短散在元件的筛选方法及其在鲸类和爬行类系统发育与进化研究中的应用

短散在元件(short interspersed repetitive elements,SINEs)是广泛分布于真核生物基因组中的一种反转录转座子。近年来越来越多的研究表明SINEs对基因组的结构、功能和进化起着重要作用,是研究物种系统发育和种群生物学的一个良好分子标记。本文简单介绍了SINEs的特征、基本结构、分离和鉴定,以及近年来SINEs标记在系统发育与进化研究中的应用。     

EST分子标记开发及在比较基因组学中的应用

数量迅速增加的EST(expressed sequence tags)为分子标记的开发提供了宝贵的资源。与来自于基因组DNA开发的传统标记相比,以EST为基础的分子标记是一种新型分子标记,具有其显著的优势,如开发简便、信息量高和通用性好等,在多方面都有重要的利用价值。本文详细地介绍了目前基于EST开发的5类分子标记以及基于生物信息学方法的开发策略,这些标记包括EST-PCR、EST-SSR、EST-SNP、EST-RFLP和EST-AFLP。此外,对这些标记在比较基因组学研究中的应用进行了评述,包括比较作图、遗传多样性评价及系统发育研究等。     

基因组结构信息在动物系统发育研究中的应用

随着人类基因组和一些模式生物、重要经济生物以及大量微生物基因组测序的完成,生物学整体研究业已进入基因组时代.最近5～10年以来,利用基因组结构信息进行系统发育推断的研究形成了分类学和进化生物学中的前沿领域之一.相对于核苷酸或氨基酸序列中的突变而言,基因组的结构变化--内含子的插入/缺失、反转录子的整合、签名序列、基因重复以及基因排序等--是更大空间(或者时间空间)尺度上的相对稀缺的系统发育信息,一般用于科和科以上阶元间的亲缘关系研究.基因组全序列的获得和其中各基因位置的确定有利于将基因组中不同层次的系统发育信息综合起来,利用全面分子证据(total molecular evidence;包括基因组信息,DNA、RNA、蛋白质的序列信息,RNA和蛋白质的高级结构等)进行分子系统学研究.     

单分子荧光检测技术的发展及其在植物生物学研究中的应用

单分子荧光检测技术是利用荧光基团对目的分子标记后,在单分子水平成像并追踪分子的构象变化、动力学特征以及分子之间相互作用的研究方法.相较于传统分子生物学和遗传学的研究手段,单分子检测技术可以对单个分子的动态和特性进行分析,特别是瞬时或偶发性的事件,从而更加深入地挖掘在群体测量中被掩盖的信息.该技术已广泛应用于动物细胞生物...     

全长rDNA簇在蝽类昆虫生命树构建中的应用前景(昆虫纲,半翅目)

在昆虫纲中,生命树计划正在以目级阶元中的分类单元为单位逐步推进.针对这一大的背景,以及高级阶元和种级阶元分子系统学研究间脱节现状,提出以rDNA簇为一组分子标记、并且在未来高级阶元系统发育研究中将目前选取少量代表类群的做法改为将尽量多的物种包含到一棵系统发育树中的建议.其中首先简要介绍了rDNA簇的结构及其中各分子标记在分子系统学研究中的应用价值,随后以蝽类昆虫为例,有针对性地总结了rDNA簇中不同基因序列已有数据的丰富程度及其在分子系统学研究中的应用情况.首次给出了蝽类昆虫28S rRNA近全长序列的二级结构模型.基于对18S rRNA和28S rRNA二级结构研究所积累的认识,强调了18S rDNA和28S rDNA内部不同区段之间变异模式和应用价值的差异,论证了未来在生命树构建中深化对rDNA簇中各基因进行联合应用的合理性和可行性.     

蝶类线粒体基因组学研究进展

蝶类所蕴含的生态和形态多样性信息十分丰富,并一直作为进化生物学和生态学研究的模型系统之一。随着分子生物学的发展,分子生物学技术被广泛应用于蝶类系统学研究。但随着研究的深入,简单的分子片段已不能满足研究的需求,需要挖掘新的分子标记。近年来,线粒体全基因组已成为蝶类分子系统学研究中的重要分子标记之一,并广泛应用于蝶类各阶元的研究中。就蝶类线粒体基因组的测序进展、基因组的结构特征、线粒体基因(蛋白质编码基因、tRNA基因、rRNA基因)的特征、A+T富集区的特征、基因重叠现象及线粒体基因组在分子系统学方面的应用进行了概述,同时也分析了线粒体基因组在应用中存在的一些问题。     

AFLP分子标记及其应用(综述)

本文简述ＡＦＬＰ分子标记的原理、方法与特点,并综述其在植物遗传多态性及系统发育学研究、基因定位及高密度遗传图谱（或物理图谱）构建和品种鉴定及抗性育种特征性状的分子标记中的应用现状和前景。     

DNA在鸟类分子系统发育研究中的应用

鸟类分子系统发育研究中常用的DNA技术有DNA杂交、RFLP和DNA序列分析等。DNA杂交技术曾在鸟类中有过大规模的应用,并由此诞生了一套新的鸟类分类系统。在鸟类的RFLP分析中,用的最多的靶序列是线粒体DNA。DNA序列分析技术被认为是进行分子系统发育研究最有效、最可靠的方法。在DNA序列分析中,线粒体基因应用最广泛,但由于其自身的一些不足,近年来,不少学者把目光投向了核基因,将线粒体基因和核基因结合起来进行系统发育研究。目前在鸟类分子系统发育中,应用较多的核基因是scnDNA,其内含子可以用于中等阶元水平的系统研究,而外显子主要用于高等阶元的系统研究。除了分子标记自身的问题之外,鸟类分子系统发育研究中还存在着方法上的问题,包括分子标记的选择,样本数量以及数据处理等。今后鸟类分子系统发育研究应该更加注重方法的标准化。     

分子遗传标记技术在兔遗传多样性分析中的应用

实验兔是重要的实验动物之一,在医药领域发挥重要作用。各种分子遗传标记的出现为实验兔系统发育、种群遗传结构分析以及质量控制等各个领域提供了更为简便、可靠的研究手段。但目前,国内实验兔遗传质量不稳定,遗传背景不明确,严重制约着实验兔的应用。本文对各种分子标记在兔遗传多样性中的应用进行综述,以为实验兔遗传检测方法的建立提供帮助。     

完全树构建中的关键领域:rRNA 序列与超级树

20年来,分子系统学在理论和实践方面都有飞速的发展.随着可用分子标记和所涉及阶元数量的增多和范围的扩大,以及计算能力的进步,人们对完全树(universal tree)将地球上所有物种囊括在内、描述其间的亲缘关系的系统发育树的憧憬正在逐步成为现实.由于rDNA/rRNA是惟一作为所有细胞生命形式所共有的分子标记,其在构建完全树的过程中具有不可替代的作用.近5年,超级树(supertree)的技术逐步完善,已经在若干类群中有良好的应用,形成了系统发育与进化生物学领域的研究前沿之一,为最终获得完全树奠定了坚实的基础.     

Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments

The sequencing and analysis of multiple housekeeping genes has been routinely used to phylogenetically compare closely related bacterial isolates. Recent studies using whole-genome alignment (WGA) and phylogenetics from >100 Escherichia coli genomes has demonstrated that tree topologies from WGA and multilocus sequence typing (MLST) markers differ significantly. A nonrepresentative phylogeny can lead to incorrect conclusions regarding important evolutionary relationships. In this study, the Phylomark algorithm was developed to identify a minimal number of useful phylogenetic markers that recapitulate the WGA phylogeny. To test the algorithm, we used a set of diverse draft and complete E. coli genomes. The algorithm identified more than 100,000 potential markers of different fragment lengths (500 to 900 nucleotides). Three molecular markers were ultimately chosen to determine the phylogeny based on a low Robinson-Foulds (RF) distance compared to the WGA phylogeny. A phylogenetic analysis demonstrated that a more representative phylogeny was inferred for a concatenation of these markers compared to all other MLST schemes for E. coli. As a functional test of the algorithm, the three markers (genomic guided E. coli markers, or GIG-EM) were amplified and sequenced from a set of environmental E. coli strains (ECOR collection) and informatically extracted from a set of 78 diarrheagenic E. coli strains (DECA collection). In the instances of the 40-genome test set and the DECA collection, the GIG-EM system outperformed other E. coli MLST systems in terms of recapitulating the WGA phylogeny. This algorithm can be employed to determine the minimal marker set for any organism that has sufficient genome sequencing.     

Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next‐generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra‐individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos.     

Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers

Variation in substitution rates among evolutionary lineages (among-lineage rate variation or ALRV) has been reported to negatively affect the estimation of phylogenies. When the substitution processes underlying ALRV are modeled inadequately, non-sister taxa with similar substitution rates are estimated incorrectly as sister species due to long-branch attraction. Recent advances in modeling site-specific rate variation (heterotachy) have reduced the impacts of ALRV on phylogeny estimation in several empirical and simulated datasets. However, the addition of parameters to the substitution model reduces power to estimate each parameter correctly, which can also lead to incorrect phylogeny estimation. A potential solution to this problem is to identify the levels of ALRV that negatively impact phylogeny estimation such that molecular markers with non-deleterious levels of ALRV can be identified. To this end, we used analyses of empirical and simulated gene datasets to evaluate whether levels of ALRV identified in a mitochondrial genomic dataset for salamanders negatively impacted phylogeny estimation. We simulated data with and without ALRV, holding all other evolutionary parameters constant, and compared the phylogenetic performance of both simulated and empirical datasets. Overall, we found limited, positive effects of ALRV on phylogeny estimation in this dataset, the majority of which resulted from an increase in substitution rate on short branches. We conclude that ALRV does not always negatively impact phylogeny estimation. Therefore, ALRV can likely be disregarded as a criterion for marker selection in comparable phylogenetic studies.     

The road less traveled: Phylogenetic perspectives in primatology

Interest in phylogeny is increasing in many areas of evolutionary biology. One area of evolutionary anthropology that has not yet fully embraced this growth in phylogenetic thinking, however, is the study of primate behavior and ecology.¹ The predominant framework for behavioral studies of primates over the last three decades has been socioecological. The goals have been to identify broad correlations between species' behaviors and current environmental conditions. As such, the socioecological approach has been largely nonhistorical, taking little account of phylogeny. In contrast, phylogenetic approaches view the behavior of contemporary taxa within an explicitly historical framework. Although socioecology has proven extremely productive, there are many reasons to think that research in primatology could be profitably supplemented by a phylogenetic perspective.^2,3     

A phylogenomics approach for selecting robust sets of phylogenetic markers

Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and analysis of a relatively small sample of marker genes. The selection of these phylogenetic markers should ideally be based on accurate predictions of their combined, rather than individual, potential to accurately resolve the phylogeny of interest. Here we present and validate a new phylogenomics strategy to efficiently select a minimal set of stable markers able to reconstruct the underlying species phylogeny. In contrast to previous approaches, our methodology does not only rely on the ability of individual genes to reconstruct a known phylogeny, but it also explores the combined power of sets of concatenated genes to accurately infer phylogenetic relationships of species not previously analyzed. We applied our approach to two broad sets of cyanobacterial and ascomycetous fungal species, and provide two minimal sets of six and four genes, respectively, necessary to fully resolve the target phylogenies. This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life.     

The lemur revolution starts now: The genomic coming of age for a non-model organism

Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman’s primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman’s career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies – many of which were conducted by Goodman himself – have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates.     

A study of the utility of convergent characters for phylogeny reconstruction: do ecomorphological characters track evolutionary history in Anolis lizards?

The reconstruction of phylogeny requires homologous similarities across species. Characters that have been shown to evolve quickly or convergently in some species are often considered to be poor phylogenetic markers. Here I evaluate the phylogenetic utility of a set of morphological characters that are correlated with ecology and have been shown to evolve convergently in Anolis lizards in the Greater Antilles. Results of randomization tests suggest that these “ecomorph” characters are adequate phylogenetic markers, both for Anolis in general and for the Greater Antillean species for which ecomorphological convergence was originally documented. Explanations for this result include the presence of ecomorphologically similar species within evolutionary radiations within islands, some monophyly of ecomorphs across islands, and the existence of several species that defy ecomorphological characterization but share phylogenetic similarity in some ecomorph characters.     

Novel classification and biogeography of Leptolejeunea (Lejeuneaceae,Marchantiophyta) with implications for the origin and evolution of the Asian evergreen broad-leaved forests

Although recent molecular phylogenetic analyses have greatly improved our understanding of the classification of the large liverwort family Lejeuneaceae, the frequent incongruencies between morphology-based taxonomy and molecular phylogeny have hindered our understanding of evolutionary diversification within the group. Here we focus on Leptolejeunea (Spruce) Steph., a pantropical epiphyllous genus in Lejeuneaceae with 40 species. Phylogenetic studies on the genus have been hampered by insufficient taxon sampling, leaving the deep phylogenetic relationships within this group unresolved. We present the most comprehensive phylogenetic analysis of the genus to date with sampling of over 80% of species, including the enigmatic Leptolejeunea spinistipula (Mizut.) X.L.He endemic to Borneo. Based on data from three molecular markers with representatives of Leptolejeunea and its allies, Leptolejeunea appeared to be monophyletic following the exclusion of L. spinistipula and its transfer to Soella R.L.Zhu, L.Shu, Qiong He & Y.M.Wei. A total-evidence approach was taken to resolve the backbone phylogeny of Leptolejeunea and a first infrageneric classification of Leptolejeunea, including a new subgenus and three new sections, is proposed based on integrated molecular and morphological evidence. Reconstruction of the evolutionary history showed a wide ancestral area of Leptolejeunea during the Paleogene that arose in mainland Asia, followed by an accelerated speciation rate. Across the biogeographical history of Leptolejeunea, long-distance dispersal had profound effects on population expansion. Our findings suggest that Australasia is a source of biodiversity of Asian evergreen broad-leaved forests that have been established since the Oligocene and rose after the early Miocene.     

Developing a series of conservative anchor markers and their application to phylogenomics of Laurasiatherian mammals

The availability of numerous universal markers and suitable phylogenetic analysis methods are both very important for phylogenomics inference. Based on PCR amplification, a total of 122 markers, which were amplified in 19 representative species, were developed for Laurasiatherian phylogenomics. Subsequently, we illustrated the utility of these newly developed markers using a subset of eight markers. We showed that both 'supermatrix' and 'supertree' trees generated similar topology, which accorded with the current understanding of the Laurasiatherian phylogeny in most aspects. Thus, markers developed here would be likely to make a contribution to resolving evolutionary relationships and inferring evolutionary histories of the Laurasiatherian mammals in the future.     

The new phylogeny of eukaryotes

Molecular phylogeny has been regarded as the ultimate tool for the reconstruction of relationships among eukaryotes-especially the different protist groups-given the difficulty in interpreting morphological data from an evolutionary point of view. In fact, the use of ribosomal RNA as a marker has provided the first well resolved eukaryotic phylogenies, leading to several important evolutionary hypotheses. The most significant is that several early-emerging, amitochondriate lineages, are living relics from the early times of eukaryotic evolution. The use of alternative protein markers and the recognition of several molecular phylogeny reconstruction artefacts, however, have strongly challenged these ideas. The putative early emerging lineages have been demonstrated as late-emerging ones, artefactually misplaced to the base of the tree. The present state of eukaryotic evolution is best described by a multifurcation, in agreement with the 'big bang' hypothesis that assumes a rapid diversification of the major eukaryotic phyla. For further resolution, the analysis of genomic data through improved phylogenetic methods will be required.