Phylogenetic relationships in the Pterygiella complex (Orobanchaceae) inferred from molecular and morphological evidence

The Pterygiella complex, i.e. Pterygiella, Phtheirospermum, Pseudobartsia and Xizangia, is controversial in terms of both its relationships and taxonomic status. The genera of the complex are all species‐poor and endemic to eastern Asia. In this study, we sampled all taxa in the complex for seven genic regions [atpB‐rbcL, atpH‐I, psbA‐trnH, rpl16 intron, trnL‐F, trnS‐G and internal transcribed spacer (ITS)], which were analysed separately and in combination. We examined capsule and seed morphology of these genera using scanning electron microscopy (SEM). Our results indicate that the complex is polyphyletic and comprises two clades. The first, designated ‘Pterygiella complex I’, includes only Phtheirospermum japonicum. This clade is uniquely diagnosed by its papery yellow capsule and reticulate secondary thickening on the seed coat. The second clade, ‘Pterygiella complex II’, includes Phtheirospermum tenuisectum, P. parishii, P. muliense, Pseudobartsia, Xizangia and Pterygiella. These taxa share a coriaceous capsule. Pterygiella is monophyletic and is characterized by eglandular, unicellular, pilose hairs on the capsule and hook‐like protuberances on the horizontal ridges of the striate or reticulate seed coat. Excluding P. japonicum, the remaining taxa of Phtheirospermum cluster together and are sister to Pterygiella. Xizangia bartschioides and Pseudobartsia yunnanensis are separated from Pterygiella and Phtheirospermum, respectively, and are supported as genera by molecular and morphological evidence. © 2013 The Linnean Society of London     

Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data

Doradidae is a putatively monophyletic group of South American freshwater catfishes containing 30 extant genera and 72 valid species. Only one study to date has attempted to estimate phylogenetic relationships among doradids. This morphological analysis partitioned species into two basal genera ( Wertheimeria and Francisodoras ) and a crown group of three subfamilies (Platydoradinae, Astrodoradinae and Doradinae) whose relationships were unresolved. No subsequent work has been done to resolve the subfamilial trichotomy or to assess whether postulated intergeneric relationships are accurate. We address this problem with complete sequences (2.5 kilobases, kb) of mitochondrial 12S and 16S rRNA genes and partial (1.3 kb) sequences of the nuclear elongation factor-1 alpha (EF1α) gene from representatives of 23 doradid genera (43 species) and 13 outgroups from additional siluriform families. Phylogenetic analysis of these data yields strong support for the monophyly of Doradidae and Astrodoradinae (as well as other relationships), but otherwise shows significant conflict with morphological results. A partial re-examination of published morphological data indicates that many characters may have been incorrectly polarized and many taxa have incorrect state assignments. Our results provide a framework for ongoing efforts to describe the species-level diversity of this poorly understood neotropical family.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 551–575.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

甜菜树属--我国云南产山柚子科一原始新属及其植物地理学意义

报道了我国云南红河流域山柚子科的一个原始新属－－甜菜树属,该属具大型圆锥花序,两性,是Ｌｅｐｉｏｎｕｒｕｓ,Ｍｅｌｉｅｎｔｈａ和Ｃｈａｍｐｅｕｅｉａ３个单型属的祖型,远远无疑起源于康滇古陆即今之云南高原,其发现对山柚子科的起源分化具重要意义。     

Determination of phylogenetic position ofPipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Phylogenetic relationships within Serpulidae (Sabellida, Annelida) inferred from molecular and morphological data

We assessed phylogenetic relationships within Serpulidae (including Spirorbinae) using parsimony and Bayesian analyses of 18S rDNA, the D1 and D9−D10 regions of 28S rDNA, and 38 morphological characters. In total, 857 parsimony informative characters were used for 31 terminals, 29 serpulids and sabellid and sabellariid outgroups. Following ILD assessment the two sequence partitions and morphology were analysed separately and in combination. The morphological parsimony analysis was congruent with the results of the 2003 preliminary analysis by Kupriyanova in suggesting that a monophyletic Serpulinae and Spirorbinae form a clade, while the remaining serpulids form a basal grade comprising what are normally regarded as Filograninae. Bremer support values were, however, quite low throughout. In contrast, the combined analyses of molecular and morphological data sets provided highly resolved and well-supported trees, though with some conflict when compared to the morphology-only analysis. Spirorbinae was recovered as a sister group to a monophyletic group comprising both 'filogranin' taxa ( Salmacina , Filograna , Protis , and Protula ) and 'serpulin' taxa such as Chitinopoma , Metavermilia , and Vermiliopsis . Thus the traditionally formulated subfamilies Serpulinae and Filograninae are not monophyletic. This indicates that a major revision of serpulid taxonomy is needed at the more inclusive taxonomic levels. We refrain from doing so based on the present analyses since we feel that further taxon sampling and molecular sequencing are required. The evolution of features such as the operculum and larval development are discussed.     

Position of enigmatic miniature trichomycterid catfishes inferred from molecular data (Siluriformes)

Trichomycteridae is a well‐corroborated catfish family that comprises about 300 valid species distributed in eight subfamilies. The phyletic status of the Trichomycterinae is uncertain, with different hypothesis regarding the position of the miniaturized Trichomycterus hasemani group. This group comprises four valid species, and neither its monophyly nor its positioning among the Trichomycteridae was tested in a phylogenetic framework. Bayesian Inference and Maximum Likelihood analyses of a molecular data set comprising the mitochondrial genes 12S and 16S and the nuclear genes H3, MYH6 and RAG2 (2983 bp) for 26 taxa highly supported the miniature catfish T. hasemani group as monophyletic and sister to the Tridentinae, consequently recognized as a new genus of this subfamily. Potamoglanis gen. nov. is diagnosed by seven character states: an angle of 35–40° between the main longitudinal axis of the head and the main axis of the autopalatine; thin tubular shape of the second ceratobranchial; presence of six or seven anal‐fin rays; eyes dorsally placed on head; opercular and interopercular odontodes patches not juxtaposed; absence of a distal process on the hyomandibula and presence of a long process on the anterior region of the hyomandibula. Potamoglanis gen. nov is similar to the Tridentinae genera by the presence of a wide cranial fontanelle; presence of a short ventral process in the opercular bone and by the origin of the dorsal fin placed in a vertical through the anal‐fin origin.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Phylogenetic origin of Beckmannia （Poaceae） inferred from molecular evidence

The phylogenetic origin of Beckmannia remains unknown. The genus has been placed within the Chlorideae, Aveneae （Agrostideae）, Poeae, or treated as an isolate lineage, Beckmanniinae. In the present study, we used nuclear internal transcribed spacer （ITS） and chloroplast trnL-F sequences to examine the phylogenetic relationship between Beckmannia and those genera that have assumed to be related. On the basis of the results of our studies, the following conclusions could be drawn： （i） Beckmannia and Alopecurus are sister groups with high support; and （ii） Beckmannia and Alopecurus are nested in the Poeae clade with high support. The results of our analysis suggest that Beckmannia should be placed in Poeae.     

Phylogenetic relationships of the Clavelinidae and Pycnoclavellidae (Ascidiacea) inferred from mtDNA data

Abstract. The phylogenetic relationships within the Order Aplousobranchiata (Ascidiacea) are largely unexplored. In this work, we study the phylogenetic status of the genera Clavelina and Pycnoclavella. Traditionally, both genera had been included in the family Clavelinidae, until the new family Pycnoclavellidae was defined, removing the genus Pycnoclavella from Clavelinidae. Not all authors accept the validity of Clavelina and Pycnoclavella as distinct genera, let alone their belonging to different families. In addition, the assignment of species to these genera, as well as to the genus Archidistoma , has been controversial. We analyzed sequences of the mitochondrial gene cytochrome c oxidase subunit I belonging to ten species of Pycnoclavella (including several formerly assigned to Archidistoma and Clavelina ), 11 species of Clavelinidae, and ten species of other aplousobranch genera belonging to seven families, plus two outgroups. Two different tree construction methods (maximum likelihood and Bayesian inference) showed similar results. Pycnoclavella and Clavelina appeared in distinct clades but formed a monophyletic group relative to representatives of the main families of the order Aplousobranchiata. Our phylogenetic results indicate that both genera are valid but should be included within a single family, with the name Clavelinidae having precedence. The monotypic clavelinid genus Nephtheis branches in our trees within the clade of the genus Clavelina. Our results also confirm that some forms assigned to Archidistoma and Clavelina have been misplaced and belong to the genus Pycnoclavella. Pycnoclavella martae n.sp. is described.     

Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)

Drosophila is the genus responsible for the birth of experimental genetics, but the taxonomy of drosophilids is difficult because of the overwhelming diversity of the group. In this study, we assembled sequences for 358 species (14 genera, eight subgenera, 57 species groups, and 65 subgroups) to generate a maximum‐likelihood topology and a Bayesian timescale. In addition to sampling an unprecedented diversity of Drosophila lineages, our analyses incorporated a geographical perspective because of the high levels of endemism. In our topology, Drosophila funebris (Fabricius, 1787) (the type species of Drosophila) is tightly clustered with the pinicola subgroup in a North American clade within subgenus Drosophila. The type species of other drosophilid genera fall within the Drosophila radiation, presenting interesting prospects for the phylogenetic taxonomy of the group. Our timescale suggests that a few drosophilid lineages survived the Cretaceous–Palaeogene (K‐Pg) extinction. The drosophilid diversification began during the Palaeocene in Eurasia, but peaked during the Miocene, an epoch of drastic climatic changes. The most recent common ancestor of the clades corresponding to subgenera Sophophora and Drosophila lived approximately 56 Mya. Additionally, Hawaiian drosophilids diverged from an East Asian lineage approximately 26 Mya, which is similar to the age of the oldest emerging atoll in the Hawaiian–Emperor Chain. Interestingly, the time estimates for major geographical splits (New World versus Asia and Africa versus Asia) were highly similar for independent lineages. These results suggest that vicariance played a significant role in the radiation of fruit flies. © 2013 The Linnean Society of London     

Phylogenetic relationships in the tribe Oxyptilini (Lepidoptera,Pterophoridae, Pterophorinae) based on morphological data of adults

The monophyly of the tribe Oxyptilini and phylogenetic relationships of the genera embraced in this tribe were examined using 171 (75 binary and 96 multistate) characters of adult morphology. The study material included 98 species of 30 genera, representing all previously recognized genera of Oxyptilini, together with the genera Sphenarches, Antarches, Diacrotricha, and Cosmoclostis, four species of Oidaematophorini, three species of Platyptiliini, as well as three and two other species belonging to Pterophorini and Exelastini respectively. Two Agdistis species were used as outgroups. The cladistic analysis resulted in six equally parsimonious trees. A majority of the recovered synapomorphic characters have previously been used in the taxonomy of the subfamily. However, 25 novel characters were found. The monophyly of Oxyptilini was supported, although only with homoplastic characters and low amounts of tree confidence; the genera Capperia, Procapperia, Paracapperia, Oxyptilus, Megalorhipida, and Trichoptilus were found to be nonmonophyletic; Sphenarches and Antarches were recovered as members of Oxyptilini; the two genera Cosmoclostis and Diacrotricha were placed out of Oxyptilini, inside the tribe Pterophorini; and close affinity of the genus Dejongia to Stangeia, Stenodacma, Megalorhipida, Trichoptilus, and Buckleria species was revealed. Four new combinations, Cosmoclostis lanceata (Arenberger) comb. nov. , Nippoptilia regulus (Meyrick) comb. nov. , Capperia tadzhica (Zagulajev) comb. nov. , and Buckleria negotiosus (Meyrick) comb. nov. are proposed; Capperia insomnis Townsend was considered as a senior synonym of Procapperia hackeri Arenberger syn. nov. , Buckleria negotiosus (Meyrick) as a senior synonym of Buckleria vanderwolfi Gielis syn. nov. , and Oxyptilus variegatus Meyrick syn. nov. as a junior synonym of Oxyptilus secutor Meyrick. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 484–547.     

Phylogenetic relationships in European erpobdellid leeches (Hirudinea: Erpobdellidae) inferred from restriction-site data of the 18S ribosomal gene and ITS2 region

The PCR-amplified 185 rRNA gene and ITS2 region were used for a restriction-site analysis to infer phylogenetic relationships among European representatives of the leech family Erpobdellidae and to test the phylogenetic reliability of the morphological characters used in this family till now. Fragment patterns produced by 11 restriction endonucleases in the 18S rRNA gene and by nine in the ITS2 region showed a higher interspecific variation in the latter than in the former genome component. No intraspecific variation could be detected, even among geographically very distant populations, except for the two supposed subspecies Trocheta b. bykowskii and T. b. krasense . The estimated overall nucleotide divergence (d) was lower in the genus Erpobdella (d = 0.015–0.061) than in the genera Dina and Trocheta (d = 0.049–0.090). E. testacea and E. monostriata do not seem to be as closely related to each other as previously thought; their pairwise nucleotide divergence (0.061) is highest within the genus Erpobdella . The nucleotide divergence between T. b. bykowskii and T. b. krasense (0.090), which greatly resemble each other morphologically, was surprisingly high. Phylogenetic trees were inferred via neighbour-joining and maximum parsimony methods. The trees support the monophyly of Erpobdellidae and the subdivision into two groups according to the pattern of annulation (the Erpobdella clade and the Dina-Trocheta clade). Further subdivision based on annulation patterns and other morphological characters is not supported. There was no molecular evidence for the monophyly of the genus Dina and the monophyly of the genus Trocheta .     

Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia,Muridae) inferred from molecular data,with description of a new species

Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus), Chiromyscus langbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscus thomasi sp. n.     

Reappraisal ofDiplolabellum coreanum (orchidaceae) as inferred from molecular data

The taxonomic treatment of a monotypic genus,Diplolabellum, has been disputed by various authors. Maekawa (1935) described the genus on the basis ofOreorchis coreana IFinet. Because distribution of its plants is very limited, i.e., to Jeju Island of the South Korean Peninsula, it has not been well studied. To reappraise the phylogenetic relationship ofDiplolabellum coreanum Finet, we obtained ITS,matK, trnT-trnL, andtrnL-trnF sequences from several species ofOreorchis and related genera. Sequence analysis showed thatD. coreanum is closely related to one group ofOreorchis that consists ofO. patens Lindle andO. fargesii Finet. Therefore, our molecular data support treating the species asO. coreana rather than asD. coreanum, even though the latter genus is distinct fromOreorchis in morphological characters such as callus, pedicel, column, and caudicle.     

基于多基因序列和形态性状的牡丹组种间关系

牡丹被认为是中国的国花,具有很高的医学、观赏和经济价值.野生牡丹被认为是栽培牡丹的野生祖先,因此弄清牡丹组的种间亲缘关系具有重要的理论和实践意义.由于受到信息量的限制,根据单基凼数据或形态数据往往无法对牡丹组的种间关系得到明确的结果.本研究用12份样品代表野生牡丹组(Paeonia section Moutan DC.,Paeoniaceae)8个种,利用包括核基因(Adh1A、Adh2和GPAT)和叶绿体基因(trnS-trnG和rps16-trnQ)的DNA序列以及形态性状的多套数据来探讨野牛牡丹的种间关系.合并分析得到具高支持率的牡丹组物种间的系统发育关系.结果表明,芍药属牡丹组8个野生种分为两个亚组,即肉质花盘亚组subseet.Delavayanae和革质花盘亚组subsect.Vaginatae.肉质花盘亚组包括滇牡丹P delavayi和大花黄牡丹P.ludlowii;革质花盘亚组包括其余6个种.革质花盘亚组中,四川牡丹P.decomposita ssp.decomposita和紫斑牡丹P. rockii ssp. rockii关系密切;卵叶牡丹P.qiui和矮牡丹P. jishanenMs关系密切;银屏牡丹P. suffruticosa ssp.yinpingmudan与风丹P. ostii关系 密切,并且后两个分支为姊妹群.