Phylogenetic relationships within the fern genus Hymenophyllum s.l. (Hymenophyllaceae, Filicopsida): contribution of morphology and cytology

The phylogenetic relationships of Hymenophyllum and its segregate genera Cardiomanes, Hymenoglossum, Rosenstockia, Serpyllopsis and Microtrichomanes are addressed, using 31 morphological characters of the sporophyte and one cytological character. As expected, this study reveals considerable morphological heterogeneity within the genus sensu lato, but several apomorphic changes allow support for some clades. Four unresolved taxa, Cardiomanes, Hymenoglossum, Diplophyllum and Mecodium pro parte are probably the most basal elements in Hymenophyllum. The analysis also suggests the polyphyly of Mecodium, and two unexpected associations: Sphaerocionium together with Microtrichomanes; and a broad clade composed of subg. Hymenophyllum, Hemicyatheon and Craspedophyllum, genera Rosenstockia and Serpyllopsis, and subsect. Leptocionium and Amphipterum. These associations appear justified by morphological, cytological or geographical data, and most of them are in agreement with preliminary molecular results.     

碎米蕨属的系统学研究——基于4种叶绿体DNA序列片段

碎米蕨属(Cheilosoria Trevis.)隶属碎米蕨类, 由于形态上的趋同进化, 使得该类群的系统分类一直存在争议。该研究对该碎米蕨属植物的4种叶绿体DNA序列片段(rbcL/matK/rps4/rps4-trnS)进行PCR扩增和序列分析, 再结合其它相关类群, 用贝叶斯法和最大似然法构建系统树并探讨其系统发育关系。结果表明, 碎米蕨属不是一个单系类群, 旧世界分布的碎米蕨属植物(薄叶碎米蕨除外)均聚在亚洲Cheilanthes群内, 与粉背蕨属(Aleuritopteris Fée)等类群形成不同亚支。该属孢子形态具有明显异质性。薄叶碎米蕨(Cheilosoria tenuifolia (Burm. f.) Trevis.)与亚洲其它碎米蕨属植物的系统位置相距甚远, 且与隐囊蕨(Notholaena hirsuta (Poir.) Desv.)聚为完全支持的分支, 两者可能均为大洋洲起源, 并属于另一类群。美洲和旧世界分布的碎米蕨属植物关系较远, 二者可能代表了不同的演化路线。     

The sporophyte-less filmy fern of eastern North America Trichomanes intricatum (Hymenophyllaceae) has the chloroplast genome of an Asian species

Trichomanes intricatum, the sporophyte-less filmy fern of the eastern United States, has been considered to be a species whose sporophyte generation has become extinct or is possibly still present among the many species of Trichomanes s.l. in the new world tropics but unable to grow in a temperate climate. A close relationship to Asian species has heretofore not been considered. Comparison of rbcL and rps4-trnS sequences to species of Trichomanes s.l. reveals that T. intricatum shares its chloroplast genome with Crepidomanes schmidtianum of eastern Asia. Because C. schmidtianum is a sterile triploid and the ploidy level of T. intricatum is unknown, several scenarios leading to their sharing of these maternally inherited genes must be explored.     

Pteridryaceae: A new fern family of Polypodiineae (Polypodiales) including taxonomic treatments

We undertook phylogenetic analyses to resolve the relationships of Pteridrys and related taxa based on six plastidmarkers (atpA, atpB, matK& rps16-matK, rbcL, rps4& rps4-trnS, and trnL & trnL-F) and nuclear pgiC.We included 195 accessions representing approximately 147 species in 38 genera, and seven of the nine families in Polypodiineae (eupolypods I). Tectariaceae s.l. (i.e., Arthropteris, Draconopteris, Hypoderris, Malaifilix, Pteridrys, Tectaria, and Triplophyllum in addition to Polydictyum) is recovered asmonophyletic (97% maximum likelihood bootstrap value), but with low (<50%) maximum parsimony jackknife value. The family Tectariaceae s.l. is therefore the only family in ferns without a corresponding non-parametric-based strong support in spite of our data totaling 9616 aligned base pairs. Tectariaceae s.l. can not be unambiguously recognized by any of the 13morphological characters analyzed. However, if the clade composed of Draconopteris, Malaifilix, Polydictyum, and Pteridrys (DMPP) is recognized as a distinct family, at least four morphological characters enable the distinction of the DMPP clade from its sister clade. Considering the uncertainty in the monophyly, the diagnosability, and the deep divergence, we propose to establish a new family, Pteridryaceae, to accommodate the DMPP clade. Species of Pteridryaceae share mostly the following characteristics: erect to suberect rhizomes, reduced basal pinnae, anastomosing or free venation, absence of catenate hairs at the leaf surface, and perine ornamentation lacking spines or spinules. Identification keys are provided for the four genera and 31 species of the DMPP clade (or Pteridryaceae). Reflecting the presented results, the recognition of Arthropteridaceae is the preferred taxonomic status of the Arthropteris clade.     

中国篦齿蕨属植物（水龙骨科）一新组合种

根据叶绿体rbcL和rps4-trnS序列及叶脉类型、孢子纹饰特征等证据,栗柄水龙骨Polypodiodes microrhizoma（C.B.Clarke ex Baker）Ching属于篦齿蕨属Metapolypodium Ching的范畴,因此将其组合到篦齿蕨属MetapolypodiumChing之下更合理。文中报道了该新组合种,即栗柄篦齿蕨Metapolypodium microrhizomum（C.B.Clarke ex Baker）S.G.Lu et L.H.Yang。     

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

? Premise of the study: The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. ? Methods: The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. ? Key results: Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. ? Conclusions: Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.     

云南铁角蕨与泸山铁角蕨的关系:来自叶绿体rbcL、trnL-F和rps4-trnS序列的证据

云南铁角蕨Asplenium yunnanense与泸山铁角蕨Asplenium lushanense的分类是一个悬而未决的问题。本文对云南铁角蕨与泸山铁角蕨及近缘类群的叶绿体rbcL基因和trnL-F、rps4-trnS基因间隔区序列进行PCR扩增和序列分析;并与已经发表的铁角蕨属植物的相应序列进行比较,发现云南铁角蕨与泸山铁角蕨的rbcL基因和trnL-F、rps4-trnS基因间隔区序列之间均未表现出差异,因此叶绿体DNA序列的证据不能将云南铁角蕨与泸山铁角蕨分开,从而从分予系统学方而证明云南铁角蕨与泸山铁角蕨是一对亲缘关系非常近的物种。     

Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data

This study examined in detail the rbcL sequence and morphological support for subfamilial relationships and monophyly of Lecythidaceae. Initially we needed to establish relationships of Lecythidaceae among other dicot families. To complete this we examined 47 rbcL sequences of 25 families along with molecular observations from several large analyses of rbcL data. All analyses strongly support the monophyly of the asterid III grouping. This analysis revealed Lecythidaceae to be paraphyletic and indicated potential outgroup relationships with Sapotaceae. Once relationships had been evaluated using molecular data we then concentrated on analyzing separate and combined morphological and molecular databases. The topology of the morphological data set was similar to the rbcL sequence and combined data sets except for the positioning of Napoleonaeoideae, Grias, Gustavia, and Oubanguia. According to the combined results, Planchonioideae, Lecythidoideae. and Foetidioideae are monophyletic, whereas the subfamily Napoleonaeoideae are paraphyletic. Nested within Napolconaeoideae, we found Asteronthos forms a strongly supported clade with Oubanguia (Scytopetalaceae). Foetidia, the only genus of Foetidioideae, is sister to Planchonioideae, and this clade is sister to Lecythidoideae. The [(Planchonioideae, Foetidioideae) Lecythidoideae are sister to Asteranthos/Oubanguia. Napoleonaeoideae are sister to the rest of Lecythidaceae.     

Molecular phylogeny of horsetails (<Emphasis Type="Italic">Equisetum</Emphasis>) including chloroplast <Emphasis Type="Italic">atpB</Emphasis> sequences

Equisetum is a genus of 15 extant species that are the sole surviving representatives of the class Sphenopsida. The generally accepted taxonomy of Equisetum recognizes two subgenera: Equisetum and Hippochaete. Two recent phylogenetical studies have independently questioned the monophyly of subgenus Equisetum. Here, I use original (atpB) and published (rbcL, trnL-trnF, rps4) sequence data to investigate the phylogeny of the genus. Analyses of atpB sequences give an unusual topology, with E. bogotense branching within Hippochaete. A Bayesian analysis based on all available sequences yields a tree with increased resolution, favoring the sister relationships of E. bogotense with subgenus Hippochaete.     

Using restriction-site variation of PCR-amplified cpDNA genes for phylogenetic analysis of tribe Cheloneae (Scrophulariaceae)

Data from restriction-site variation of three PCR-amplified chloroplast genic regions (trnK, rps2, and rbcL) were used to assess the utility of PCR-based methodology for phylogenetic reconstruction. Seventeen genera from tribe Cheloneae s.l. (Scrophulariaceae), and one genus each from Solanaceae, Acanthaceae, and Bignoniaceae, representing 32 taxa, were sampled. Phylogenetic reconstruction, based on a combined data set of 138 variable restriction sites, revealed a monophyletic clade of North American Cheloneae, which were not inconsistent with a polyphyletic Scrophulariaceae. Separate analyses of individual genie regions were unable to completely resolve the phylogeny, but were adequate for resolving relationships of major clades among the taxa sampled. We suggest that analysis of PCR-product restriction-site variation is useful for phylogenetic reconstruction above the species level.     

Phylogenetic relationships in Cyperus L. s.l. (Cyperaceae) inferred from plastid DNA sequence data

The phylogeny of Cyperus and allied genera has been reconstructed using cladistic analysis of plastid rbcL gene, rps16 intron, trnL intron, and trnL-F intergenic spacer sequence data in 40 species of tribe Cypereae. Cyperus s.s. as currently circumscribed is not monophyletic because ten cyperoid genera are embedded within it. Eucyperoid Cyperus species (with a C₃ anatomy, e.g. C. involucratus ) and the genera Courtoisina , Kyllingiella and Oxycaryum form a clade that is sister to a clade comprising chlorocyperoid species (with a C₄ anatomy, e.g. C. papyrus ) and the genera Alinula , Ascolepis , Kyllinga , Lipocarpha , Pycreus , Remirea and Sphaerocyperus . The position of two species is uncertain; C . tenellus is resolved in a clade together with Isolepis although with typical cyperoid spikelets, whereas I. humillima is not resolved near either Isolepis or Cyperus s . l . © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 145–153.     

Phylogeny and character evolution of the Neotropical fern genus <Emphasis Type="Italic">Stigmatopteris</Emphasis> (Dryopteridaceae)

We did a phylogenetic analysis on 21 of the 23 species of Stigmatopteris, a neotropical montane genus of wet forest floors. The analysis was based on four plastid markers: rbcL, rps4-trnS, trnG-trnR, and trnL-trnF. Two of the most closely related families to the Dryopteridaceae (Didymochlaenaceae and Hypodematiaceae) and 12 dryopteroid genera were used as outgroups. Eight morphological characters were mapped on the resulting tree. Stigmatopteris was recovered as monophyletic and sister to a clade formed by polystichoid ferns such as Arachniodes, Dryopteris, and Polystichum. Synapomorphies that distinguish Stigmatopteris are 1-pinnate-pinnatifid laminae, visible punctate glands in the mesophyll, the presence of hydathodes, uniseriate cilia on the scale margins, and loss of indusia. Within the genus are two main clades. The first consists of four species characterized by pinnae long-decurrent in at least the distal third of the lamina. The second consists of the remaining 17 species in the analysis and has no known morphological synapomorphies. Nested within this second clade is a subclade of six species endemic to southeastern Brazil. Anastomosing veins, a character often used in keys to distinguish the species, evolved three times within the genus.     

A global molecular phylogeny of the fern genus Trichomanes (Hymenophyllaceae) with special reference to stem anatomy

To establish a basis for future taxonomic revisions and to infer the evolutionary traits of Trichomanes s.l. , one of two large filmy fern genera, molecular phylogenetic analyses were conducted using chloroplast rbcL sequences. Sampling covered most of the global distribution range of this genus throughout the tropical and temperate zones, as well as all taxonomically significant species by the addition of 51 samples principally from Asia. The evolution of eight selected characters, which were adopted as taxonomic keys and/or putatively reflect morphological regression, was optimized on the retrieved most parsimonious rbcL trees, together with new observations on the stem anatomy of 45 species. The eight robust clades retrieved within Trichomanes in the rbcL phylogeny conflict with the existing classifications. Our results also suggest that the cup-shaped sorus, the primary diagnostic character of the genus, appears in parallel in the Hymenophyllum lineage, as demonstrated by Pleuromanes (typified by Trichomanes pallidum ) included in the lineage. The suggestion that the regressive character states are homoplastic apomorphies in the evolution of the frond size, stem thickness, root system, and stem anatomy (stele and cortex) probably illustrates a strong tendency towards adaptive evolutionary transition in Trichomanes . © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 1–27.     

扁苞蕗蕨和长柄蕗蕨的细胞分类学研究

本文首次报道了四川产扁苞蕗蕨和长柄蕗蕨的染色体及孢子发生情况。它们的染色体数目分别为 n=26和n=28,都是有性生殖的二倍体。染色体基数26在蕗蕨属的发现进一步证明了它和膜蕨属、厚壁蕨属的密切亲缘关系。这两种蕗蕨的孢子囊通常形成128个孢子及少数256个孢子的情况被描述,它们应该被看成是有性生殖真蕨,尤其是在膜蕨科和薄囊真蕨中的其他较原始的类群中的正常的孢子发生路线。     

A plastid gene phylogeny of the non-photosynthetic parasitic <Emphasis Type="Italic">Orobanche</Emphasis> (Orobanchaceae) and related genera

The phylogenetic relationships of the non-photosynthetic Orobanche sensu lato (Orobanchaceae), which includes some of the economically most important parasitic weeds, remain insufficiently understood and controversial. This concerns both the phylogenetic relationships within the genus, in particular its monophyly or lack thereof, and the relationships to other holoparasitic genera such as Cistanche or Conopholis. Here we present the first comprehensive phylogenetic study of this group based on a region from the plastid genome (rps2 gene). Although substitution rates appear to be elevated compared to the photosynthetic members of Orobanchaceae, relationships among the major lineages Cistanche, Conopholis plus Epifagus, Boschniakia rossica (Cham. & Schltdl.) B. Fedtsch., B. himalaica Hook. f. & Thomson, B. hookeri Walp. plus B. strobilacea A. Gray, and Orobanche s. l. remain unresolved. Resolution within Orobanche, however, is much better. In agreement with morphological, cytological and other molecular phylogenetic evidence, five lineages, corresponding to the four traditionally recognised sections (Gymnocaulis, Myzorrhiza, Orobanche, Trionychon) and O. latisquama Reut. ex Boiss. (of sect. Orobanche), can be distinguished. A combined analysis of plastid rps2 and nuclear ITS sequences of the holoparasitic genera results in more resolved and better supported trees, although the relationships among Orobanche s. l., Cistanche, and the clade including the remaining genera is unresolved. Therefore, rps2 is a marker from the plastid genome that is well-suited to be used in combination with other already established nuclear markers for resolving generic relationships of Orobanche and related genera.     

Molecular phylogenetic analysis of Passifloraceae sensu lato (Malpighiales) based on plastid and nuclear DNA sequences

A phylogenetic analysis of Passifloraceae sensu lato was performed using rbcL, atpB, matK, and 18S rDNA sequences from 25 genera and 42 species. Parsimony analyses of combined data sets resulted in a single most parsimonious tree, which was very similar to the 50% majority consensus tree from the Bayesian analysis. All nodes except three were supported by more than 50% bootstrap. The monophyly of Passifloraceae s.l. as well as the former families, Malesherbiaceae, Passifloraceae sensu stricto, and Turneraceae were strongly supported. Passifloraceae s.s. and the Turneraceae are sisters, and form a strongly supported clade. Within Passifloraceae s.s., the tribes Passifloreae and Paropsieae are both monophyletic. The intergeneric relationships within Passifloraceae s.s. and Turneraceae are roughly correlated with previous classification systems. The morphological character of an androgynophore/gynophore is better used for characterizing genera grouping within Passifloraceae s.s. Other morphological characters such as the corona and aril are discussed.     

A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data

The monophyly of the Peltophorum group, one of nine informal groups recognized by Polhill in the Caesalpinieae, was tested using sequence data from the trnL-F, rbcL, and rps16 regions of the chloroplast genome. Exemplars were included from all 16 genera of the Peltophorum group, and from 15 genera representing seven of the other eight informal groups in the tribe. The data were analyzed separately and in combined analyses using parsimony and Bayesian methods. The analysis method had little effect on the topology of well-supported relationships. The molecular data recovered a generally well-supported phylogeny with many intergeneric relationships resolved. Results show that the Peltophorum group as currently delimited is polyphyletic, but that eight genera plus one undescribed genus form a core Peltophorum group, which is referred to here as the Peltophorum group sensu stricto. These genera are Bussea, Conzattia, Colvillea, Delonix, Heteroflorum (inedit.), Lemuropisum, Parkinsonia, Peltophorum, and Schizolobium. The remaining eight genera of the Peltophorum group s.l. are distributed across the Caesalpinieae. Morphological support for the redelimited Peltophorum group and the other recovered clades was assessed, and no unique synapomorphy was found for the Peltophorum group s.s. A proposal for the reclassification of the Peltophorum group s.l. is presented.     

Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup

Closely related outgroups are optimal for rooting phylogenetic trees; however, such ideal outgroups are not always available. A phylogeny of the marattioid ferns (Marattiaceae), an ancient lineage with no close relatives, was reconstructed using nucleotide sequences of multiple chloroplast regions (rps4 + rps4-trnS spacer, trnS-trnG spacer + trnG intron, rbcL, atpB), from 88 collections, selected to cover the broadest possible range of morphologies and geographic distributions within the extant taxa. Because marattioid ferns are phylogenetically isolated from other lineages, and internal branches are relatively short, rooting was problematic. Root placement was strongly affected by long-branch attraction under maximum parsimony and by model choice under maximum likelihood. A multifaceted approach to rooting was employed to isolate the sources of bias and produce a consensus root position. In a statistical comparison of all possible root positions with three different outgroups, most root positions were not significantly less optimal than the maximum likelihood root position, including the consensus root position. This phylogeny has several important taxonomic implications for marattioid ferns: Marattia in the broad sense is paraphyletic; the Hawaiian endemic Marattia douglasii is most closely related to tropical American taxa; and Angiopteris is monophyletic only if Archangiopteris and Macroglossum are included.