DNA条形编码在蚜虫类昆虫中的应用

2003年提出的DNA条形编码技术给生物分类研究带来了空前的繁荣,众多学者对此进行了分析和讨论.蚜虫类昆虫具有多型、转主寄生等复杂的生物学特性,其形态特征多有特化或退化,因此,DNA条形编码在蚜虫类昆虫中的应用必将给蚜虫分类学研究带来巨大的活力.文章总结了国际DNA条形编码技术的研究进展和现状,并展望了DNA条形编码在蚜虫类昆虫研究中应用的方向,该研究技术主要用于对蚜虫物种快速准确的鉴定、解决多型性问题、发现隐存分类单元,探讨蚜虫种间的系统发育关系、蚜虫与寄主植物的关系,解释蚜虫地理分布格局和推测近期分化物种的成因等.     

DNA条形码技术及其在保护生物学中的应用

物质文明及生活水平的提升为人类带来诸多好处的同时,也使人们越来越清晰地意识到保护生物多样性及生态系统稳定性的重大意义.DNA条形码技术作为现今生物分类学中重要的分子技术,可以快速准确地鉴定物种.多国科学家都在致力于对DNA条形码的研究,以便能共同组建数据库.将现有物种正确分类并期望用于发现新种,为生物的保护及生态系统的维护作出巨大贡献.细胞色素C氧化酶亚单位I(COI)是现在动物种类鉴定中最常用的基因之一.综述DNA条形编码技术的产生、原理、发展概况与操作及其在保护动物分类中的应用.阐明该技术在保护生物学中应用的意义与可行性,并讨论DNA条形编码在生物分类应用中可能存在的问题.     

DNA条形编码技术在动物分类中的研究进展

DNA条形编码(DNA Barcoding)技术是一种新的生物分类方法,它是分子生物学和生物信息学相结合的产物。这一概念认为,就像在商店里扫描仪读取条形码那样,对地球上每一种生物也能通过快速分析其DNA中的一小段(线粒体细胞色素C氧化酶Ⅰ亚基,mt COI)加以识别。在最近3年里,该技术已成为生物分类学中研究的热点。理论上,DNA条形编码在生物分类鉴定中具有重要作用,但目前国际上对其的争论也不少。综述了DNA条形编码技术的产生、发展概况、原理与操作及其在动物分类中的应用,突出了该技术在寄生虫分类中应用的意义与可行性,并讨论了DNA条形编码在生物分类应用中可能存在的问题。     

西花蓟马检测鉴定技术研究进展

西花蓟马是一种世界性的入侵害虫,2003年首次在北京发现,目前仅在我国局部地区发生。其危害严重,潜在适生区广,且具有进一步扩散蔓延的趋势。快速准确的检测鉴定技术是防止其进一步扩散蔓延,保障我国农业生产健康发展的必要前提。综合相关报道,用于西花蓟马的检测鉴定技术包括传统的形态学特征鉴定法、由此衍生的计算机软件识别法,以及分子检测技术,如RAPD-PCR法、DNA序列分析法、PCR-RFLP法、SCAR分子标记技术、实时荧光定量PCR检测技术以及蛋白质分析技术等。其中,基因芯片和DNA条形编码技术作为新兴的物种鉴定手段,在西花蓟马等入侵物种的检测鉴定中具有广阔的应用前景。     

北京地区7种常见嗜尸性蝇类的COI基因序列分析及DNA条形码的建立

嗜尸性蝇类在命案死亡时间和现场推断方面有着十分重要的应用, 而DNA 条形编码技术能摆脱对虫卵和幼虫的饲养以及后续物种鉴定方面专业知识的依赖, 有助于实现现场采集蝇类样本的快速鉴定。本研究采集了北京地区7个嗜尸性蝇类优势种共77个个体的样本, 测定了所有个体线粒体DNA 上细胞色素C氧化酶亚基Ⅰ（COI）基因1 120 bp的序列。基于序列的系统发生分析显示, 同一物种不同个体的序列均以高达99%的支持值聚集在一起。序列间的分歧统计表明这些蝇类在物种内的个体分歧不超过1%, 而不同物种间的净分歧均超过7.74%, 最高可达14.85%。滑动窗口分析表明, 在整个序列区段种间差异位点存在较平均的分布。通过测定COI基因的序列, 建立了北京地区7个嗜尸性蝇类优势种的DNA条形码, 据此实现了对这些物种准确、快速、简单的区分和鉴定, 同时也为后续应用于物种鉴定的种属特异性位点之筛选提供了基础数据。     

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.     

环境DNA宏条形码在生物多样性研究与监测中的应用

环境DNA宏条形码(eDNA metabarcoding)技术通过提取水体、土壤、空气中的环境DNA,使用引物PCR扩增与高通量测序,进行物种鉴定与生物多样性评估.作为一种新的监测技术,相比于传统监测技术更加快捷、准确以及对自然环境的破坏小,因此在一定程度上改变了我们调查地球生物多样性的方式.本文综述了环境DNA宏条形...     

地黄属植物的DNA条形码研究

地黄属(Rehmannia)为玄参科(Scrophulariaceae)药用植物,广泛分布于中国中东部及北部地区。由于地黄属植物经历了快速成种,导致其属内物种间形态性状差异较小,运用传统的形态学分类方法已难以准确地鉴定物种,近年来迅速发展起来的DNA条形码技术为快速、准确地鉴别物种提供了新思路。本研究选用3个叶绿体DNA非编码区片段(trn L-trn F、trn M-trn V和trn S-trn G)及核基因ITS片段,运用PWG-distance和TreeBuilding两种方法对地黄属5个物种75个个体进行了DNA条形码分析。结果表明:单个叶绿体DNA片段或核基因ITS片段对地黄属物种的鉴别率较低(0%~20%),组合的叶绿体DNA片段分辨能力虽然高于单个DNA片段,但并不能将地黄属5个物种完全区分开;trn S-trn G+ITS片段组合的分辨率可达100%,能够将地黄属5个物种准确区分,与所有叶绿体DNA片段和核基因ITS片段组合(trn L-trn F+trn M-trn V+trn S-trn G+ITS)的辨别率相同,因此推荐trn S-trn G+ITS作为地黄属植物的标准条形码。此外,利用DNA条形码鉴别物种时,可采用叶绿体DNA片段和核DNA片段组合的方法来提高物种鉴定的成功率。     

DNA技术在海洋食品物种鉴定中的应用

随着分子生物学技术的发展, 海洋食品物种鉴定方法由原来的蛋白质水平深入到了DNA水平。目前应用于海洋食品物种鉴定的DNA技术主要是FINS(Forensically informative nucleotide sequencing)、PCR-RFLP和物种特异性PCR标记技术等, 能够实现对新鲜、冰冻、腌制或灌装食品物种进行鉴定, 而对混合样本的鉴定及量化分析是尚待解决的一个问题。基因数据库对物种鉴定的影响也越来越大, 是海洋加工食品物种鉴定可利用的另一种重要信息资源。文章综述了DNA技术在海洋食品物种鉴定中的应用研究进展, 并展望DNA技术在海洋食品检测中的发展趋势。     

药用植物DNA条形码鉴定研究进展

DNA条形码是利用相对较短的标准DNA片段对物种进行快速准确鉴定的一门技术。DNA条形码技术可以从分子水平弥补传统鉴定方法的一些不足。该技术具有良好的通用性,使得物种鉴定过程更加快速,已经广泛应用于动物物种的鉴定研究中。近年来,随着药用植物DNA条形码鉴定研究的快速发展,逐渐形成了药用植物和植物源中药材鉴定的完善体系。本文综述了DNA条形码技术鉴定药用植物的原理,介绍了中草药传统鉴定方法及其缺陷、使用DNA条形码技术鉴定植物源药材的意义以及DNA条形码在药用植物鉴定中的应用,对其应用前景进行了展望。     

Matthew effect in counting the number of species

The number of species in an area is a fundamental parameter in species-area theory. Besides sampling size and statistical extrapolation, the inaccurate number of species can intensify the existing controversy on the species richness—productivity and extinction rate overestimate/underestimate. This problem can be caused by Matthew effect from sampling process and taxonomic identification: it is much easier to identify and record common species than rare species. Therefore, it is necessary to prevent and control the Matthew effect, which can distort the number of species (especially the rare species) and the individuals of each species.     

CONTRASTING THE UNDERLYING PATTERNS OF ACTIVE TRENDS IN MORPHOLOGIC EVOLUTION

Gastropod evolution during the early Paleozoic featured active trends (i.e., differential replacement of morphologies) for at least three shell characters. Selective sorting, either of individual organisms or of whole species, is an obvious mechanism for such active trends. Sorting of individuals should result in a disproportionate number of ancestor to descendant transitions being in the same direction as the trend, whereas sorting of species should result in species with particular morphologies producing more daughter species. Sorting of species can occur over long periods of time or it can be concentrated over a particular interval, such as an extinction event. Constraints on morphologic evolution also can drive trends, especially in cases where it is easier to produce a particular morphology than it is to change it. Finally, active trends can be artifacts of unrelated differential diversification within a clade (i.e., species hitchhiking), which might result from sorting of species based on phylogenetically associated characters or simply by chance. Unlike other active trends, trends attributable to species hitchhiking do not support hypotheses about selection or evolutionary constraints.     

Progress toward a general species concept

New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals.     

Mutualism and evolutionary multiplayer games: revisiting the Red King

Coevolution of two species is typically thought to favour the evolution of faster evolutionary rates helping a species keep ahead in the Red Queen race, where ‘it takes all the running you can do to stay where you are’. In contrast, if species are in a mutualistic relationship, it was proposed that the Red King effect may act, where it can be beneficial to evolve slower than the mutualistic species. The Red King hypothesis proposes that the species which evolves slower can gain a larger share of the benefits. However, the interactions between the two species may involve multiple individuals. To analyse such a situation, we resort to evolutionary multiplayer games. Even in situations where evolving slower is beneficial in a two-player setting, faster evolution may be favoured in a multiplayer setting. The underlying features of multiplayer games can be crucial for the distribution of benefits. They also suggest a link between the evolution of the rate of evolution and group size.     

Absence of evidence is not evidence of absence

Imperfect detection of a species is often a problem when attempting to establish its presence or absence at a set of locations. Failing to find the required evidence that a species is present at a location does not imply that the species is absent, merely that it has not been found. Some of the consequences of imperfect detection is that assessments of factors influencing species presence/absence can be misleading, and how certain can one be that the species is really absent given it has not detected at a location. In this talk I shall briefly review some of the consequences of imperfect detection, methodological advances that enable the detection process to be explicitly accounted for, and practical ways in which the required additional information can be collected.     

On interacting populations that disperse to avoid crowding: The effect of a sedentary colony

An analysis is given of a model for two interacting species, one mobile and the other sedentary, in which the mobile one disperses to avoid crowding. The spatial distribution of the mobile species over the habitat, as it evolves with time, is studied. In particular it is shown that a colony of the sedentary species can form an effective barrier against the spreading mobile species, and prevent it from entering certain parts of the habitat.     

The functional importance of parasites in animal communities: many roles at many levels?

Past research on parasites and community ecology has focussed on two distinct levels of the overall community. First, it has been shown that parasites can have a role in structuring host communities. They can have differential effects on the different hosts that they exploit, they can directly debilitate a host that itself is a key structuring force in the community, or they can indirectly alter the phenotype of their host and change the importance of the host for the community. Second, certain parasite species can be important in shaping parasite communities. Dominant parasite species can directly compete with other parasite species inside the host and reduce their abundance to some extent, and parasites that alter host phenotype can indirectly make the host more or less suitable for other parasite species. The possibility that a parasite species simultaneously affects the structure of all levels of the overall community, i.e. the parasite community and the community of free-living animals, is never considered. Given the many direct and indirect ways in which a parasite species can modulate the abundance of other species, it is conceivable that some parasite species have functionally important roles in a community, and that their removal would change the relative composition of the whole community. An example from a soft-sediment intertidal community is used to illustrate how the subtle, indirect effects of a parasite species on non-host species can be very important to the structure of the overall community. Future community studies addressing the many potential influences of parasites will no doubt identify other functionally important parasite species that serve to maintain biodiversity.     

A stochastic biodiversity model with overlapping niche structure

The niche is a fundamental ecological concept that underpins many explanations of patterns of biodiversity. The complexity of niche processes in ecological systems, however, means that it is difficult to capture them accurately in theoretical models of community assembly. In this study, we build upon simple neutral biodiversity models by adding the important ingredient of overlapping niche structure. Our model is spatially implicit and contains a fixed number of equal-sized habitats. Each species in the metacommunity arises through a speciation event; at which time, it is randomly assigned a fundamental niche or set of environments/habitats in which it can persist. Within each habitat, species compete with other species that have different but overlapping fundamental niches. Species abundances then change through ecological drift; each, however, is constrained by its maximum niche breadth and by the presence of other species in its habitats. Using our model, we derive analytical expressions for steady-state species abundance distributions, steady-state distributions of niche breadth across individuals and across species, and dynamic distributions of niche breadth across species. With this framework, we identify the conditions that produce the log-series species abundance distribution familiar from neutral models. We then identify how overlapping niche structure can lead to other species abundance distributions and, in particular, ask whether these new distributions differ significantly from species abundance distributions predicted by non-overlapping niche models. Finally, we extend our analysis to consider additional distributions associated with realized niche breadths. Overall, our results show that models with overlapping niches can exhibit behavior similar to neutral models, with the caveat that species with narrow fundamental niche breadths will be very rare. If narrow-niche species are common, it must be because they are in a non-overlapping niche or have countervailing advantages over broad-niche species. This result highlights the role that niches can play in establishing demographic neutrality.     

Gamete interaction: Is it species‐specific?

Reproductive isolation is pivotal to maintain species separation and it can be achieved through a plethora of mechanisms. In addition, the development of barriers to gamete interaction may drive speciation. Such barriers to interspecific gamete interaction can be prezygotic or postzygotic. Considering the great diversity in animal species, it is easy to assume that regulation of the early steps of fertilization is critical to maintain species identity. One prezygotic mechanism that is often mentioned in the literature is that gamete interaction is limited to gametes of the same species. But do gametes of all animals interact in a species‐specific way? Are gamete interactions completely species‐specific or perhaps just species‐restricted? In species in which species‐restrictions have been described, is the interspecies barrier at one major step in the fertilization process or is it a combination of partially restricted steps that together lead to a block in interspecific fertilization? Are the mechanisms used to avoid interspecific crosses different between free‐spawning organisms and those with internal fertilization? This review will address these questions, focusing on prezygotic barriers, and will describe what is known about the molecular biology that may account for species‐limited gamete recognition and fertilization. Mol. Reprod. Dev. 73: 1422–1429, 2006. © 2006 Wiley‐Liss, Inc.     

Strong species‐environment feedback shapes plant community assembly along environmental gradients

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species‐environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species‐environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species‐environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species‐environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species‐environment feedback on community assembly.