对吴征镒等（2002）提出的“八纲系统”中一些问题的评论

最近吴征镒等发表的被子植物“多系_多期_多域”的“八纲”新分类系统,是以该系 统作者自己人为截取早白垩世时间横断面并认为在这个横断面上存在8条主传代线为基础建 立的。“八纲系统”在祖先式样及其起源时间和地点方面缺乏证据,各主传代线相互之间及 其与被子植物共同祖先的关系也基本没有说明。由于没有接受植物系统发育重建研究中共同 遵守的共同祖先原理,而且混淆使用了“单系”和“多系”的概念,可以认为“八纲 系统”是人为性很强的被子植物分类系统。     

以演化时间为新增指标构建真菌分类系统

随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征（“单系+表型特征”）对不同的分类等级命名是最为普遍的方法。历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步。然而系统发育重建所揭示的单系类群并没有相应的标准来对应于纲目科属等种上分类等级,所以并不能直接转换为分类系统,且在分类实践中,由于不同分类学家在决定各个单系类群对应的分类等级时采用的尺度不同、依据不一,严重影响分类系统的科学性和稳定性。随着分子钟分析方法的出现,实现了对现生生物类群演化时间的估算,所以在系统发育、表型特征研究的基础上,把演化时间作为真菌分类的新增指标来划分和命名种上分类等级的方法（“单系+表型特征+演化时间”）得以应用。本文回顾了首次利用这种方法重建蘑菇属分类系统的工作,目前研究所揭示的担子菌门和子囊菌门从门至科各分类等级的演化时间范围,及利用演化时间为新增指标在分类命名中的应用;分析了影响演化时间估算可靠性的关键因素及对策。我们认为在构建分类系统的研究中增加演化时间指标,使新分类系统体现类群进化过程中的时间维度,能更全面反映类群的进化历程,促进分类系统的科学性和稳定性。     

重构符合自然历史的演化树是系统生物学的终极目标

从自然历史的角度,对单系群、特征、系统发育和自然分类系统的概念做出了澄清和解释。自然分类是仅包含单系群全体成员和它们之间亲缘发育关系和自然演化过程的分类。只有包括所有成员在内的单系群才能称为一个自然分类系统。目前生物系统学主要使用分支分析方法重建自然历史演化过程。在编写算法语言和程序时,作者常将注意力集中在形态和分子数据的获得、运算过程和算法的改进,而忽略了支序分类学的简约原则等假设前提和它的理论缺陷。由此在系统发育重建的过程中存在2个常见的误区:(1)在一个单系类群中包括的成员不完全却声称是一个自然系统;(2)将通过数学和程序运算出来的"简约"或最"似然"的亲缘发育关系当作自然系统。自然单系类群往往具有漫长的演化历史,人类无法直接观察和在实验室中重复。利用支序分类原理构建的单系类群的发育关系只是一个单系类群之间的最"简约"或最"似然"的亲缘发育关系,并不能真正反映自然历史的本来面目。古生物学虽然有较好的时空框架,但可提供的特征数量和精度不够。现生生物的各种特征和遗传数据虽然相对充分,但对于具有较长演化历史的类群,由于缺失了大量关键成员,推导出的系统发育关系可能都是并系或复系,无法构成一个自然系统。因此只用现生生物宏观和基因组信息重构具有较长演化历史的生物类群的自然系统是无法实现的。只有利用分子和形态的全证据,从宏观和微观两个层面、古代和现代相结合,采用多种技术和研究手段对一个单系类群的全体成员进行研究,才能真正做到自然分类。在这个过程中可以利用6个原则对分类系统是否符合自然历史发展进行检验。     

六足总纲系统发育研究进展与新分类系统

简要综述了昆虫分纲、分目的历史变化,包括昆虫分目多少的变化,昆虫是纲级还是总纲级阶元的变化,昆虫各目分类地位系统排列的变化以及六足总纲系统发育研究进展。根据近10年来形态特征与分子测序数据相结合的系统发育研究,整理出六足总纲与系统发育支序分析相一致的分类系统,对昆虫35目的分类运用了10个分类阶元。在此基础上,删减次要分类阶元,提出简明分类系统,既反映每个高级分类单元的单系性,明晰各目的共祖近度,又减少了分类阶元层次,方便各分类单元的识别与鉴定。六足总纲Hexapoda分为4纲:原尾纲Protura(包括蚖目Acerentomata、华蚖目Sinentomata、古蚖目Eosentomata),弹尾纲Collembola(包括弹尾目Collembola),双尾纲Diplura(包括双尾目Diplura),昆虫纲Insecta。昆虫纲分为单髁亚纲SubclassMonocondylia(包括石蛃目Archaeognatha)与双髁亚纲SubclassDicondylia。双髁亚纲分为衣鱼部DivisionZygentoma(包括衣鱼目Zygentoma)与有翅部DivisionPterygota。有翅部分为10个总目、27目。     

旋唇纲系统发育基因组学分析支持瘦尾虫属归于散毛目

根据传统形态学特征的系统分类学研究,将瘦尾虫属(Uroleptus)归入尾柱目(Urostylida).但是,基于单基因和多基因联合的分子系统发育学分析支持瘦尾虫属与散毛目内部类群的亲缘关系更近.为进一步探讨旋唇纲(Spirotrichea)内部类群的系统发育关系以及瘦尾虫属的系统发育地位,我们对四种旋唇纲纤毛虫(澳大利亚速体虫(Notohymena australis)、瘦尾虫属未定种(Uroleptus sp.)、弹跳虫属未定种(Halteria sp.)和楯纤虫属未定种(Aspidisca sp.))进行单细胞转录组测序,并基于151个直系同源基因的51 596个氨基酸位点对旋唇纲开展更全面的系统发育基因组学分析.分析结果支持旋唇纲中四个亚纲单系:寡毛亚纲与环毛亚纲聚为姐妹枝,腹毛亚纲与这两个亚纲的亲缘关系更近,游仆亚纲位于旋唇纲的基部.尾柱目非单系,瘦尾虫属与散毛目中的尖毛虫科聚为一支,系统发育基因组学分析结果支持瘦尾虫属归于散毛目.     

从核糖体RNA基因序列探讨双尾虫的系统进化

双尾虫是否单系, 以及双尾虫与其他六足动物系统关系是多年来动物分类学家争议的一个关键问题. 测定了双尾虫的两大类群: 康虫八类和铗虫八类, 以及原尾虫、跳虫和蝗虫等核糖体RNA基因18SrDNA全序列和28SrDNA部分序列(D3~D5区), 并选用甲壳动物卤虫为外群, 采用最大简约(MP)法构建分子系统树. 结果表明: (ⅰ) 18SrDNA和28SrDNA数据整合分析含有较强的系统发育信息, 支持双尾虫单系性观点; (ⅱ) 双尾虫与原尾虫在系统树中构成姊妹群, 且支持率很高.     

从形态分类到准分支系统分类——修订版Treatise双壳纲卷分类系统简介

修订版Treatise双壳纲卷首卷即将正式出版,其分类系统的纲要已提前公开发表。在古生物学家、现代生物学家和分子生物学家的共同努力下,终于顺利地实现了化石和现生双壳类分类系统的初步融合,与1969版的形态分类相比,整个分类系统已经面目全非。为此,有必要全面介绍其分类方法和原则,介绍新分类系统带来的种种重大变化。新分类系统将进化学派的系统发育概念与分支系统分析方法的合理内核有机结合,发挥后者在方法论方面的优势,摒弃其系统发育即分岐演化的错误概念和某些不合理的分类学原则,如拒绝接受并系群和姐妹群必须具有相同级序等;充分发挥林奈系统的长处并加以改进,形成由共同衍征主导同时也考虑前进演化的林奈式级序体系,准分支系统分类方法由此形成。新方法兼顾分支发生和进化级这两个不同的方面,注重恢复可能的祖-裔关系;主要根据系统树但借鉴分支图方法来确定级序格架,将级序与系统树的分枝点对应,即与衍征的分歧时间对应,使级序的划分不再主观任意;一般将姐妹分类单元置于同一级序,必要时将并系群与其后裔类群置于同一级序,而姐妹群则可能被置于不同的级序。采用近亲单元和准近亲单元分别作为无级序的单系群和并系群的标识,解决了将化石分类群融入现代生物分类系统的技术难题,可简化并有效地保持分类系统的稳定性。新方法使双壳纲完成从形态分类向准分支系统分类的转变,这代表着分类学未来发展的新趋势,而林奈式级序体系则为林奈系统今后的改革提供了新的范例。     

基于mtDNA和rDNA基因序列的中国按蚊属塞蚊亚属种类的系统发育研究（双翅目：蚊科）

【目的】应用mtDNA和rDNA基因特征重建中国按蚊属塞蚊亚属已知种类的系统发育关系, 以阐明亚属内各蚊种的亲缘关系。【方法】对采自中国的按蚊属塞蚊亚属Anopheles (Cellia) 20种蚊的mtDNA-COⅡ和 rDNA-28S-D3序列进行测定和分析, 以按蚊属按蚊亚属Anopheles (Anopheles)的中华按蚊An. (An.) sinensis和赫坎按蚊An. (An.) hyrcanus为外群, 采用COⅡ和D3单基因, 以及“COⅡ+D3”联合数据组以邻接法（NJ）、 最大简约法（MP）、 最大似然法（ML）和贝叶斯法（BI）等重建这些种类的系统发育树。【结果】 mtDNA-COⅡ和rDNA-28S-D3序列的长度范围分别为685 bp和375～410 bp, 在塞蚊亚属蚊种间的遗传距离分别为0.015～0.117和0.003～0.111。各系统树显示外群被合理分开,除在COⅡ树中新塞蚊系为并系外,各系均聚为单系群,新迈蚊系和迈蚊系亲缘关系最近。联合数据组构建的系统合意树显示中国塞蚊亚属各蚊种形成4支,除伪威氏按蚊与多斑按蚊种团未聚为单系群外,其他各种团和复合体成员种均分别聚在一起,各分支的置信值均大于50%。【结论】本研究获得的分子系统发育树清楚地显示了中国按蚊属塞蚊亚属各种类及系之间的系统发育关系, 对其分类和防治研究具有参考价值。     

序列的证据

线蕨属Colysis植物主要分布于亚洲热带和亚热带地区, 少数种类分布至非洲、澳大利亚(昆士兰)及新几内亚地区。自1849年成立以来, 线蕨属的分类范畴和系统位置一直有待确定。本文利用叶绿体基因组的rbcL、rps4基因和rps4-trnS基因间隔区序列, 运用最大简约法和贝叶斯方法分析了线蕨属及其近缘类群的系统演化关系。研究结果显示: (1)线蕨属和薄唇蕨属Leptochilus (含似薄唇蕨属Paraleptochilus)组成一个支持率很高的单系分支(C-L Clade), 但是薄唇蕨属的成员位于线蕨属的不同支系内, 支持线蕨属和薄唇蕨属合并为一个属; (2)瘤蕨属Phymatosorus单独形成一个单系分支; (3)星蕨属Microsorum是一个多系类群, 除Microsorium linguiforme、M. varians和M. pustulatum与马来群岛的Lecanopteris聚在一起外, 其他的星蕨属成员均位于不同的支系上。本文的系统发育分析结果为线蕨属和薄唇蕨属的分类处理提供了分子系统学的证据。     

关于停止使用"同翅目Homoptera" 目名的建议

长期以来,在我国昆虫学界,“同翅目Homoptera”和半翅目Hemiptera一直被作为2个并列的昆虫目被广泛使用。传统的“同翅目”被分为3亚目10总科,即鞘喙亚目Coleorrhyncha(包括膜翅蝽总科Peloridioidea)、胸喙亚目Stemorrhyncha(包括木虱总科Psylloidea、粉虱总科Aleyrodoidea、蚧总科Coccoidea和蚜总科Aphidoidea)和头喙亚目Auchenorrhyncha[包括蜡蝉子亚目Fulgoromorpha(包括蜡蝉总科Fulgoroidea)和蝉子亚目Cicadomorpha(包括蝉总科Cicadoidea、沫蝉总科Cercopoidea、叶蝉总科Cicadelloidea和角蝉总科Membracoidea)]。近年来,形态学及分子学特征数据的支序分析研究表明,木虱总科、粉虱总科、蚧总科、蚜总科、蜡蝉总科、蝉总科、沫蝉总科、角蝉总科都是单系群;鞘喙亚目、胸喙亚目、蝉子亚目及蜡蝉子亚目也都是单系群,其相互之间的系统发育关系为：胸喙亚目 (蝉子亚目 (蜡蝉子亚目 (鞘喙亚目 异翅亚目(蝽类)))),它们共同组成了单系的半翅目Hemiptera。系统发育分析表明,在半翅目中,鞘喙亚目与异翅亚目具有最近的亲缘关系,蜡蝉子亚目与鞘喙亚目 异翅亚目是姊妹群,蝉子亚目是蜡蝉子亚目 (鞘喙亚目 异翅亚目)的姐妹群,胸喙亚目是半翅目中最早和最原始的一个分枝。因此传统的“同翅目”并不是一个自然的单系类群,而是一个人为的并系类群。目前,在国际昆虫学界,“同翅目”作为一个人为的并系类群已得到公认和普遍接受,并已不再作为昆虫纲的一个有效目被使用。然而,“同翅目”作为昆虫纲的一个有效目在国内一直被广泛使用,为此,作者建议我国的昆虫学工作者今后应停止使用“同翅目”这一人为的并系目名而使用单系的半翅目目名,即将长期以来一直置于“同翅目”的木虱、粉虱、蚧虫、蚜虫、蝉、沫蝉、叶蝉、角蝉及蜡蝉类昆虫与蝽类昆虫一起作为半翅目的成员对待。     

A critique on the “Eight_Class System” of the classification of Angiosperms proposed by Wu et al.

Some critical comments are made on the “Eight-Classs System” of the classification of angiosperms recently proposed by Wu et al., which the aut hors claimed to be a “polyphyletic-polytopic” system. This system is established based on the hypothesis that there have existed eight principal lineages of angiosperms by the end of the Early Cretaceous. However, this hypothesis has not been supported by any neobotanical and paleobotanical evidence. There lationship among the eight lineages and their relationship with the common ances tor of angiosperms are not clearly clarified in the system. Having failed to follow the principle of common ancestry in the reconstruction of angiosperm phylogeny and having misinterpreted the concepts of monophyly and polyphyly, the “Eight-Class System” of the classification of angiosperms is considered to be an artificial one.     

Ernst Haeckel (1834–1919) and the monophyly of life

Ernst Haeckel, who first introduced the term ‘monophyly’ into the biological literature, has in the past been appealed to in adjudication of the modern use of that concept. A contextual analysis of his writings reveals an inconsistent use of the term ‘monophyly’ by Haeckel. Morphological phylogeny was decoupled in Haeckel’s thinking from the evolutionary history of taxa. Monophyly could mean the derivation of one taxon from another, ancestral one, where these taxa could be species or of supraspecific rank. Monophyly could also mean the phylogenetic differentiation of a diversity of organismal ‘forms’ (morphologies) from a common primitive ‘form’ (morphological stage). And finally, monophyly, as also polyphyly, could apply to the origin of specific anatomical structures, in which case the monophyly/polyphyly of anatomical structures needed not to correlate with the monophyly/polyphyly of the taxon characterized by these structures. With respect to the issue of the unity and reality of monophyletic taxa, Haeckel’s writings again are indeterminate as is his stance on the monophyletic origin of life.     

Molecular phylogeny of fire ants of the Solenopsis saevissima species-group based on mtDNA sequences

The systematics of South American fire ants (Solenopsis saevissima species-group) has been plagued by difficulties in recognizing species and their relationships on the basis of morphological characters. We surveyed mtDNA sequences from 623 individuals representing 13 described and undescribed species within the species-group and 18 individuals representing other major Solenopsis lineages to generate a phylogeny of the mitochondrial genome. Our analyses support the monophyly of the S. saevissima species-group, consistent with a single Neotropical origin and radiation of this important group of ants, as well as the monophyly of the socially polymorphic species within the group, consistent with a single origin of polygyny (multiple queens per colony) as a derived form of social organization. The mtDNA sequences of the inquiline social parasite S. daguerrei form a clade that appears to be distantly related to sequences from the several host species, consistent with the view that advanced social parasitism did not evolve via sympatric speciation of intraspecific parasites. An important general finding is that species-level polyphyly of the mtDNA appears to be the rule in this group of ants. The existence of multiple divergent mtDNA lineages within several nominal species (including the pest S. invicta) suggests that the pattern of widespread polyphyly often stems from morphological delimitation that overcircumscribes species. However, in two cases the mtDNA polyphyly likely results from recent interspecific hybridization. While resolving species boundaries and relationships is important for understanding general patterns of diversification of South American fire ants, these issues are of added importance because invasive fire ants are emerging as global pests and becoming important model organisms for evolutionary research.     

Phylogenetic relationships within Aglaopheniidae (Cnidaria,Hydrozoa) reveal unexpected generic diversity

Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner‐Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo‐Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1‐5.8S rRNA gene‐ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.     

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.     

Relationships among "ancient araliads" and their significance for the systematics of Apiales

The relationship between the angiosperm families Apiaceae and Araliaceae (order Apiales) has been difficult to resolve, due in large part to problems associated with taxa characterized by a mixture of features typical of both families. Among such confounding groups are the araliads Delarbrea, Pseudosciadium, Myodocarpus, Mackinlaya, and Apiopetalum and many members of Apiaceae subfamily Hydrocotyloideae. Traditional systems have often envisioned these taxa as phyletic intermediates or bridges between the two families. To reevaluate the phylogenetic position of the "intermediate" araliad genera, molecular data were collected from nuclear (rDNA ITS) and plastid (matK) sequences from a complete or near-complete sampling of species in each genus. When analyzed with samples representing the other major clades now recognized within Apiales, results confirm and expand the findings of previously published studies. The five araliad "intermediates" are placed within two well-supported clades clearly segregated from the "core" groups of both Apiaceae and Araliaceae. These segregate clades closely parallel traditional definitions of the araliad tribes Myodocarpeae (Delarbrea, Pseudosciadium, and Myodocarpus) and Mackinlayeae (Mackinlaya and Apiopetalum), and relationships among the species within these clades are largely supported by morphological and anatomical data. Based on these results, Myodocarpeae and Mackinlayeae may best be treated as distinct families. This approach would render four monophyletic groups within Apiales, to which a fifth, Pittosporaceae, cannot at present be excluded. Sampling of taxa from Hydrocotyloideae remains preliminary, but results confirm previous studies indicating the polyphyly of this subfamily: hydrocotyloid taxa may be found in no fewer than three major clades in Apiales.     

Phylogeny and the “polyphyletic-polychronic-polytopic” system of classification of angiosperms— A response to Fu De-Zhi

The historical development of the concepts of genealogy, phylogeny, mo nophyly and polyphyly is briefly reviewed. The different implications of the tw o most controversial terms in taxonomic and evolutionary literature, “monophyly " and “polyphyly", are     

Using molecules and morphology to infer the phylogenetic relationships and evolutionary history of the Dirini (Nymphalidae: Satyrinae), a tribe of butterflies endemic to Southern Africa

The first empirically supported phylogenetic hypothesis of relationships for the southern African endemic butterfly tribe Dirini is presented. Data derived from the morphology and ecology of the adults and immature stages (33 characters), and portions of the mitochondrial gene cytochrome oxidase I (COI) and the nuclear genes elongation factor 1α (EF1α) and wingless (WG) (totalling 1734 bp) were used to infer the relationships of the in‐group genera. An expanded molecular dataset using four genera from the Nymphalini and Satyrini to root the tree, and three genera from the Melanitini to test the monophyly of the tribe, was analysed using parsimony and Bayesian methods. Estimates of divergence times were calculated using two fossil calibrations under a relaxed molecular clock model. The monophyly of the tribe and each in‐group genus were strongly supported. Key findings are the sister‐taxon relationship of Aeropetes and Tarsocera, the apparent simultaneous or nearly simultaneous radiation of four lineages, the polyphyly of the species within Torynesis, and the apparent trans‐Atlantic dispersal of the ancestors of Manataria about 40 Ma. Estimates of divergence times indicate that the tribe has undergone two major radiations since its origin: the first when they left forest habitats in the mid–late Oligocene, shortly after the radiation of the grasses (Poaceae), and the second in the early‐middle Pliocene, coinciding with the aridification of southern Africa and the spread of conditions that favoured C₄ grasses over the C₃ grasses that dirine larvae prefer to eat. The high species diversity within the tribe appears to be partly a taxonomic artefact that may have resulted from the misinterpretation of climate‐related phenotypic variation within extant species. Relocation and breeding experiments should test this hypothesis.     

Phylogenetic analysis of the tribe Bovini (Mammalia: Artiodactyla)

A matrix of 57 (mainly cranial) characters and 32 taxa of fossil and Recent Bovini (buffaloes, bison and cattle) has been analysed using the parsimony program HENNIG86. Among the best established results are the exclusion of Parabos , polyphyly of Leptobos , monophyly of the Bos sensu lato + buffaloes group (a clade including all Recent Bovini), probable monophyly of the Bubalina and Syncerina, and the close relationship between bison and yak. Some other interesting questions raised include the apparent absence of a close link between Pliocene African bovines (except "Leptobos" syrticus ) and later African buffaloes, and the possible monophyly of Pelorovis oldowayensis+Bos sensu lato .