中国薄叶卷柏复合群的物种划分

卷柏属(Selaginella)是石松类植物中最大的属, 也是分类难度较大的类群之一。该属的物种划分主要基于形态特征, 但许多近缘种在形态上很难区分。近年来, 已有大量分子证据被用于各植物类群的分类学研究, 但目前未发现一套适合卷柏属物种鉴定的分子标记。薄叶卷柏复合群(S. delicatula group)是卷柏属下鉴定较为困难的类群, 包括了薄叶卷柏(S. delicatula)、黑顶卷柏(S. picta)和瓦氏卷柏(S. wallichii) 3个物种, 主要分布于亚洲的热带和亚热带地区。为了探讨薄叶卷柏复合群内物种的亲缘关系和评估不同分子标记在卷柏属分类学研究中的应用价值, 本研究对该复合群物种进行广泛取样, 共收集到73个个体, 并选取3个叶绿体基因(rbcL, psbA和atpI)和2个核基因(26S nrDNA和pgiC)片段进行系统树的构建及叶绿体单倍型分析。研究发现, 基于叶绿体和核基因构建的系统发生关系存在冲突: 叶绿体基因树上薄叶卷柏个体分为两个分支(A和B), 薄叶卷柏B分支与薄叶卷柏A-S. picta分支呈姐妹关系, 并且rbcL单倍型分析结果也表明薄叶卷柏A和B两个分支存在明显分化; 而核基因结果则支持该复合群3个物种各自的单系性, 其中, S. delicatula分支与S. picta分支为姐妹群, S. wallichii与S. delicatula-S. picta分支为姐妹关系。在对复合群分布区大量标本的观察以及野外群体调查的基础上, 评估了植株茎和枝的分枝方式、孢子叶、营养叶(侧叶、中叶和腋叶)和孢子表面纹饰等形态性状的分类学价值。结果表明, 薄叶卷柏A和B分支的样本仅在植株分枝方式和大孢子表面纹饰上存在差异, 但无法依靠小孢子表面纹饰、孢子叶穗和营养叶形态等特征进行区分。基于现有证据, 薄叶卷柏复合群至少可划分为薄叶卷柏、黑顶卷柏和瓦氏卷柏3种, 但彻底澄清该复合群的物种划分还需要获取模式标本产地的材料和细胞学证据。最后, 建议在未来卷柏属的分类学研究集中于该属分类复杂的复合群, 结合使用形态学、细胞学、分子生物学(同时使用核基因和叶绿体分子标记)及地理分布等整合证据来进行物种划分。     

The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics

Cryptic species of passerine birds lack notable morphological differentiation and can best be identified by molecular and bioacoustic markers. Here we investigate seven cryptic species of the golden-spectacled warbler (Seicercus burkii complex) with respect to territorial song and cytochrome-b (cyt-b) sequences. Their phylogenetic relations to other Seicercus species and to members of the genus Phylloscopus are inferred by the same methods. Three separate lineages of Seicercus are nested within different branches of the molecular Phylloscopus tree. The S. burkii complex is a monophyletic unit comprising seven species (S. burkii s. str., S. whistleri, S. valentini, S. soror, S. omeiensis, S. tephrocephalus and S. affinis). S. xanthoschistos turned out to be a close relative of Phylloscopus davisoni within the P. reguloides group. Two isolated sister taxa, S. grammiceps and S. castaniceps, also branch together with the P. reguloides group. Within the S. burkii complex the overall haplotype and nucleotide diversity is highest in taxa from the Chinese middle and upper mountain belt (S. valentini, S. omeiensis and S. soror), indicating at least partially restricted gene flow in these species. This is explained by the fragmentation of high-altitude habitats in China while in the Himalayas the vicariant species S. whistleri inhabits a more continuous mountain belt at the same altitude. For the Chinese species from medium and high altitudes, past range expansion is indicated by significantly negative Tajima Ds. According to pairwise genetic distances, most species of the S. burkii complex have diverged 5 myr ago, the most recent split between S. burkii and S. tephrocephalus is dated 2 myr ago. Coalescence times for haplotype lineages of the different species range from 9 up to 12 myr, and between 5 and 6 myr for S. burkii and S. tephrocephalus.

Within Seicercus divergence of song features such as frequency parameters and syntax structures correlate with genetic distances between taxa. The three cyt-b lineages of Seicercus correspond to different clusters in a discriminant analysis by acoustic parameters. Common syntax structures of territorial song in the Phylloscopus/Seicercus assemblage are: (1) an introductory element derived from specific calls and (2) a syntax of trills and repeated element groups or a combination of both. There are clear indications that these song structures have repeatedly emerged, were lost or were altered in different branches of the phylogenetic tree at different times. Absolute differences between taxa in frequency parameters or in an acoustic divergence index increase significantly with growing genetic distances. However, due to multiple parallel evolution phylogenetic information provided by single acoustic traits decreases with increasing numbers of taxa involved in the investigation.     

A taxonomic study of phlebioid fungi (Basidiomycota)

The genus Phlebia has long been regarded as a polyphyletic or paraphyletic taxon, including distinct groups of more closely related species. Consequently, the delimitation of the genus has been given different interpretations and several rearrangements have been proposed by various authors. In the present study, DNA sequences (25S, rDNA) were obtained for twenty species of the genus Phlebia and a phylogenetic analysis was performed. Because of the presumably paraphyletic nature of the genus, different outgroups were used for different sets of taxa. A core group of species, including the type Ph. radiata , is well distinguished. For the delimitation of the genus, however, the wider scope of a more weakly supported clade is proposed. This clade also includes Phlebiopsis gigantea and its combination in Phlebia is reaffirmed. Two species, Ph. griseoflavescens and Ph. tristis , are distinctly separated from this clade and should be removed from the genus. Morphological characters were used in a separate phylogenetic analysis but the result did not conform with analysis from sequence data.     

Phylogenetic relationships among Chilean Sophora species

Phylogenetic affinities among Chilean Sophora species are not clear. We suggest a new hypothesis for the origin of the section Edwardsia on the basis of parsimony analysis, which allows a South American origin to be established for the species of this section. The seed alkaloid composition did not provide useful information for the filiation of Edwardsia species, and the shortest tree was obtained using morphological characters only. Two branches are clearly distinguishable by the pubescence of the leaflets and the flag/wings length ratio: one of them includes S. chrysophylla, S. tetraptera, S. toromiro, S. howinsula and S. denudata; the other one includes S. macnabiana, S. microphylla, S. masafuerana, S. prostrata and S. fernandeziana. In contrast, S. macrocarpa, an ancient element of the South American flora, is closely related to species belonging to the section Sophora represented in the region by S. tomentosa, S. linearifolia and S. rhynchocarpa. Sections Calia and Styphnolobium are clearly related to each other, both morphologically and chemically.     

Integrating coalescent-based species delimitation with ecological niche modeling delimited two species within the Stewartia sinensis complex (Theaceae)

Accurate species delimitation is the key to precise estimation of species diversity and is fundamental to most branches of biology. Unclear species boundaries within species complexes could lead to the underestimation of species diversity. However, species delimitation of species complexes remains challenging due to the continuum of phenotypic variations. To robustly examine species boundaries within a species complex, integrative approaches in phylogeny, ecology, and morphology were applied to the Stewartia sinensis complex (Theaceae) endemic to China. Multispecies coalescent-based species delimitation using 572 nuclear ortholog sequences (anchored enrichment) supported reciprocal phylogenetic monophyly of the northern lineage (NL) and southern lineage (SL), which were not sister clades. Niche equivalency and similarity tests demonstrated significant climatic niche differentiation between NL and SL with observed Warren et al.'s I = 0.0073 and Schoener's D = 0.0021. Species distribution modeling also separated their potential distribution. Morphometric analyses suggested significant interlineage differentiation of multiple traits including the ratio of length and width, leaf width, and pedicel length, although overall similarity did not differ. Based on the integrative species concept, two distinct species were proposed with legitimate names of Stewartia gemmata for SL and S. sinensis for NL. Our empirical study of the S. sinensis complex highlights the importance of applying multiple species criteria, in particular the underappreciated niche differentiation, to species delimitation in species complexes pervasive in plants.     

A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology

Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF-rpl32, rpl32-trnL, and psbM-psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS-derived and cpDNA-derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.     

Genetic relationship between Salix exigua and other North American willows (Salix L.): Evidence from allozyme variation

Starch gel electrophoresis was used to examine the allozyme variation and the genetic relationship between Salix exigua and other North American willows. A total of 149 clonal collections comprising six willow species were analyzed for 26 putative isozyme loci. Genetic distances between species were estimated and used for distance analysis of species relationships. Individual alleles were used as characters for cladistic analysis of phylogenetic inference. Distance analysis indicates that S. exigua has approximately equal divergence to both subgenus Salix and Vetrix. Results of cladistic analysis suggest that S. exigua may be a separate group isolated from all other willows. Based on evidence of allozyme variation, it is suggested that the taxonomic placement of S. exigua within subgenus Salix need to be revised.     

Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota)

Fruiting body guided sequence analysis of mycorrhizal root-tip mycelia is a powerful yet relatively sparsely explored method for species-level identification of mycorrhizal fungi. It is used in this study to indicate mycorrhizal associations in the corticioid (resupinate) genus Sistotrema of the cantharelloid clade through phylogenetic analysis of the ITS and nuLSU rDNA regions of two spatiotemporally co-occurring Sistotrema fruiting bodies and ectomycorrhizal root tips. The genus Sistotrema is confirmed to be polyphyletic, and the mycorrhizal species form a strongly supported monophyletic clade together with the stipitate genus Hydnum. The remaining lineages of Sistotrema may well be saprotrophic, the nutritional mode traditionally attributed to the genus, but the phylogenetic analyses show that they should be excluded from Sistotrema. The cantharelloid clade contains several mycorrhizal genera, but no symbiotic associations have previously been demonstrated for Sistotrema.     

Phylogeny of the millipede genus Sphaeriodesmus Peters, 1864 (Polydesmida: Sphaeriodesmidae) based on morphological characters

In order to understand the evolutionary relationships among the species encompassed within the genus Sphaeriodesmus Peters, 1864, a cladistic analysis including 63 species was conducted. Ninety-five morphological characters were used for the phylogenetic reconstruction. The results suggested that the current composition of the genus Sphaeriodesmus does not circumscribe a monophyletic group; instead, the genera Eusphaeriodesmus, Colobodesmus, and Proeilodesmus are here synonymized under Sphaeriodesmus. Although raw morphological data had suggested the genus Lophocyclus as the sister taxon of Sphaeriodesmus, the phylogenetic analysis under implied weight identified the genus Cyphodesmus as the taxon most closely related to Sphaeriodesmus. Sphaeriodesmus isolatus Chamberlin, 1940 is a subjective synonym of Sphaeriodesmus conformans Chamberlin, 1925. The putative subdivisions previously proposed within Sphaeriodesmus do not hold as monophyletic either. Low stability was observed concerning the higher-level phylogenetic relationships of Sphaeriodesmus. Sphaeriodesmus crucis (Loomis, 1974), S. mecistonyx (Hoffman, 1990), and S. triramus (Kraus, 1954) are new combinations.     

Revisiting of Carex sect. Confertiflorae s.l. (Cyperaceae): New data from molecular and morphological evidence and first insights on Carex biogeography in East Asia

Carex sect. Confertiflorae s.l. is a medium-sized species group (ca. 40 species) with its center of diversity in E Asia (China and Japan). According to morphological traits, the section has been proposed to split into two sections (sects. Confertiflorae sensu Ohwi and Molliculae Ohwi) up to five different ones (sects. Confertiflorae s.s., Molliculae, Dispalatae Ohwi, Ischnostachyae Ohwi, and Alliiformes Akiyama). Recent phylogenetic reconstructions showed Confertiflorae s.l. not to be monophyletic, as species traditionally considered part of it were found to belong to other clades, whereas species traditionally ascribed to other sections were nested within it. In this study, we investigated the phylogenetic structure, morphological affinities, and biogeographic history of sect. Confertiflorae s.l. We employed a taxon-based approach to explore the morphological affinities of the species considered in sect. Confertiflorae and compared the micromorphology of the nutlets of almost all the taxa using SEM. We included 40 samples representing 31 species/subspecies of sect. Confertiflorae s.l. and used two nuclear (ETS and ITS) and three plastid (trnL-F, matK, and rpl32-trnL ^UAG) molecular markers to reconstruct the phylogeny of the group. The phylogenetic analyses confirmed the polyphyly of sect. Confertiflorae s.l., whose representatives were found within five distinct clades. From these, two clades, sect. Confertiflorae and sect. Molliculae, were found to be closely related and contained the majority of the species. The composition of the two clades agreed with the morphological structure of the group, and we confirmed an exclusive combination of features (namely color of basal sheaths, presence of bract sheath, peduncle of lowest spike, inflorescence sex distribution, shape of pistillate glume apex, and color and veins of utricle, among others) characterizing each of the two clades. The origin of the two clades was found to be in the early Pliocene; however, the majority of the diversification events within each clade took place during the Pleistocene. This illustrates that although Asia has been regarded as having little potential ecological space for Carex to diversify due to its climate stability, groups of sedges sub-endemic from that area may have a fairly recent origin related to glaciations. We proposed the rearrangement of sect. Confertiflorae as previously conceived as three independent sections: the monotypic Alliiformes, sect. Molliculae, and sect. Paludosae.     

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.     

国产柳属繁柳组植物叶脉序研究及其分类学意义

采取脉络法,对柳属（Salix）繁柳组（Sect.Denticulatae C.K.Schneid.）17种及1变种进行叶片脉序观察。结果表明：繁柳组植物叶脉序类型均为直行羽状脉,表现出较高的一致性。该组植物均有二级间脉,但类型各有不同;三级脉及较高级脉序大体有三种类型;网眼发育完善或不完善;盲脉偶有不分枝;不同种之间网眼的发育以及盲脉分枝具有显著差异,是有价值的分类性状。根据聚类分析,繁柳组植物叶脉序分为两种类型：草地柳（S.praticola Hand.-Mazz.ex Enander）类型及腹毛柳（S.delavayana Hand.-Mazz.）类型,研究结果与形态学结果基本一致,但叶脉序提供了新的分类学性状,可为柳属植物疑难种的分类寻找新的依据。     

Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov

The genus Chlamydomonas (including Chloromonas) is one of the largest green algal genera comprising more than 600 species. To initiate a comprehensive analysis of the phylogeny and systematics of the genus, we determined nuclear-encoded SSU rRNA sequences from 32 strains of Chlamydomonas, Chloromonas and Chlorogonium with emphasis on oogamous taxa and related strains, and incorporated these into global molecular phylogenetic analyses of 132 strains of Chlorophyceae. In addition, we studied the morphology and reproduction of oogamous and related strains by light microscopy. We recognize and designate 18 monophyletic lineages (clades) within the Chlorophyceae, 11 of which are confined to the CW (basal bodies displaced clockwise) subgroup. The majority of clades recognized within the Chlorophyceae do not correspond to any of the traditional classification systems, which are still largely based on the organization level. Strains assigned to Chlamydomonas and Chloromonas were found in seven different clades confirming the polyphyly of the two genera as presently conceived. To initiate the taxonomic revision of Chlamydomonas, C. reinhardtii is proposed as the conserved type of the genus. In consequence, species in clades other than the clade containing C. reinhardtii must be transferred to other genera, a process initiated in this contribution. The oogamous strains studied represent a monophyletic lineage, which is described as Oogamochlamys gen. nov. comprising three species (O. gigantea, O. zimbabwiensis and O. ettlii spec. nov.). The sister clade to Oogamochlamys consists of isogamous strains characterized by chloroplasts with incisions and is described as Lobochlamys gen. nov. with two species (L. culleus and L. segnis). Another clade is characterized by asteroid or perforated, parietal chloroplasts and contains the type species of Chloromonas (C. reticulata). Thus, the polyphyletic Chloromonas (traditionally defined as “Chlamydomonas without pyrenoids”) can be legitimized as a monophyletic genus by restriction to this clade and is here emended on the basis of chloroplast characters (the clade contains strains with or without pyrenoids thus rejecting the character “absence of pyrenoids”).     

Analyzing the radiation of the proenkephalin gene in tetrapods: cloning of a Bombina orientalis proenkephalin cDNA.

Analyzing the Radiation of the Proenkephalin Gene in Tetrapods: Cloning of a Bombina orientalis Proenkephalin cDNA: A proenkephalin cDNA was cloned from the brain of the anuran amphibian, Bombina orientalis (Family: Discoglossidae). This cDNA is 1358 nucleotides in length, and contains an open reading frame that codes for 251 amino acids. Within the open reading frame there are seven opioid (YGGF) sequences. There were five Met-enkephalin (YGGFM) sequences that are flanked by sets of paired basic amino acid proteolytic cleavage sites and two C-terminally extended Met-enkephalin sequences: YGGFMRGY and YGGFMRF. No Leu-enkephalin sequences were found in B. orientalis proenkephalin. It was possible to align the amino acid sequences of proenkephalin from several vertebrate taxa (human, Australian lungfish, B. orientalis, Xenopus laevis, Spea multiplicatus) by inserting a minimum of nine gaps. This alignment was then used to analyze the corresponding nucleotides for each proenkephalin sequence using maximum likelihood. This analysis yielded a single tree. In this tree, the Australian lungfish sequence was the outgroup or the tetrapod ingroup. The amphibian sequences form a clade separate from the human sequence. The bootstrap value for the amphibian clade was 100%. Within the amphibian clade the Bombina sequence was the sister group to a clade composed of the X. laevis and S. multiplicatus sequences. The bootstrap value for the X. laevis/S. multiplicatus clade was 94%. Collectively, these data indicate that the sequence of Bombina proenkephalin may be more similar to the proposed ancestral anuran proenkephalin sequence, than either X. laevis or S. multiplicatus proenkephalin.     

Phylogenetics of paniceae (poaceae)

Paniceae demonstrate unique variability of photosynthetic physiology and anatomy, including both non-Kranz and Kranz species and all subtypes of the latter. This variability suggests hypotheses of independent origin or reversals (e.g., from C(4) to C(3)). These hypotheses can be tested by phylogenetic analysis of independent molecular characters. The molecular phylogeny of 57 species of Paniceae was explored using sequences from the grass-specific insert found in the plastid locus rpoC2. Phylogenetic analyses confirmed some long-recognized alliances in Paniceae, some recent molecular phylogenetic results, and suggested new relationships. Broadly, Paniceae were found to be paraphyletic with Andropogoneae, Panicum was found to be polyphyletic, and Oplismenus hirtellus was resolved as the sister group to the remaining ingroup species. A particularly well-supported clade in the rpoC2 tree included four genera with non-Kranz species and three with distinctively keeled paleas. As previously suggested, the PCK (phosphoenol pyruvate carboxykinase) C(4) subtype arose once within Paniceae. All clades with non-Kranz species had Kranz ancestors or sister taxa suggesting repeated loss of the Kranz syndrome.