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.     

Molecular phylogeny of the ranid frogs from Southwest India based on the mitochondrial ribosomal RNA gene sequences

The Western Ghats of Southwestern India are known as one of the world's "hotspots" of biodiversity. We collected frog specimens from the family Ranidae and investigated the phylogenetic relationships among ranid species, particularly among the Fejervarya, a genus whose morphological diagnostic characteristics and phylogenetic features remain little known. We analyzed partial sequences of the mitochondrial 12S (428 bp) and 16S rDNAs (549 bp). Results showed that the members of Fejervarya form a monophyletic group with the genera Hoplobatrachus and Euphlyctis among ranid genera. This confirms the recent allocation of Fejervarya, including it within the subfamily Dicroglossinae. The mitochondrial rDNA data in our study also appeared to be useful as a marker to distinguish Fejervarya species without morphological differences. The phylogenetic tree based on the 16S rDNA sequence showed a correlation between Fejervarya phylogenies and their geographic distributions. Lastly, our results suggested the recent occurrence of a radiation event of Fejervarya species in the Indian-Sri Lankan region.     

Molecular systematics of Helicoma, Helicomyces and Helicosporium and their teleomorphs inferred from rDNA sequences

Three genera of asexual, helical-spored fungi, Helicoma, Helicomyces and Helicosporium traditionally have been differentiated by the morphology of their conidia and conidiophores. In this paper we assessed their phylogenetic relationships from ribosomal sequences from ITS, 5.8S and partial LSU regions using maximum parsimony, maximum likelihood and Bayesian analysis. Forty-five isolates from the three genera were closely related and were within the teleomorphic genus Tubeufia sensu Barr (Tubeufiaceae, Ascomycota). Most of the species could be placed in one of the seven clades that each received 78% or greater bootstrap support. However none of the anamorphic genera were monophyletic and all but one of the clades contained species from more than one genus. The 15 isolates of Helicoma were scattered through the phylogeny and appeared in five of the clades. None of the four sections within the genus were monophyletic, although species from Helicoma sect. helicoma were concentrated in Clade A. The Helicosporium species also appeared in five clades. The four Helicomyces species were distributed among three clades. Most of the clades supported by sequence data lacked unifying morphological characters. Traditional characters such as the thickness of the conidial filament and whether conidiophores were conspicuous or reduced proved to be poor predictors of phylogenetic relationships. However some combinations of characters including conidium colour and the presence of lateral, tooth-like conidiogenous cells did appear to be predictive of genetic relationships.     

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.     

A molecular phylogeny of Panicum (Poaceae: Paniceae): tests of monophyly and phylogenetic placement within the Panicoideae

Panicum L. is a cosmopolitan genus with approximately 450 species. Although the genus has been considerably reduced in species number with the segregation of many taxa to independent genera in the last two centuries, Panicum remains a heterogeneous assemblage, as has been demonstrated in recent years. The genus is remarkably uniform in its floral characters but exhibits considerable variation in anatomical, physiological, and cytological features. As a result, several classifications, and criteria of what the genus should really include, have been postulated in modern literature. The purpose of this research, based on molecular data of the chloroplast ndhF gene, is to test the monophyly of Panicum, to evaluate infrageneric classifications, and to propose a robust phylogenetic hypothesis. Based on the present results, previous morphological and molecular phylogenetic studies, and inferred diagnostic morphological characters, we restrict Panicum sensu stricto (s.s.) to the former subgenus Panicum and support recognition of Dichanthelium, Phanopyrum, and Steinchisma as distinct genera. We have transfered other species of Panicum to other genera of the Paniceae. Most of the necessary combinations have been made previously, so few nomenclatural changes have been required. The remaining species of Panicum sensu lato (s.l.) are included within Panicum incertae sedis representing isolated species or species grouped within monophyletic clades. Additionally, we explore the performance of the three codon position characters in producing the supported phylogeny.     

Comparison of ribosomal dna nucleotide sequences of the mosquito genera Aedes and Ochlerotatus (Diptera: Culicidae: Aedini)

Nucleotide rDNA sequences of 9 species of the mosquito genus Ochlerotatus and 2 species of the genus Aedes were obtained and compared. Variation both within and between these genera was characterized. The phylogenetic relationships among the studied species of Ochlerotatus generally correspond to the grouping of species based on morphological characters.     

Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence

Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.     

A new species group in the genus Dichaetophora Duda (Diptera: Drosophilidae) based on a phylogenetic analysis, with descriptions of four new species from China

A new species group, the sinensis group, is established within the genus Dichaetophora, based on a phylogenetic analysis of 37 adult morphological characters from 26 drosophilid species, including ten known species of Dichaetophora; four newly described species (Di. abnormis, Di. hainanensis, Di. bicornis, and Di. sinensis spp. nov. from China); and some representatives of related genera (Drosophila, Hirtodrosophila, and Scaptomyza).     

Evolutionary relationships within the Neotropical, eusporangiate fern genus Danaea (Marattiaceae)

Genera within the eusporangiate fern family Marattiaceae have long been neglected in taxonomic and systematic studies. Here we present the first phylogenetic hypothesis of relationships within the exclusively Neotropical genus Danaea based on a sampling of 60 specimens representing 31 species from various Neotropical sites. We used DNA sequence data from three plastid regions (atpB, rbcL, and trnL-F), morphological characters from both herbarium specimens and live plants observed in the field, and geographical and ecological information to examine evolutionary patterns. Eleven representatives of five other marattioid genera (Angiopteris, Archangiopteris, Christensenia, Macroglossum, and Marattia) were used to root the topology. We identified three well-supported clades within Danaea that are consistent with morphological characters: the "leprieurii" clade (containing species traditionally associated with the name D. elliptica), the "nodosa" clade (containing all species traditionally associated with the name D. nodosa), and the "alata" clade (containing all other species). All three clades are geographically and ecologically widely distributed, but subclades within them show various distribution patterns. Our phylogenetic hypothesis provides a robust framework within which broad questions related to the morphology, taxonomy, biogeography, evolution, and ecology of these ferns can be addressed.     

Phylogenetic relationships of the genus Dugesia (Platyhelminthes, Tricladida, Paludicola)

A phylogenetic analysis was performed on the genera and subgenera within the freshwater triclad family Dugesiidae, based on 19 terminal taxa and 17 morphological characters. The phylogenetic tree proposed has length of 27 steps and consistency index of 0.66. This phylogenetic hypothesis implies that the current genus Dugesia is paraphyletic and that its subgenera Girardia, Schmidiea and Dugesia S.S. should be elevated to the rank of genus. The genera Cura, Spathula and Neppia are presumed monophyletic by default because the database was unable to provide autapomorphies for any of these genera. The genera Dugesia S.S. and Neppia share sistergroup relationship. Several characters are discussed which were previously considered to be of phylogenetic importance but were not included in the present analysis. It is emphasized that sensory organs form potentially useful set of phylogenetic characters for the Dugesiidae.     

The phylogeny of the Trypanosomatidae: the molecular and morphological approaches

The results of comparative analysis of two phylogenetic trees of the trypanosomatids based on morphological and molecular characters are discussed. The morphological dendrogram was based on 33 ultrastructural characters, 6 light microscope characteristics and 8 biological characters. Molecular UPGMA dendrogram depicting differences (Dice distance) between examined trypanosomatids is based on the universally primed PCR polymorphisms. The general topology of both dendrograms are similar, with the Trypanosoma at the base. The genus Wallaceina appears to be monophyletic. In a contrary, the genera Leptomonas, Crithidia and Herpetomonas look like artificial groups according to both methods used. The cyst-forming homoxenous trypanosomatids from insects represent a monophyletic clade, which seems to be a separate genus. Two species of within genus Wallaceina are arranged as a separate subgenus.     

石山苣苔属(苦苣苔科)花形态演化及分类学意义

石山苣苔属(苦苣苔科)约30种,主要分布于我国南部的石灰岩地区.目前该属已知物种数虽少但花形态极其多样,是该科中分类最为困难的类群之一.基于分子证据,其它8个属中花形态迥异的一些物种被并入石山苣苔属.然而,该属花形态的演化趋势缺乏系统性的研究,传统分类对属的界定与分子系统学研究结果相矛盾的原因,以及是否有形态特征支持新界定的石山苣苔属还不清楚.该研究中,总共编码了19种石山苣苔属植物和9种报春苣苔属植物的35个形态特征,其中包括26个花部形态特征,在分子系统树上追踪了它们的演化路径.结果表明:无论属内还是属间,多数花部形态特征,尤其以往属的分类界定特征,在演化过程中变化频繁且发生了高度同塑性演化,这是导致传统形态分类不自然的关键因素.此外,在观察研究的所有特征中,花丝和柱头的差异可能在石山苣苔属植物共同祖先中经历了演变,或可用于区分石山苣苔属与其姐妹报春苣苔属的大多数种类.因此,在苦苣苔科植物的分类学研究中应当慎用这些花部性状作为分类依据,而且应对形态特征进行广泛地观察研究,在密集的取样和分辨率更高、更可靠的系统树上追踪它们的演化规律.更为重要的是,需要进一步研究导致复杂形态性状演化的内在分子调控机理和外在的自然选择动力,最终更加深入地理解石山苣苔属等典型喀斯特植物的演化过程和机理.     

Phylogeny of the genus Peperomia (Piperaceae) inferred from the trnK/matK region (cpDNA)

The genus Peperomia is one of the largest genera of basal angiosperms, comprising about 1500-1700 pantropically distributed species. The currently accepted infrageneric classification divides Peperomia into nine subgenera and seven sections. This classification is based on some 200 species, primarily using fruit morphology. The monophyly of these infrageneric taxa has never been tested and molecular phylogenetic studies of a representative sampling within Peperomia do not exist. This paper provides the first molecular phylogeny for the genus Peperomia. Monophyletic clades within Peperomia are identified and previously used morphological characters are critically reviewed. We show that the importance of some morphological characters has been overestimated and that some of these characters presumably have evolved several times independently. Only one previously described subgenus has been confirmed to be monophyletic.     

A phylogeny of the ITS and ETS for Montanoa (Asteraceae: Heliantheae)

A phylogeny of the genus Montanoa based on the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) is presented. Each of the two clades revealed by the Bayesian and parsimony analyses has approximately half of the number of species in the genus. One lineage is composed mostly of central and southern Mexican species whereas the other lineage contains those species endemic to Mesoamerica and South America. The molecular phylogeny is compared to previous phylogenetic hypotheses based on morphological characters. Key features in the structure of the capitulum such as pale morphology, heavily used in the past to construct hypotheses of relationship within the genus, are viewed as of minimal value to circumscribe natural groups. The relationships of Montanoa to other genera in the Heliantheae are briefly discussed.     

A multilocus phylogeny of the desmid genus Micrasterias (Streptophyta): evidence for the accelerated rate of morphological evolution in protists

Micrasterias, the name of which is derived from the Greek for 'little star', comprises possibly the most spectacularly shaped desmids (Desmidiales, Streptophyta). Presently, the genus Micrasterias includes about 60 traditional species, the majority of which were described in the early 19th century. We used a comprehensive multigene dataset (including SSU rDNA, psaA, and coxIII loci) of 34 Micrasterias taxa to assess the relationships between individual morphological species. The resulting phylogeny was used to assess the patterns characterizing the morphological evolution of this genus. The phylogenetic analysis led to the recognition of eight well-resolved lineages that could be characterized by selected morphological features. Apart from the members of Micrasterias, three species belonged to different traditional desmid genera (Cosmarium, Staurodesmus, and Triploceras) and were inferred to be nested within the genus. Morphological comparisons of these species with their relatives revealed an accelerated rate of morphological evolution. Mapping morphological diversification of the genus on the phylogenetic tree revealed profound differences in the phylogenetic signal of selected phenotypic features. Whereas the branching pattern of the cells clearly correlated with the phylogeny, cell complexity possibly reflected rather their adaptive morphological responses to environmental conditions. Finally, ancestral reconstruction of distribution patterns indicated potential origin of the genus in North America, with additional speciation events occurring in the Indo-Malaysian region.     

<Emphasis Type="Italic">Subsessila turbinata</Emphasis> gen. et. sp. nov. (Beltraniaceae), a <Emphasis Type="Italic">Beltrania</Emphasis>-like fungus from Thailand

A new monotypic Beltrania-like genus, Subsessila, with its type species S. turbinata, is described, illustrated and compared with similar genera. The new genus is introduced in the family Beltraniaceae based on phylogenetic analysis and morphological characters. Subsessila can be easily distinguished from other Beltrania-like genera by dark setae arising from radially lobed basal cells, mostly lacking macronematous conidiophores. Conidiogenous cells are ampulliform or doliiform and produce turbinate to clavate conidia with rostrate proximal end and rounded distal end. Evidence for establishment of the new genus is provided based on morphological comparison and DNA sequence data analyses.     

23种伞形科植物果实形态及其分类学意义

该实验采用徒手切片法对伞形科17属23种植物的果实进行了外部形态和解剖特征的观察,结果表明:伞形科果实有背腹压扁、两侧压扁和不压扁3种类型;侧棱有宽、有窄;油管的分布有棱槽单油管型和棱槽多油管型;花柱基多数为圆锥状,少数种的花柱基为扁平垫状;萼齿明显或不明显。通过进一步对属间和属内果实解剖特征的比较得出:(1)果实表面被钩刺或刚毛及果棱特征在属间差异明显,在属内表现出一致性,可作为伞形科属间分类的依据。(2)果实横切面的形状、胚乳腹面的凹凸以及萼齿的形态特征在属内种间的分类研究中有重要的意义。基于果实形态特征,编制了17属23种植物的分种检索表。     

Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae)

Recent advances in molecular systematics of the ferns make it possible to address long-standing questions about classification of the major fern genera, such as the worldwide genus Polystichum (Dryopteridaceae), comprising at least 200 species. In this study we examined rbcL sequences and morphological characters from 55 fern taxa: 34 were from Polystichum and 21 were from other genera in the Dryopteridaceae. We found that Phanerophlebia, possibly including Polystichopsis, is the sister group to Polystichum sensu lato (s.l.), including Cyrtomium. Polystichum as commonly recognized is paraphyletic. Our results lead us to suggest recognizing the clade of earliest diverging Polystichum species as a distinct genus (Cyrtomidictyum) and to continue to recognize Cyrtomium as a separate genus, leaving a monophyletic Polystichum sensu stricto (s.s.). We resolved a tropical American clade and an African clade within Polystichum s.s. However, the resemblance between the once-pinnate, bulb-bearing calciphilic species found in Asia and the West Indies appears to be the result of convergent evolution. Optimizing our morphological character transformations onto the combined phylogeny suggests that the common ancestor of Polystichum s.l. and Phanerophlebia had evolved the common features of the alliance, including ciliate petiole-base scales, once-pinnate fronds, ultimate segments with scarious tips, peltate indusia, and microscales.     

Systematics of the genera of Bodotriidae (Crustacea: Cumacea)

The cumacean family Bodotriidae includes 382 species in 31 genera grouped in three subfamilies: Bodotriinae, Mancocumatinae and Vaunthompsoniinae. Generic diagnoses are based on few characters that often have overlapping states among genera, complicating the understanding of the relationships within the group. The goals of this study are to illuminate the phylogenetic relationships among the genera of the Bodotriidae using morphological characters and to review the systematics of the family. For this purpose, all species within each genus were studied from the literature to code all the variability of genera for 109 variable morphological characters. Phylogenetic analyses show that there is independent reduction of the pleopods in two clades from a plesiomorphic state of five pairs, while the number of exopods of peraeopods has been reduced gradually in more derived groups of bodotriids. The subfamily Bodotriinae is the most derived and the Vaunthompsoniinae the most basal, and is paraphyletic with the Mancocumatinae embedded within it. No discriminatory characters were found between the subfamilies Mancocumatinae and Vaunthompsoniinae and they are not clearly separated in the phylogeny. Mancocumatinae is synonymized with Vaunthompsoniinae and all the genera of the former Mancocumatinae should be included within Vaunthompsoniinae. Analyses of character evolution justify a few other taxonomic changes. All genera were redescribed based on all the coded characters and a complete list of all valid species for each genus is included. Finally, dichotomous keys for identification to genus level are provided.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 1–58.     

雪雀属系统发育关系的研究（雀形目：文鸟科)

雷雀属Montifringilla7种36个形态特征作为分类单元,进行支序分析。以麻雀属Passer、石雀属Petronia部分种类作为比较外群,讨论雪雀属的分类地位及其与近缘属麻雀属、石雀属系统发育关系;分析了雪雀属内种间的系统发育。支序分析的结果表明雪雀属为单系群,建议将雪雀属划分成两个亚属,讨论了雪雀属种类在进货上的位置,在3个近缘属的系统发育关系中,麻雀属类群较原始,雪雀属类群较进化,石雀属在进货中介于二之间。