尺度、不同分类单元、不同粒径谱、不同生态类群和不同测度方法等多个方向展开,而这些领域的应用研究是浮游动物多样性最具前景的方向.     

Molecules and migration: biogeographical studies in cruciferous plants

In the past two decades our understanding of plant biogeography has been improved substantially by the introduction of various molecular marker systems. Especially within the angiosperms, maternally inherited chloroplast DNA based data sets have elucidated not only genetic relatedness but also geographic structuring of genetic variation. These findings were based on the observation that DNA molecules might mutate during migration, which consequently found its manifestation in the term phylogeography introduced in the late 80s by John Avise. However, other markers such as codominantly inherited allozymes were used before the advent of DNA techniques and were used in theoretical population genetic studies. In actual phylogeographic studies, highly variable markers, such as AFLPs (amplified fragment length polymorphisms), were needed to unravel recent species histories (e.g. pleistocenic differentiation). The levels of molecular variation at such markers are closer to that of allelic variation measured with allozymes. Hence, an increasing number of studies have relied on highly polypmorphic markers, such as DNA microsatellite loci. Herein, we try to present an overview on the various biogeographic and phylogeographic studies using various molecular (including isozyme) markers and methodological approaches to analyse them, concentrating on studies done with representatives of the Brassicaceae family.