叶蝉科昆虫分子系统发育的研究进展

从基因组DNA的提取、研究的基因片段、PCR引物选用、扩增条件以及叶蝉科不同阶元的分子系统发育分析等方面,综述叶蝉科(半翅目:叶蝉科)昆虫分子系统发育的研究进展。目前角顶叶蝉类的研究成果相对较多,大叶蝉亚科次之,其余类群的研究较少或无。线粒体基因与核基因序列联合分析以及线粒体全序列分析以及基因序列与形态数据相结合分析,分子鉴定叶蝉与共生菌之间的协同进化的研究,将是叶蝉分子系统学未来发展的主要研究手段。     

山西省苹果树腐烂病菌的种群结构分析

为明确山西省苹果树腐烂病菌的分布与组成,本研究采集并分离得到来自山西省8个苹果树种植区有代表性的78株腐烂病菌,通过形态特征观察及利用2个DNA片段（ITS和EF1α）构建系统发育树等方法对其遗传结构进行了研究。结果表明山西省苹果树腐烂病由苹果黑腐皮壳菌Valsa mali和梨黑腐皮壳菌Valsa pyri 2个致病种所致,其中V. pyri是优势种,分布于山西省各个苹果树种植区,占菌株总数的58.97%。以山西省8个苹果树种植区腐烂病菌各个种的相对频率进行聚类分析,欧式距离9作为聚类分割点将其种群结构分为3类。第Ⅰ类包括忻州、朔州2个苹果树种植区,V. pyri为该类型苹果树种植区的致病菌、相对频率为100%。第Ⅱ类包括晋城、长治、临汾、太原、运城5个苹果树种植区,V. pyri是这5个种植区的优势种。第Ⅲ类包含晋中1个苹果树种植区,V. mali是该种植区的优势种。     

真核生物系统发育和多样性概观

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.     

Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationships as compared to a complete species level analysis. These changes in topology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as single terminals, and (3) incongruence in the data set. We examine the effects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (Mammalia: Phocidae). Incongruence among characters can produce changes in topology by shifting the ‘balance of power’ among groups of characters when supraspecific taxa are represented as single terminals. In the absence of homoplasy, the correct topology is maintained. Of the three methods for representing supraspecific taxa, the ‘ancestral’ method, which explicidy infers the common ancestor of the group corresponding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa were represented. This agrees with theoretical predictions. The ‘democratic’ and ‘exemplar’ methods, which represent the higher level taxon through a survey of all or one of its extant constituent species, respectively, were not as effective in maintaining the correct topology. Although both occasionally provided correct answers, their occurrences were largely unpredictable. The success of the exemplar method varies with the species selected. The simultaneous representation of two or more higher level taxa produced interactive effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects occurred with all three methods, albeit to a lesser degree for the ancestral method. Changes in topology were observed regardless of whether the higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately, there does not seem to be a reliable way to determine when a paraphyletic group has been included in the analysis (e.g. through bootstrap values or indices measuring homoplasy). The implications of these findings for phylogenetic analyses of molecular data are also discussed.     

The Impact of Molecular Methods on the Systematics of Angiosperms

A comparison is made between the systematics of selected orders and families based on morphology and other “classical” characters on the one hand, and the results of molecular methods on the other hand. It can be shown that taxa defined by a broad array of characters from morphology, anatomy, embryology and phytochemistry usually are confirmed by molecular results. On the other hand a family like the Saxifragaceae s.l. delimited solely on the basis of floral morphology has been shown to be grossly polyphyletic. Some quite surprising results of the molecular analyses usually agree with some embryological or phytochemical characters, and sometimes even with characters of vegetative morphology and anatomy. As a special case “unequal ancient splits” are discussed, where one clade contains few genera and species usually retaining many primitive characters, and the other shows great diversity and contains the more advanced members.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF

Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.     

Molecular phylogeny of the Rhinotermitidae

Summary. Relationships among genera in the termite family Rhinotermitidae and their relationship to the families Termitidae and Serritermitidae were investigated based on analysis of three mitochondrial genes: COI, COII and 16S rDNA. Maximum Parsimony (MP) bootstrap analysis of each of these genes indicated a low level of phylogenetic incongruence between them, and thus they were combined and analysed by MP and Bayesian analysis. Six main lineages were clearly identified, however relationships among these were not well defined. Tentative support was found for the Rhinotermitid genera Coptotermes, Heterotermes and Reticulitermes being the sister group to the Termitidae, rendering the Rhinotermitidae paraphyletic. The species Serritermes serrifer and Glossotermes oculatus were found to group with strong support, in agreement with the recent transfer of the latter species to the family Serritermitidae based on morphological characteristics. No support was found for the Rhinotermitidae being paraphyletic with respect to the Serritermitidae. A number of disagreements were found between the molecular tree and traditional classifications of genera within subfamilies.Received 20 February 2004; revised 2 April 2004; accepted 19 April 2004.     

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies

Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to ‘microlepidopteran’ groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.