Phylogeny and divergence time estimation of the genus Didymodon (Pottiaceae) based on nuclear and chloroplast markers

Didymodon Hedw., with approximately 140 species in the family Pottiaceae, is distributed nearly throughout the world, with the greatest diversity and important ecological functions in drought lands and alpine ecosystems. Several studies involving morphology, molecular systematics, and macro-systematic analysis have addressed the infrageneric classification of Didymodon, but controversy over the position of the infrageneric and species classification remains due to its high degree of morphological variation in micro-habitats and strong sensitivity to climate change at regional and global scale. To date, only a few phylogenetic studies have been conducted with an incomplete number of Didymodon species; further, there is no study published regarding the divergence time of Didymodon. Consequently, we conducted a comprehensive phylogenetic analysis of Didymodon species, sampling a total of 107 species, based on one nuclear (ITS) and five chloroplast DNA. Moreover, divergence time analysis was conducted to infer the age of origin and divergence of Didymodon species. Our results presented the largest scale phylogenetic relationship of Didymodon to date and resolved the phylogenetic status of some controversial taxa and the new species. The divergence time estimation showed that Didymodon species originated around the early Cretaceous, and the diversification was concentrated in the Cretaceous and Eocene. Paleoclimate and environmental change have a direct impact on the origin and divergence of Didymodon species by shaping their morphology, resource availability and ecological niche. Our study will help understand species origin and speciation of Didymodon as well as reflecting species adaptability and experience to historical events.     

中国灵芝属真菌的多样性与资源

灵芝属是大型真菌的一个重要类群,具有重要的经济价值、生态价值和文化价值。尽管国内外对灵芝属真菌的研究较多,但灵芝属真菌的分类一直存在诸多问题,我国过去报道的灵芝属真菌有114个分类单元,但其中很多的分类地位存在争议。本文基于凭证标本,确认我国目前发现的灵芝种类有40种,其中具有ITS分子序列的种类有39种,其他74个分类单元或为同物异名或为待定种。本文提供的中国39种灵芝的ITS序列可为今后准确鉴定灵芝的野生和栽培种类提供依据。     

The identification of vahlkampfiid amoebae by ITS sequencing

We have determined the internal transcribed spacer (ITS) sequences (including the 5.8S ribosomal DNA) of 30 strains of 14 species belonging to eight vahlkampfiid genera. Each previously described species has a specific ITS sequence, except for Tetramitus aberdonicus, Tetramitus thorntoni, and Tetramitus jugosus, which have identical ITS sequences. The latter three may therefore constitute a single species despite their apparent phenotypic differences. The ITS sequence appears to be conserved within a species. The species Willaertia magna appears to be ubiquitous. The 5.8S rDNA sequences of Singhamoeba horticola and Learamoeba waccamwensis indicate that they do not represent different genera, but both belong to the genus Tetramitus. The ITS sequences of 16 undescribed vahlkampfiid isolates were determined. Based on these sequences, seven isolates were identified as belonging to described species, while nine probably represent seven new species. Five of these presumed new species belong to the genus Tetramitus, and one each to the genera Vahlkampfia and Paravahlkampfia.     

Molecular phylogenetics and diagnosis of Anisakis, Pseudoterranova, and Contracaecum from northern Pacific marine mammals

Individual specimens of Anisakis, Pseudoterranova, and Contracaecum collected from marine mammals inhabiting northern Pacific waters were used for comparative diagnostic and molecular phylogenetic analyses. Forty-eight new sequences were obtained for this study of 14 Anisakis taxa, 8 Pseudoterranova taxa, 4 Contracaecum taxa, and 4 outgroup species. Partial 28S (LSU) and complete internal transcribed spacer (ITS-1, 5.8S, ITS-2) ribosomal DNA was amplified by the polymerase chain reaction and sequenced. Sequences of ITS indicated that Pseudoterranova specimens from Zalophus californianus (California sea lion), Mirounga angustirostris (northern elephant seal), Phoca vitulina (harbor seal), Enhydra lutris (sea otter), and Eumetopias jubatus (Steller's sea lion) exactly matched P. decipiens s. str., extending the host and geographic range of this species. Anisakis from northern Pacific marine mammals were most closely related to members of the A. simplex species complex. Comparison of Anisakis ITS sequences diagnosed the presence of A. simplex C in 2 M. angustirostris hosts, which is a new host record. Anisakis specimens from Phocoena phocoena (harbor porpoise), Lissodelphis borealis (Pacific rightwhale porpoise), and E. jubatus included 3 ITS sequences that did not match any known species. Contracaecum adults obtained from Z. californianus were most closely related to C. ogmorhini s.l. and C. rudolphii, but ITS sequences of these Contracaecum specimens did not match C. ogmorhini s. str. or C. margolisi. These novel Anisakis and Contracaecum ITS sequences may represent previously uncharacterized species. Phylogenetic analysis of LSU sequences revealed strong support for the monophyly of Anisakinae, Contracaecum plus Phocascaris, Pseudoterranova, and Anisakis. Phylogenetic trees inferred from ITS sequences yielded robustly supported relationships for Pseudoterranova and Anisakis species that are primarily consistent with previously published phenograms based on multilocus electrophoretic data.     

Systematic Rearrangement of Korean <Emphasis Type="Italic">Scirpus</Emphasis> L. s.l. (Cyperaceae) as Inferred from Nuclear ITS and Chloroplast <Emphasis Type="Italic">rbcL</Emphasis> Sequences

The genus Scirpus L. s.l. (Cyperaceae) has been accepted as a polyphyletic taxon by most plant taxonomists. This genus was separated into different genera by several different authors: Scirpus s. str., Trichophorum Pers., Bolboschoenus (Asch.) Palla, Schoenoplectus (Rchb.) Palla, and Schoenoplectiella Lye. The heterogeneity of Korean Scirpus s.l. has not yet been studied. We examined 17 taxa of Korean Scirpus s.l. by morphological characters and phylogenetic analyses based on nuclear ITS and chloroplast rbcL sequences. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian method provided sufficient resolution. The phylogeny revealed the polyphyly of Korean Scirpus s.l. with five distinct clades. These clades correspond to Bolboschoenus, Schoenoplectus s.str., and Schoenoplectiella, Scirpus s.str., and Trichophorum, respectively. These five genera were delimited in terms of the morphology of tuber, bract, and inflorescence. By virtue of our findings, we suggest that the 17 taxa of Korean Scirpus s.l. should be placed into five genera as follows: Bolboschoenus (two species), Schoenoplectus (three species), Schoenoplectiella (six species), Scirpus s.str. (five species), and Trichophorum (one species).     

大小兴安岭地区红菇属物种多样性及其地理成分

红菇属(Russula)真菌广泛分布于世界各地并与多种植物根系共生形成外生菌根, 对于森林生态系统的多样性维持与群落构建具有重要的作用。我国东北大小兴安岭地区是欧亚和美洲北温带地区生物群落交流的关键地区之一, 但该地区有关外生菌根真菌的区系研究较少。本研究对采自大小兴安岭的96份红菇标本进行了形态学鉴定和ITS序列分析, 通过结合世界范围内红菇属代表性物种(146个种)的ITS序列构建了红菇属系统发育图谱。结果表明, 大小兴安岭地区红菇属有46个分类单元, 其中包括37个种和9个未定种。对大小兴安岭地区37种红菇的地理成分分析表明, 北温带分布成分有13种、温带-热带共有成分8种、欧亚成分9种、世界广布成分7种。本研究表明大小兴安岭地区的红菇具有丰富的物种多样性, 而且具有明显的北温带区系特征, 同时也具有一定的区域特殊性。     

Unravelling evolutionary relationships between epifoliar Meliolaceae and angiosperms

Epifoliar fungi are a group of poorly studied fungal symbionts that coinhabit the surface of living plants. Meliolaceae is the largest group of epifoliar fungi and has been considered as obligate parasites. We investigated the taxonomy of Meliolaceae and the coevolutionary events with their host plants using time-calibrated cophylogeny based on large subunit, small subunit, and internal transcribed spacer (ITS) sequence data obtained from 17 different fungal taxa and rbcL, ITS, and trnH-psbA sequence data from their corresponding hosts. Nine new fungal species are introduced in this paper and Appendiculella is synonymized under Asteridiella. The dominant coevolutionary events during the Cretaceous and Cenozoic are cospeciation and host shift, respectively. We hypothesize that the evolutionary history of epifoliar fungi can be divided into three major periods: origins of families, formations of genera, and diversification of species. The rise of angiosperms prompted the evolution of modern epifoliar fungi and the diversification of orders of Angiospermae fostered the formation of epifoliar fungal genera. Phylogenetically, epifoliar fungal genera can be delimited according to their coevolutionary patterns and divergent periods.     

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.     

Delimitation of the genus Schizachyrium (Poaceae,Andropogoneae) based on molecular and morphological data

Schizachyrium (Poaceae, Andropogoneae) includes about 60 species distributed in tropical and subtropical regions of the world. In all recent molecular phylogenies of Andropogoneae, representatives of Schizachyrium appear closely related to Andropogon species. The objective of this study was to contribute to the delimitation of Schizachyrium. We performed a phylogenetic study including 38 taxa (>63%) of Schizachyrium, along with representatives of related genera, mainly of Andropogon, yielding a total of 49 taxa. This is the first phylogenetic analysis to include the type species of Schizachyrium, S. condensatum. DNA sequences of two plastid markers (ndhF and trnL-F) were analyzed under Bayesian methods. The results indicate that Schizachyrium is not monophyletic: 26 of the 38 Schizachyrium taxa analyzed are placed in a Schizachyrium s.s. clade that includes the type species of the genus, while 10 taxa are related to Andropogon species and two other species, S. delavayi (from China and India) and S. jeffreysii (from Africa), appear clearly separated. Additionally, 58 morphological characters (41 qualitative and 17 quantitative) were scored for the same 49 taxa and analyzed under the parsimony criterion. Character optimizations showed that (i) the reduced pedicellate spikelets, (ii) with lower glume less than or equal to 0.5 mm wide, (iii) awned, and (iv) without lemma and palea support the Schizachyrium s.s. clade. We propose these four characters as diagnostic features for the delimitation of Schizachyrium s.s.     

Phylogeny of the Spiny African Daisies (Compositae, tribe Arctotideae, subtribe Gorteriinae) based on trnL-F, ndhF, and ITS sequence data

The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215 species) and many species in the Cape Floristic Region. It is divided into two subtribes: Arctotidinae (ca. 5 genera, 85 species) and Gorteriinae (ca. 8 genera, 130 species). The monophyly of the genera within the subtribe Gorteriinae and their relationship to one another was investigated using 71 samples/212 sequences including 64/141 of which are newly reported from three phylogenetic markers, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS). The outgroup was composed of seven members from the sister subtribe. Results show the subtribe Gorteriinae to be divided into three monophyletic groups, the Gazania-Hirpicium-Gorteria group, the Didelta group, and the Berkheya-Cullumia group. Within these three groups are 13 sub-groups, one of which has sub-clades. The genus Berkheya Ehrh. is paraphyletic, falling into five different sub-groups. The two monotypic genera, Cuspidia and Heterorhachis are not nested within any of the Berkheya clades. Hirpicium and Cullumia each have most of their taxa in a monophyletic group, but they also have one or two taxa associated with other clades. Four of the five sub-groups of Berkheya have morphologically recognizable shared characters, such as habit and spines that have been recognized by past studies. However, the grouping of one species with Didelta is difficult to explain. Support for the major clades and most of the sub-groups is strong but the relationships among some of the terminal taxa are variable.     

Length Variation of the Nuclear Ribosomal DNA Internal Transcribed Spacer in the Genus Abies,with Reference to Its Systematic Utility in Pinaceae

The internal transcribed spacer (1TS) region (1TS1, ITS2 and 5.8S rDNA) of the nuclear ribosomal DNA (nrDNA) was amplified via PCR in 28 taxa of Abies Mill. The amplified fragments showed length polymorphism among species, with species from Central America and two species from North America having a length of approximately 2 500 base pairs (bp) and the remaining taxa having a length of approximately 1 700 bp based on 100 bp and 1 kb ladder standard markers. The complete sequencing of ITS of Abies bracteata showed that the shorter type is 1 697 bp (1TS1 is 1 296 bp, 5.8S + 1TS2 is 401 bp). For the longer one, the partial rrs1 and complete 5.8S + ITS2 sequencing revealed that thelength of 5.8S + ITS2 is the same as that of the shorter type. The length difference of ITS in Abies is mainly due to the length difference in the ITS1 region, a result similar to the previous findings in other genera of Pinaceae. Variation in ITS length seems well correlated with morphological and geographic characters in Abies, suggesting that the length variation may be a phylogenetically informative character within the genus, long ITS was also found in other genera of Pinaceae in the previous studies. The long length of ITS in the family makes the sequencing of the region and subsequent alignment of sequences among species or genera more difficult than in taxa with short ITS, such as angiosperms. Although the length variation of ITS in the genus Abies is significant, the homogenous of ITS sequence between the longer one and the shorter one is obvious if the insertion in the longer ITS is ignored.     

中国丝膜菌属李玉丝膜菌组一新种：李玉丝膜菌

本研究报道了丝膜菌属的一个新种：李玉丝膜菌,该种采自中国吉林省蒙古栎林中,其主要特征为担子体小型、幼时具蓝紫色调,菌盖强水浸状、具条纹,担孢子近球形。该种在系统发育树中形成一个独立的分支,与斑丝膜菌组形成姐妹关系,但遗传关系较远,属于新组李玉丝膜菌组。本文对新分类单元进行了详细描述,并对其系统发育上相近的物种进行了比较。     

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.     

利用核核糖体DNA内转录间隔区(ITS)探讨广义羽藓科系统发育

利用核核糖体DNA ITS序列,探讨了苔藓植物广义羽藓科的系统发育,摸索出适于扩增ITS片段的最适反应条件。实验共得到广义羽藓科6个种的ITS序列,它们分别是：Abieti-nela abietina(AJ417494),Anomodon minar(AJ344145),Chaopodium aciculum(AJ315968),Tuidium pristocalyx(AJ416443),Thuidium assimile(AJ416442),Herpetineuron toccoae(AJ315967),其中后5个种是国际上首次得到的。本文利用ITS序列构建羽藓科7属、11种植物的系统发育树,据Bootstrap严格一致树表明：广义的羽藓科为并系发育,可分为两个主要的分支,牛舌藓属Anomodon,羊角藓属Herpetineuron和多枝藓属Happohymenium等为一支,而山羽藓属Abietinella,羽藓属Thuuidium,沼羽藓属Helodium和麻羽藓属Claopodium等为另一主要分支,从分子水平上支持了据形态特征把原牛舌藓亚科的牛舌藓属,羊角藓属,多枝藓属提升为牛舌藓科的结论。     

中国冬青卫矛叶斑上的假尾孢菌

卫矛科Celastraceae植物上已报道尾孢类真菌10种,其中包括假尾孢属Pseudocercospora真菌7种。在对中国尾孢类真菌的调查研究中,采集到寄生在冬青卫矛Euonymus japonicus上的3种假尾孢菌,其中2个为新种,即冬青卫矛假尾孢Pseudocercospora euonymi-japonici和北京假尾孢P. beijingensis。本文对这2个新种和Pseudocercospora cf. destructiva提供了形态描述、图及与近似种区别的讨论。采用ITS、tef1-α、act和rpb2 4个片段的序列构建了系统发育树。     

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.     

Phylogeny of calcareous dinoflagellates as inferred from ITS and ribosomal sequence data

The phylogenetic relationships of calcareous dinoflagellates (i.e., Calciodinellaceae and Thoracosphaera) are investigated. Molecular data from the ribosomal 5.8S rRNA and highly conserved motifs of the ITS1 show Calciodinellaceae s.l. to be monophyletic when few non-calcareous taxa are included. They segregate into three monophyletic assemblages in a molecular analysis that considers the 5.8S rRNA and both the Internal Transcribed Spacer regions ITS1 and ITS2: a clade comprising species of Ensiculifera and Pentapharsodinium (E/P-clade), Scrippsiella s.l. (including fossil-based taxa such as Calciodinellum and Calcigonellum), and a heterogeneous group (T/P-clade) of calcareous (e.g., Thoracosphaera) and non-calcareous taxa (e.g., the highly toxic Pfiesteria). The potential to produce calcareous structures is considered as apomorphic within alveolates, and non-calcareous taxa nesting with calcareous dinoflagellates may have reduced calcification secondarily. Molecular results do not contradict general evolutionary scenarios provided by previous morphological (mainly paleontological) investigations.     

Phylogeny of the genus Lophozia (Dumort.) Dumort. s. str. inferred from nuclear and chloroplast sequences ITS1-2 and TRNL-F

Maximum parsimony and maximum likelihood phylogenetic trees were constructed for 21 taxa of Lophozia s. str. and the related genera, Schistochilopsis (5 species), Protolophozia elongate, and Obtusifolium obtusum based on pooled nuclear ITS 1-2 and chloroplast trnL-F DNA sequences. The trees were characterized by similar topology. It was demonstrated that the genus Lophozia s. str. was monophyletic, excluding L. sudetica, which deserved isolation into a distinct cryptic genus. The species distribution among the clades disagreed with the sections distinguished based on anatomical and morphological data. The relationships within the genus Schistochilopsis were consistent with the sectioning of the genus, based on morphological characters. Analysis of molecular data provided more precise definition of the systematic position of a number of taxa. Small genetic divergence of geographically distant forms was demonstrated.     

Phylogeny of Orthotrichum s.l. and Ulota s.l. (Orthotrichaceae,Bryophyta): Insights into stomatal evolution

Orthotrichum Hedw. s.l. and Ulota Mohr s.l. are two of the most speciose genera of the xerophytic moss family Orthotrichaceae. We reconstructed the phylogeny of these two genera using three data matrices: (i) organellar genomes and 33 taxa; (ii) six loci from three genomes and 144 taxa; and (iii) two plastid loci and 163 taxa. The present phylogeny, based on the maximum sampling of genes or taxa to date, generally confirms the new classification of Orthotrichum and Ulota, and indicated that all Ulota species, except Ulota phyllantha Brid., form a clade and three lineages comprise the cryptoporous Orthotrichum clade. We provided new morphological characters that support the present division of the two genera. Ancestral state reconstruction of stoma indicates that superficial stomata in Orthotrichum represent a plesiomorphic character and semi-immersed stomata were derived from immersed stomata. The results also suggest that immersed stomata independently arose once in Orthotrichum, whereas semi-immersed stomata probably arose more than once. Molecular dating analysis reveals that the occurrence of immersed stomata is probably related to arid environments during the early Oligocene to late Miocene, whereas the appearance of semi-immersed stomata might be associated with the mesic–xeric or semiarid environments during the middle Miocene to Pliocene. Ancestral state reconstruction of habitat indicates that the saxicolous habitat is apomorphic and independently evolved multiple times in Orthotrichum and Ulota, which supports the former hypothesis. Considering morphological statistics, the development of the cryptopore in Orthotrichum could provide increased resilience to dry habitats, and might promote their habitat shift during evolution.