A MOLECULAR APPROACH TO THE CIRCUMSCRIPTION AND EVALUATION OF SOME GENERA SEGREGATED FROMPARMELIAS. LAT.

New sequences have been produced of the ITS rDNA region of twenty-nine species ofParmeliaceae, and analysed by neighbour-joining maximum likelihood distance analysis, and maximum parsimony analysis. Twelve monophyletic groups have been identified, most of which correspond to proposed generic segregated fromParmelias. lat.ParmeliaandParmelina,Melanelia, andPuncteliaappear as independent monophyletic groups; the type species of the two latter genera were, however, not included in the analysis. The parsimony analysis does not supportXanthoparmeliaas a monophyletic group separate fromNeofuscelia, andRimelia reticulatais nested withinParmotrema. Parmelinopsis horrescensis more closely related toHypotrachyna revolutathan toParmelina. Genetic distance values suggest thatFlavoparmelia caperatais closer toParmotremathan to other taxa included, and thatPlatismatia glaucaandHypogymnia tubulosaare closer toParmelias. lat. than to thePhysciaceae. However, there is no conclusive support for any of the latter groupings in the parsimony analysis. We conclude that the ITS region contains valuable information for studying generic delimitations within the familyParmeliaceae, but our study suggests that this region will not conclusively resolve within-family relationships in this group.     

Molecular Systematics of Bats of the Genus Myotis (Vespertilionidae) Suggests Deterministic Ecomorphological Convergences

Based on extensive phenetic analyses, bats of the genus Myotis have been classically subdivided into four major subgenera each of which comprise many species with similar morphological and ecological adaptations. Each subgenus thus corresponds to a distinct “ecomorph” encompassing bat species exploiting their environment in a similar fashion. As three of these subgenera are cosmopolitan, regional species assemblages of Myotis usually include sympatric representatives of each ecomorph. If species within these ecomorphs are monophyletic, such assemblages would suggest extensive secondary dispersal across geographic areas. Conversely, these ecomorphological adaptations may have evolved independently through deterministic processes, such as adaptive radiation. In this case, phylogenetic reconstructions are not expected to sort species of the same ecomorph into monophyletic clades. To test these predictions, we reconstructed the phylogenetic history of 13 American, 11 Palaearctic, and 6 other Myotis species, using sequence data obtained from nearly 2 kb of mitochondrial genes (cytochrome b and nd1). Separate or combined analyses of these sequences clearly demonstrate the existence of several pairs of morphologically very similar species (i.e., sibling species) which are phylogenetically not closely related. None of the three tested subgenera constitute monophyletic units. For instance, Nearctic and Neotropical species currently classified into the three subgenera were clustered in a single, well-supported monophyletic clade. These species thus evolved independently of their ecological equivalents from the Palaearctic region. Independent adaptive radiations among species of the genus Myotis therefore produced strikingly similar evolutionary solutions in different parts of the world. Furthermore, all phylogenetic reconstructions based on mtDNA strongly supported the existence of an unsuspected monophyletic clade which included all assayed New World species plus M. brandtii (from the Palaearctic Region). This “American” clade thus radiated into a morphologically diverse species assemblage which evolved after the first Myotis species colonized the Americas. Molecular reconstructions support paleontological evidence that species of the genus Myotis had a burst of diversification during the late Miocene–early Pliocene epoch.     

A morphological cladistic analysis of Lecythidoideae with emphasis on Bertholletia, Corythophora, Eschweilera, and Lecythis

A cladistic analysis was conducted to test the monophyly of Eschweilera and Lecythis as well as to examine the relationships of these two genera and their close relatives Bertholletia and Corythophora. The study included 86 species, representing all four genera and covering the range of taxonomic and morphological variation in the genera. The data matrix included 49 parsimony-informative characters derived from vegetative, floral, fruit, and seed morphology and anatomy. The results based on the consensus of all most parsimonious trees indicate that Bertholletia, Corythophora, Eschweilera, and Lecythis form a clade supported by brachyparacytic stomata, the absence of pedicels (with subsequent reversals in several clades), a two or four-locular ovary, the presence of an aril, and the absence of cotyledons. Within the clade, the monophyly of Corythophora is supported by the presence of inflorescence scales and the absence of nectar. Eschweilera is monophyletic only if E. congestiflora and E. simiorum are excluded. The monophyly of Eschweilera is supported by the presence of a two-locular ovary. Lecythis is not monophyletic, but sections Corrugata, Pisonis, and Poiteaui are monophyletic. Three species of section Lecythis are more closely related to Eschweilera, and other species of section Lecythis along with Bertholletia excelsa remain as unresolved.     

A molecular phylogeny of <Emphasis Type="Italic">Haptoglossa</Emphasis> species,terrestrial peronosporomycetes (oomycetes) endoparasitic on nematodes

Phylogenetic relationships of seven Haptoglossa isolates were analyzed by using mitochondrial COII amino acid sequences with a data set of 34 peronosporomycetes. Haptoglossa isolates formed a single clade and appeared to be basal to the clade consisting of all other peronosporomycetes. The Haptoglossa clade was divided into two subclades: one clade consisted of five aplanosporic isolates and the other included one aplanosporic and one zoosporic isolate. These results indicate that the genus Haptoglossa is monophyletic, and patterns of infection cell formation reflect more the phylogenetic relationship between the species than patterns of sporogenesis.     

利用DNA片段测序方法探究枳属和富民枳的分类地位

富民枳(Poncirus polyandra)属于芸香科(Rutaceae)枳属(Poncirus Raf.).自发表以来,分类地位一直备受争议,其中在Flora of China中认为富民枳为柑橘杂交种(Poncirus polyandra),把枳属归并于柑橘属(Citrus).该研究选取枳属的富民枳、枳(Ponci...     

Evolution and phylogenetic relationships within Porinaceae (Ostropomycetidae), focusing on foliicolous species

A phylogeny of the lichen family Porinaceae using mitochondrial SSU rDNA sequences is presented, with special focus on foliicolous taxa. Fifty specimens of 28 mostly tropical species, representing eight species groups of Porina as well as the genus Trichothelium, were analysed together with species of other members of Ostropomycetidae, and using Agyriaceae as outgroup. We performed the phylogenetic analyses with a Bayesian approach and under the criterion of maximum parsimony. Four main clades can be distinguished: the P. nitidula-group s. lat. (including Trichothelium, P. papillifera and P. rubescens), the Porina epiphylla-group s. lat. (including the P. radiata-, the P. nucula-, the P. imitatrix- and the P. epiphylla-group s. str.) and two clades of the P. rufula-group. The genus Porina as understood by all recent concepts is paraphyletic, and Trichothelium is nested within the Porina nitidula-group. The non-setose P. repanda forms a monophyletic clade with Trichothelium. The tree does not support a monophyletic origin of substrate preferences or photobiont selection. Species-specific associations with morphologically different trentepohlioid photobionts mapped on the tree suggest that closely related mycobiont species switch between different types of algae.     

Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

基于cpDNA和rDNA ITS片段分析西南地区青杨派杨树的系统发育与进化关系

西南地区青杨派杨树种质资源丰富,可为杨树遗传改良提供珍贵的基因资源,但树种之间形态学差异细微,该研究以山杨作为外类群,测定了西南地区及其他地区杨属青杨派17个种(杂种)共36份样本的3个叶绿体片段(atpF-atpH、trnL-F和matK)和核糖体ITS片段,并对其进行系统发育分析,以探讨西南地区青杨派树种的系统进化关系。结果表明:(1)在所有样本中,3个叶绿体片段atpF-atpH、trnL-F、matK的长度分别为605~634bp、957~1 010bp、819bp,3个片段拼接后的联合序列包含29个变异位点和15个信息位点;ITS片段对齐后的长度为646bp,变异位点19个,信息位点17个。(2)基于叶绿体联合序列和ITS片段的杨属青杨派树种的平均遗传距离分别为0.001 3和0.003 6。叶绿体联合片段的MP和Bayes系统树树型基本一致,青杨派树种可以划分为2组,第1组由青杨、三脉青杨、大青杨和辽杨构成;第2组中的小叶杨、小青杨、川杨、德钦杨、昌都杨、乡城杨、康定杨、西南杨、滇杨和藏川杨不能有效区分,且均与缘毛杨的遗传关系较近。(3)基于ITS的系统树与叶绿体联合片段构建的系统树差异不大,仅在于第2组中的小青杨与小叶杨、川杨等差异明显,与第1组中的树种紧密聚拢。     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.     

Taxonomy, molecular phylogeny, and ultrastructural morphology of Olpidiopsis porphyrae sp. nov. (Oomycetes, straminipiles), a unicellular obligate endoparasite of Bangia and Porphyra spp. (Bangiales, Rhodophyta)

Olpidiopsis porphyrae sp. nov., a marine oomycete endoparasite that infects the commercially cultivated red alga Porphyra yezoensis, is described and its phylogenetic position based on molecular data and ultrastructural morphology is discussed. O. porphyrae infects the host Porphyra by means of encysted zoospores. Spherical-shaped holocarpic thalli develop within the cytoplasm of its algal host, which produce monoplanetic, subapically biflagellate zoospores. The characteristic features of this isolate are the ellipsoidal, unicellular thallus and simple holocarpic zoosporangial development, which show morphological similarity with the genus Olpidiopsis. Laboratory infection experiments with a wide range of green, brown, and red algae revealed that O. porphyrae infects several stages of the bangialean red algae (the genera Bangia and Porphyra). Molecular phylogenetic analyses inferred from both SSU rRNA and cox2 genes showed O. porphyrae branched before the main saprolegnian and peronosporalean lineages within the monophyletic oomycete clade, indicating its phylogenetic separation from them. A single or double K-body-like organelle, which contains tubular inclusions, is found located to one side of the zoospore nucleus and shows similarities to homologous organelles previously described in O. saprolegniae. The ultrastructural morphology of O. porphyrae with zoospore initials containing K-bodies and tubular mitochondrial cristae is characteristic of oomycetes. Group I intron-like multiple insertions were found in the SSU rRNA gene of O. porphyrae. This is the first report of SSU group I introns in the class Oomycetes.     

Phylogeny and biogeography of Chinese and Australasian Polystichum ferns as inferred from chloroplast trnL-F and rps4-trnS sequence data

Polystichum, one of the largest genera of ferns, occurs worldwide with the greatest diversity in southwest China and adjacent regions. Although there have been studies of Chinese Polystichum on its traditional classification, geographic distributions, and even a few on its molecular systematics, its relationships to other species outside China remain little known. Here, we investigated the phylogeny and biogeography of the Polystichum species from China and Australasia. The evolutionary relationships among 42 Polystichum species found in China (29 taxa) and Australasia (13 taxa) were inferred from phylogenetic analyses of two chloroplast DNA sequence data sets: rps4-trnS and trnL-F intergenic spacers. The divergence time between Chinese and Australasian Polystichum was estimated. The results indicated that the Australasian species comprise a monophyletic group that is nested within the Chinese diversity, and that the New Zealand species are likewise a monophyletic group nested within the Australasian species. The divergence time estimates suggested that Chinese Polystichum migrated into Australasia from around 40 Ma ago, and from there to New Zealand from about 14 Ma. The diversification of the New Zealand Polystichum species began about 10 Ma. These results indicated that Polystichum probably originated in eastern Asia and migrated into Australasia: first into Australia and then into New Zealand.     

Speciation in Pyricularia inferred from multilocus phylogenetic analysis

Pyricularia isolates from various host plants were subjected to a multilocus phylogenetic analysis based on rDNA-ITS, actin, β-tubulin, and calmodulin loci. A combined gene tree resolved seven groups with 100 % BS support, suggesting that they are monophyletic groups supported concordantly by all four loci. By incorporating biological and morphological species criteria, each of the seven groups was considered to be a current species. However, phylogenetic relationships among these species were unresolved in the single-gene trees and in the combined tree. Furthermore, the transition from concordance to conflict occurred more than once in the combined gene tree. They were interpreted by assuming that Pyricularia has evolved through repeated species radiation. The transition point other than the current species limit was considered to be the limit of the former species.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

瑞香属和荛花属的数量分类研究

瑞香属和荛花属为瑞香科瑞香亚科的落叶或常绿灌木,中国西南部是瑞香属和荛花属的重要分化中心。全世界共有瑞香属95种、荛花属70种,中国分布有瑞香属52种、荛花属49种。瑞香属和荛花属的分类学研究一直存在不同程度的分歧。花盘形状和果实类型在传统分类中一直是区分瑞香属和荛花属的典型特征,而花盘形态和果实类型在2个属中存在交叉和过渡,部分植物分类学家根据这些特征将两个属进行过不同程度的归并。该研究采用数量分类法对瑞香属77种(变种)和荛花属62种(变种)植物,选取32个形态学性状进行聚类分析和主成分分析。结果表明:聚类分析和主成分分析均显示两属均未形成单系类群。在主成分分析中,前3个主成分分析的贡献值为35.56%,传统分类中用来区分两属的花盘形状、叶序及果实类型等特征对前3个主成分贡献相对较小,因此,传统分类学中对这两个属进行区分的性状并没有典型的分类学意义。同时,聚类图和主成分分析得到的散点图均不能将这两个属区分开来。数量分类研究结果显示两属植物存在明显的交叉,支持瑞香属和荛花属不是两个独立自然类群的观点。     

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.