低等六足动物系统学研究进展

低等六足动物包括原尾纲、弹尾纲和双尾纲三个类群,是探讨六足动物起源和进化问题的关键类群,近十年来成为节肢动物系统进化研究中的焦点之一。低等六足动物的系统发育地位以及它们之间的关系一直是备受争论的问题。通过介绍三类低等六足动物最新的分类系统,从经典分类学和系统发育两个方面对低等六足动物近十年来的研究进展进行了综述。迄今,对于三类低等六足动物都建立了比较完备的分类体系,原尾纲划分为3目10科,弹尾纲划分为4目30科,双尾纲划分为2亚目3总科10科。系统发育研究中,大多数的系统发育分析结果不支持传统的缺尾类假说,缺尾纲应摒弃不用。分子数据分析的结果普遍支持原尾纲与双尾纲近缘,但仍需要进一步探讨。线粒体基因组、比较胚胎学和比较精子学的研究结果表明,原尾纲可能经历了长期的趋异进化历史。最近的比较精子学研究支持了双尾纲的单系性。总之,三类低等六足动物系统学研究均取得了长足的发展,但仍然存在诸如研究人员匮乏和研究水平不均衡等问题。系统发育研究中,分子系统学研究成为关注的焦点,而基于核基因和线粒体基因的数据分别建立的系统发育假说存在分歧,亟需开发更优的数据分析方法。此外,需加强低等六足动物比较形态学、比较胚胎学、发育生物学等方面的研究,以便将来进行全证据的系统发育研究。     

Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: influence of character dependence and character choice in analyses of 28S rRNA sequences

The present analyses employ the almost complete sequence of the 28S rRNA gene to investigate phylogenetic relationships among Pancrustacea, placing special emphasis on the position of basal hexapod lineages. This study utilizes a greater number of characters and taxa of Protura, Collembola and Diplura than previous analyses to focus on conflicts in the reconstruction of the early steps in hexapod evolution. Phylogenetic trees are mainly based on Bayesian approaches, but likewise include analyses with Maximum Likelihood and Maximum Parsimony. Different analyses, including the application of a mixed DNA/RNA substitution model, were performed to narrow possible misleading effects of non-stationarity of nucleotide frequencies, saturation and character independence down to a minimum. This is the first time that a mixed DNA/RNA model is applied to analyse 28S rRNA sequences of basal hexapods. All methods yielded strong support for the monophyly of Collembola, Diplura, Dicondylia and Insecta s.str. , as well as for a cluster composed of Diplura and Protura ('Nonoculata-hypothesis'). However, the last cluster may be an artifact caused by a shared GC bias of the 28S sequences between these orders, in combination with a long branch effect. The instability of the position of the 'Nonoculata' within Pancrustacea further bears out the misleading effect of non-stationarity of nucleotide frequencies. Protura and Diplura either form the sister-group to Collembola (Entognatha) or cluster with branchiopod crustaceans. Overall, the phylogenetic signal of the complete sequences of the 28S rRNA gene favours monophyly of Hexapoda over paraphyly. However, further corroboration from independent data is needed to rule out the competing hypothesis of mutually paraphyletic Crustacea and Hexapoda.     

Brain organization in Collembola (springtails)

Arthropoda is comprised of four major taxa: Hexapoda, Crustacea, Myriapoda and Chelicerata. Although this classification is widely accepted, there is still some debate about the internal relationships of these groups. In particular, the phylogenetic position of Collembola remains enigmatic. Some molecular studies place Collembola into a close relationship to Protura and Diplura within the monophyletic Hexapoda, but this placement is not universally accepted, as Collembola is also regarded as either the sister group to Branchiopoda (a crustacean taxon) or to Pancrustacea (crustaceans + hexapods). To contribute to the current debate on the phylogenetic position of Collembola, we examined the brains in three collembolan species: Folsomia candida, Protaphorura armata and Tetrodontophora bielanensis, using antennal backfills, series of semi-thin sections, and immunostaining technique with several antisera, in conjunction with confocal laser scanning microscopy and three-dimensional reconstructions. We identified several neuroanatomical structures in the collembolan brain, including a fan-shaped central body showing a columnar organization, a protocerebral bridge, one pair of antennal lobes with 20-30 spheroidal glomeruli each, and a structure, which we interpret as a simply organized mushroom body. The results of our neuroanatomical study are consistent with the phylogenetic position of Collembola within the Hexapoda and do not contradict the hypothesis of a close relationship of Collembola, Protura and Diplura.     

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

HennigdividedInsectas.lat.(=Hexapoda)intotwowelldefinedtaxonomicgroups:Entog-nathaandEctognatha[1].ThemostdistinctivecharacterofEntognatha(includingProtura,Col-lembolaandDiplura)liesintheenclosedmouthpartscondition,whereasthepresenceofexposedmouthpartsisthemainfeatureofEctognatha(includingMicrocoryphia,Zygentomaandtheptery-goteinsects).ControversiesaboutthephylogeneticrelationshipsofhightaxaEntognathahavekeptgrowinginrecentyears,withthemonophylyofDipluraandthephylogeneticpositionsofDiplur…     

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

The monophyly of Diplura and its phylogenetic relationship with other hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNAgene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustaceanArtemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.     

双尾虫系统进化的初步探讨

双尾虫系统发生问题目前血受学者的关注。作为六足总纲中内,外颚亚纲的过渡类群,双尾虫是否单系性及其系统地位的确定是争论的焦点,也是解决六足总纲高级阶元系统关系的一个关键。文中综述了多年来双尾虫形态学和解剖学方面研究所引发的争议和达成的共识,并对近几年该方面分子系统学的工作进行了总结和初步探讨。     

On the phylogenetic position of insects in the Pancrustacea clade

The current views on the phylogeny of arthropods are at odds with the traditional system, which recognizes four independent arthropod classes: Chelicerata, Crustacea, Myriapoda, and Insecta. There is compelling evidence that insects comprise a monophyletic lineage with Crustacea within a larger clade named Pancrustacea, or Tetraconata. However, which crustacean group is the closest living relative of insects is still an open question. In recent phylogenetic trees constructed on the basis of large gene sequence data insects are placed together with primitive crustaceans, the Branchiopoda. This topology is often suspected to be a result of the long branch attraction artifact. We analyzed concatenated data on 77 ribosomal proteins, elongation factor 1A (EF1A), initiation factor 5A (eIF5A), and several other nuclear and mitochondrial proteins. Analyses of nuclear genes confirm the monophyly of Hexapoda, the clade uniting entognath and ectognath insects. The hypothesis of the monophyly of Hexapoda and Branchiopoda is supported in the majority of analyses. The Maxillopoda, another clade of Entomostraca, occupies a sister position to the Hexapoda + Branchiopoda group. Higher crustaceans, the Malacostraca, in most analyses appear a more basal lineage within the Pancrustacea. We report molecular synapomorphies in low homoplastic regions, which support the clade Hexapoda + Branchiopoda + Maxillopoda and the monophyletic Malacostraca including Phyllocarida. Thus, the common origin of Hexapoda and Branchiopoda and their position within Entomostraca are suggested to represent bona fide phylogenetic relationships rather than computational artifacts.     

Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea

Background

The phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study.

Results

Two largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda.

Conclusion

The finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods.

     

Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic

For over a century the relationships between the four major groups of the phylum Arthropoda (Chelicerata, Crustacea, Hexapoda and Myriapoda) have been debated. Recent molecular evidence has confirmed a close relationship between the Crustacea and the Hexapoda, and has included the suggestion of a paraphyletic Hexapoda. To test this hypothesis we have sequenced the complete or near-complete mitochondrial genomes of three crustaceans (Parhyale hawaiensis, Squilla mantis and Triops longicaudatus), two collembolans (Onychiurus orientalis and Podura aquatica) and the insect Thermobia domestica. We observed rearrangement of transfer RNA genes only in O. orientalis, P. aquatica and P. hawaiensis. Of these, only the rearrangement in O. orientalis, an apparent autapomorphy for the collembolan family Onychiuridae, was phylogenetically informative.We aligned the nuclear and amino acid sequences from the mitochondrial protein-encoding genes of these taxa with their homologues from other arthropod taxa for phylogenetic analysis. Our dataset contains many more Crustacea than previous molecular phylogenetic analyses of the arthropods. Neighbour-joining, maximum-likelihood and Bayesian posterior probabilities all suggest that crustaceans and hexapods are mutually paraphyletic. A crustacean clade of Malacostraca and Branchiopoda emerges as sister to the Insecta sensu stricto and the Collembola group with the maxillopod crustaceans. Some, but not all, analyses strongly support this mutual paraphyly but statistical tests do not reject the null hypotheses of a monophyletic Hexapoda or a monophyletic Crustacea. The dual monophyly of the Hexapoda and Crustacea has rarely been questioned in recent years but the idea of both groups' paraphyly dates back to the nineteenth century. We suggest that the mutual paraphyly of both groups should seriously be considered.     

植物microRNA的保守性及其分布的分析

MicroRNA(miRNA)是真核生物中具有重要调控作用的小分子非编码RNA。本文对miRNA官网miRBase数据库Release 22.1中隶属于植物界的绿藻门、苔藓植物门、蕨类植物门、裸子植物门、被子植物门共计82个物种的miRNA进行了统计分析。miRBase共收录植物miRNA 前体8 615个,成熟miRNA 10 414条,隶属于2 892个miRNA家族。绿藻门miRNA与其他4个门miRNA无同源性;对其他4个门植物miRNA的保守性进行研究,发现存在于2个植物门的miRNA家族有26个,属于中度保守miRNA家族;14个miRNA家族存在于3个及3个以上植物门中,属于高度保守miRNA家族,其中7个miRNA家族系苔藓、蕨类、裸子和被子植物共有,是植物中最保守的miRNA。分析表明,超过30个miRNA家族的植物有35种。进一步对40个中度或者高度保守miRNA在35种植物中的分布进行研究,发现miRNA家族及其成员在物种间的分布存在较大的差异。这些分布上的差异一方面反映不同植物中miRNA的研究深度不同,另一方面也反映出miRNA在植物进化过程中的适应性调整。研究不同植物中miRNA家族的分布,可在miRNA水平为植物早期进化同源性的研究提供分子依据。     

植物microRNA的保守性及其分布的分析

MicroRNA(miRNA)是真核生物中具有重要调控作用的小分子非编码RNA。本文对miRNA官网miRBase数据库Release 22.1中隶属于植物界的绿藻门、苔藓植物门、蕨类植物门、裸子植物门、被子植物门共计82个物种的miRNA进行了统计分析。miRBase共收录植物miRNA 前体8 615个,成熟miRNA 10 414条,隶属于2 892个miRNA家族。绿藻门miRNA与其他4个门miRNA无同源性;对其他4个门植物miRNA的保守性进行研究,发现存在于2个植物门的miRNA家族有26个,属于中度保守miRNA家族;14个miRNA家族存在于3个及3个以上植物门中,属于高度保守miRNA家族,其中7个miRNA家族系苔藓、蕨类、裸子和被子植物共有,是植物中最保守的miRNA。分析表明,超过30个miRNA家族的植物有35种。进一步对40个中度或者高度保守miRNA在35种植物中的分布进行研究,发现miRNA家族及其成员在物种间的分布存在较大的差异。这些分布上的差异一方面反映不同植物中miRNA的研究深度不同,另一方面也反映出miRNA在植物进化过程中的适应性调整。研究不同植物中miRNA家族的分布,可在miRNA水平为植物早期进化同源性的研究提供分子依据。     

有关节肢动物分类的几个问题

本文简要讨论了近年来有关节肢动物特别是昆虫高级分类研究中争论较大的几个关键问题,包括节肢动物的分类基础、“单肢亚门Ｕｎｉｒａｍｉａ”的单系性、六足总纲的单系性及昆虫纲（狭义）Ｉｎｓｅｃｔａ ｓ．ｓｔｒ．的范围等,以期引起我国动物学者的注意与重视。     

A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics

The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies.     

A new view of insect-crustacean relationships I. Inferences from neural cladistics and comparative neuroanatomy

Traditional hypotheses regarding the relationships of the major arthropod lineages focus on suites of comparable characters, often those that address features of the exoskeleton. However, because of the enormous morphological variety among arthropods, external characters may lead to ambiguities of interpretation and definition, particularly when species have undergone evolutionary simplification and reversal. Here we present the results of a cladistic analysis using morphological characters associated with brains and central nervous systems, based on the evidence that cerebral organization is generally robust over geological time. Well-resolved, strongly supported phylogenies were obtained from a neuromorphological character set representing a variety of discrete neuroanatomical traits. Phylogenetic hypotheses from this analysis support many accepted relationships, including monophyletic Chelicerata, Myriapoda, and Hexapoda, paraphyletic Crustacea and the union of Hexapoda and Crustacea (Tetraconata). They also support Mandibulata (Myriapoda + Tetraconata). One problematic result, which can be explained by symplesiomorphies that are likely to have evolved in deep time, is the inability to resolve Onychophora as a taxon distinct from Arthropoda. Crucially, neuronal cladistics supports the heterodox conclusion that both Hexapoda and Malacostraca are derived from a common ancestor that possessed a suite of discrete neural centers comprising an elaborate brain. Remipedes and copepods, both resolved as basal to Branchiopoda share a neural ground pattern with Malacostraca. These findings distinguish Hexapoda (Insecta) from Branchiopoda, which is the sister group of the clade Malacostraca + Hexapoda. The present study resolves branchiopod crustaceans as descendents of an ancestor with a complex brain, which means that they have evolved secondary simplification and the loss or reduction of numerous neural systems.     

Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects

Hexapoda includes 33 commonly recognized orders, most of them insects. Ongoing controversy concerns the grouping of Protura and Collembola as a taxon Ellipura, the monophyly of Diplura, a single or multiple origins of entognathy, and the monophyly or paraphyly of the silverfish (Lepidotrichidae and Zygentoma s.s.) with respect to other dicondylous insects. Here we analyze relationships among basal hexapod orders via a cladistic analysis of sequence data for five molecular markers and 189 morphological characters in a simultaneous analysis framework using myriapod and crustacean outgroups. Using a sensitivity analysis approach and testing for stability, the most congruent parameters resolve Tricholepidion as sister group to the remaining Dicondylia, whereas most suboptimal parameter sets group Tricholepidion with Zygentoma. Stable hypotheses include the monophyly of Diplura, and a sister group relationship between Diplura and Protura, contradicting the Ellipura hypothesis. Hexapod monophyly is contradicted by an alliance between Collembola, Crustacea and Ectognatha (i.e., exclusive of Diplura and Protura) in molecular and combined analyses.     

Mesoderm formation in a springtail,Tomocerus ishibashii Yosii (Collembola : Tomoceridae)

The mesoderm formation of Tomocerus ishibashii (Collembola : Tomoceridae) is described. Mesodermal cells are formed after the beginning of the formation of the primary dorsal organ, and originate from the entire region of the embryonic area. After completion of the blastodermic cuticles, cells of mesoderm and ectoderm concentrate towards a ventral midline and form a well-defined 2-layered germ band. The manner of mesoderm formation in the Collembola is similar to that in Diplura and Myriapods, except for the Chilopoda; the mesoderm of the Thysanura s. lat. and Pterygota originates from a localized zone of the embryo. Within the Hexapoda, mesoderm formation is categorized into 2 types: Type 1—unlocalized origin, in the Collembola and Diplura, and Type 2—localized origin, in the Thysanura s. lat. and Pterygota. Types 1 and 2 are thought to be plesiomorphic and apomorphic, respectively.