Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes

Inferring basal relationships among vascular plants poses a major challenge to plant systematists. The divergence events that describe these relationships occurred long ago and considerable homoplasy has since accrued for both molecular and morphological characters. A potential solution is to examine phylogenetic analyses from multiple data sets. Here I present a new source of phylogenetic data for ferns and other pteridophytes. I sequenced the chloroplast gene atpB from 23 pteridophyte taxa and used maximum parsimony to infer relationships. A 588-bp region of the gene appeared to contain a statistically significant amount of phylogenetic signal and the resulting trees were largely congruent with similar analyses of nucleotide sequences from rbcL. However, a combined analysis of atpB plus rbcL produced a better resolved tree than did either data set alone. In the shortest trees, leptosporangiate ferns formed a monophyletic group. Also, I detected a well-supported clade of Psilotaceae (Psilotum and Tmesipteris) plus Ophioglossaceae (Ophioglossum and Botrychium). The demonstrated utility of atpB suggests that sequences from this gene should play a role in phylogenetic analyses that incorporate data from chloroplast genes, nuclear genes, morphology, and fossil data.     

The morphological nature of the fertile spike in the Ophioglossaceae

KHANDELWAL, S., 1986. The morphological nature of the fertile spike in the Ophiogiossaceae. A study of a large collection of specimens belonging to 12 species of Ophioglossum revealed the presence of many abnormal structures in the tropophyll and the spike. These anomalous structures suggest that the fertile spike of Ophioglossum is derived from the modified pinnae of a compound leaf. Compound vegetative leaves are possessed by its allies Botrychium and Helminthostachys.     

Elatinaceae are sister to Malpighiaceae; Peridiscaceae belong to Saxifragales

Phylogenetic data from plastid (ndhF and rbcL) and nuclear (PHYC) genes indicate that, within the order Malpighiales, Elatinaceae are strongly supported as sister to Malpighiaceae. There are several putative morphological synapomorphies for this clade; most notably, they both have a base chromosome number of X = 6 (or some multiple of three or six), opposite or whorled leaves with stipules, unicellular hairs (also uniseriate in some Elatinaceae), multicellular glands on the leaves, and resin (Elatinacae) or latex (Malpighiaceae). Further study is needed to determine if these features are synapomorphic within the order. Malpighiaceae have previously been inferred as sister to Peridiscaceae based on rbcL sequence data, but the rbcL sequence of Whittonia is a chimera of two sequences, neither of which appears to be Whittonia. Our data from plastid (atpB, rbcL) and nuclear (18S rDNA) genes instead place Peridiscaeace as a member of the Saxifragales.     

Systematics of Vitaceae from the viewpoint of plastid rbcL DNA sequence data

A phylogenetic analysis of plastid rbcL DNA sequences for 20 species of Vitaceae s.l. (including Leeaceae) and eight outgroups from Dilleniaceae and Santalales is presented. Patterns of floral and vegetative morphology and ontogeny within the family are compared to the phylogenetic trees produced. Despite the limited sampling of large and variable genera, there is a good correspondence with hypothesized floral and vegetative ontogenetic trends, with Leea and Ampelopsis ancestral, Cissus and Ampelocissus intermediate and Vitis most derived. A clade containing Parthenocissus , Tetrastigma , Cyphostemma and Vitis is found in all shortest trees. Cyphostemma and Parthenocissus are shown to be closely related to Vitis , to which clade Tetrastigma and Cayratia comprise the sister clade. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 421–432.     

Identifying clades in Asian Annonaceae: monophyletic genera in the polyphyletic Miliuseae

The tribe Miliuseae (Annonaceae) comprises six genera distributed in Asia: Alphonsea, Mezzettia, Miliusa, Orophea, Platymitra, and Phoenicanthus. A phylogenetic study to investigate the putative monophyly of the tribe and the intergeneric relationships is presented here. Nucleotide sequences of the plastid gene rbcL, trnL intron, and trnL-trnF intergenic spacer were analyzed from 114 Annonaceae taxa, including 24 Miliuseae species and two outgroups using maximum parsimony and Bayesian inference. The two data sets (rbcL and the trnL-trnF regions) were analyzed separately and in combination. Miliuseae were found to be polyphyletic due to the position of Mezzettia and are part of a large, predominantly Asian and Central-American clade (miliusoid clade). Although intergeneric relationships were poorly resolved, all genera, except Polyalthia, were monophyletic, supporting previous generic delimitation based on morphology. A group of three Polyalthia species seems the most likely sister group of Miliusa. Several infrageneric groups of Miliusa, Orophea, and Polyalthia are supported by both molecular and morphological data. No morphological synapomorphies have yet been found for the miliusoid clade. Molecular clades within the miliusoid clade, however, can be characterized by size and the shape of the outer petals, number of ovules per carpel, and the size of the fruits.     

Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails

Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies already has provided critical insight into some long-standing questions about the evolution of land plants. Here we report on the presence of a group II intron located in the mitochondrial atp1 gene of leptosporangiate and marattioid ferns. Primary sequence data for the atp1 gene are newly reported for 27 taxa, and results are presented from maximum likelihood-based phylogenetic analyses using Bayesian inference for 34 land plants in three data sets: (1) single-gene mitochondrial atp1 (exon+intron sequences); (2) five combined genes (mitochondrial atp1 [exon only]; plastid rbcL, atpB, rps4; nuclear SSU rDNA); and (3) same five combined genes plus morphology. All our phylogenetic analyses corroborate results from previous fern studies that used plastid and nuclear sequence data: the monophyly of euphyllophytes, as well as of monilophytes; whisk ferns (Psilotidae) sister to ophioglossoid ferns (Ophioglossidae); horsetails (Equisetopsida) sister to marattioid ferns (Marattiidae), which together are sister to the monophyletic leptosporangiate ferns. In contrast to the results from the primary sequence data, the genomic structural data (atp1 intron distribution pattern) would seem to suggest that leptosporangiate and marattioid ferns are monophyletic, and together they are the sister group to horsetails--a topology that is rarely reconstructed using primary sequence data.     

Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging

Phylogenetic relationships within Fagonia were inferred from analyses of plastid trnL intron and nuclear ribosomal ITS DNA sequences. Sampling of the genus was nearly complete, including 32 of 34 species. Phylogenetic analysis was carried out using parsimony, and Bayesian model averaging. The latter method allows model-based inference while accounting for model-selection uncertainty, and is here used for the first time in phylogenetic analyses. All species of Fagonia in the Old World, except F. cretica, form a weakly supported clade, and all Fagonia species of the New World, except F. scoparia, are well supported as sister to the Old World clade. Fagonia scoparia, from Mexico, and F. cretica, from Northern Africa, are well supported as sisters to all other Fagonia species. Vicariance-dispersal analysis, using DIVA, indicated that the occurrences of Fagonia in South America and southern Africa are due to dispersals, and also, that the ancestor of Fagonia had a distribution compatible with the boreotropics hypothesis.     

Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences

Phylogenetic analyses of DNA nucleotide sequences from the plastid genes rbcL and matK were employed to investigate intergeneric relationships within Malpighiaceae. Cladistic relationships generated from the independent data matrices for the family are generally in agreement with those from the combined matrix. At the base of Malpighiaceae are several clades mostly representing genera from a paraphyletic subfamily Byrsonimoideae. Intergeneric relationships among these byrsonimoid malpighs are well supported by the bootstrap, and the tribe Galphimeae is monophyletic. There is also a well-supported clade of genera corresponding to tribes Banisterieae plus Gaudichaudieae present in all trees, and many of the relationships among these banisterioid malpighs are well supported by the bootstrap. However, tribes Hiraeae and Tricomarieae (the hiraeoid malpighs) are paraphyletic and largely unresolved. Species of Mascagnia are distributed throughout these hiraeoid clades, confirming the suspected polyphyly of this large genus. Optimization of selected morphological characters on these trees demonstrates clear phylogenetic trends such as the evolution of globally symmetrical from radially symmetrical pollen, increased modification and sterilization of stamens, and switch from base chromosome number n = 6 to n = 10.     

Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.     

Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plastid coded genes and the 18S rRNA gene.

The basal relationship of bryophytes and tracheophytes is problematic in land plant phylogeny. In addition to cladistic analyses of morphological data, molecular phylogenetic analyses of the nuclear small-subunit ribosomal RNA gene and the plastic gene rbcL have been performed, but no confident conclusions have been reached. Using the maximum-likelihood (ML) method, we analyzed 4,563 bp of aligned sequences from plastid protein-coding genes and 1,680 bp from the nuclear 18S rRNA gene. In the ML tree of deduced amino acid sequences of the plastid genes, hornworts were basal among the land plants, while mosses and liverworts each formed a clade and were sister to each other. Total-evidence evaluation of rRNA data and plastid protein-coding genes by TOTALML had an almost identical result.     

Phylogenetics of Cranichideae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences

DNA sequences from plastid rbcL and matK genes and the trnL-F region, as well as the nuclear ribosomal ITS region, were used to evaluate monophyly and subtribal delimitation of Cranichideae and generic relationships in Spiranthinae. Cranichideae are moderately supported as monophyletic, with Chloraeinae and Pterostylis-Megastylis indicated as their collective sisters. Within Cranichideae, Pachyplectroninae and Goodyerinae form a well-supported monophyletic group sister to a "core spiranthid" clade that includes, according to their branching order, Galeottiellinae, Manniellinae, and a Prescottiinae-Cranichidinae-Spiranthinae subclade. Inclusion of Galeottiella in Spiranthinae, as in previous classifications, renders the latter paraphyletic to all other spiranthid subtribes. Cranichidinae and Spiranthinae (minus Galeottiella) are monophyletic and strongly supported, but Prescottiinae form a grade that includes a strongly supported prescottioid Andean clade and a weakly supported Prescottia-Cranichidinae clade sister to Spiranthinae. Well-supported major clades in Spiranthinae identified in this study do not correspond to previous alliances or the narrowly defined subtribes in which they have been divided recently. Morphological characters, especially those that have been used for taxonomic delimitation in Cranichideae, are discussed against the framework of the molecular trees, emphasizing putative synapomorphies and problems derived from lack of information or inadequate interpretation of the characters.     

Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes

Phylogenetic interrelationships in the enlarged order Ericales were investigated by jackknife analysis of a combination of DNA sequences from the plastid genes rbcL, ndhF, atpB, and the mitochondrial genes atp1 and matR. Several well-supported groups were identified, but neither a combination of all gene sequences nor any one alone fully resolved the relationships between all major clades in Ericales. All investigated families except Theaceae were found to be monophyletic. Four families, Marcgraviaceae, Balsaminaceae, Pellicieraceae, and Tetrameristaceae form a monophyletic group that is the sister of the remaining families. On the next higher level, Fouquieriaceae and Polemoniaceae form a clade that is sister to the majority of families that form a group with eight supported clades between which the interrelationships are unresolved: Theaceae-Ternstroemioideae with Ficalhoa, Sladenia, and Pentaphylacaceae; Theaceae-Theoideae; Ebenaceae and Lissocarpaceae; Symplocaceae; Maesaceae, Theophrastaceae, Primulaceae, and Myrsinaceae; Styracaceae and Diapensiaceae; Lecythidaceae and Sapotaceae; Actinidiaceae, Roridulaceae, Sarraceniaceae, Clethraceae, Cyrillaceae, and Ericaceae.     

Phylogeny of the Polytrichales (Bryophyta) based on simultaneous analysis of molecular and morphological data

Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees were constructed with simultaneous parsimony analyses of all sequences plus morphology and separate combinations of sequence data only. Results lend support for recognition of Polytrichales as a monophyletic entity. Oedipodium griffithianum appears as a sister taxon to Polytrichales or as a sister taxon of all mosses excluding Sphagnales and Andreaeles. Within Polytrichales, Alophosia and Atrichopsis, species without the adaxial lamellae (in Atrichopsis present but poorly developed on male gametophyte) otherwise typical of the group are sister to the remaining species followed by a clade including Bartramiopsis and Lyellia, species with adaxial lamellae covering only the central portion of the leaves. Six taxa with an exclusively Southern Hemisphere distribution form a grade between the basal lineages and a clade including genera that are mostly confined to the Northern Hemisphere.     

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.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

Molecular evidence for the common origin of snap-traps among carnivorous plants

The snap-trap leaves of the aquatic waterwheel plant (Aldrovanda) resemble those of Venus' flytrap (Dionaea), its distribution and habit are reminiscent of bladderworts (Utricularia), but it shares many reproductive characters with sundews (Drosera). Moreover, Aldrovanda has never been included in molecular phylogenetic studies, so it has been unclear whether snap-traps evolved only once or more than once among angiosperms. Using sequences from nuclear 18S and plastid rbcL, atpB, and matK genes, we show that Aldrovanda is sister to Dionaea, and this pair is sister to Drosera. Our results indicate that snap-traps are derived from flypaper-traps and have a common ancestry among flowering plants, despite the fact that this mechanism is used by both a terrestrial species and an aquatic one. Genetic and fossil evidence for the close relationship between these unique and threatened organisms indicate that carnivory evolved from a common ancestor within this caryophyllid clade at least 65 million years ago.     

Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA

Familial, subfamilial, and tribal monophyly and relationships of aroids and duckweeds were assessed by parsimony and Bayesian phylogenetic analyses of five regions of coding (rbcL, matK) and noncoding plastid DNA (partial trnK intron, trnL intron, trnL-trnF spacer) for exemplars of nearly all aroid and duckweed genera. Our analyses confirm the position of Lemna and its allies (formerly Lemnaceae) within Araceae as the well-supported sister group of all aroids except Gymnostachydoideae and Orontioideae. The last two subfamilies form the sister clade of the rest of the family. Monophyly of subfamilies Orontioideae, Pothoideae, Monsteroideae, and Lasioideae is supported, but Aroideae are paraphyletic if Calla is maintained in its own subfamily (Calloideae). Our results suggest expansion of the recently proposed subfamily Zamioculcadoideae (Zamioculcas, Gonatopus) to include Stylochaeton and identify problems in the current delimitation of tribes Anadendreae, Heteropsideae, and Monstereae (Monsteroideae), Caladieae/Zomicarpeae, and Colocasieae (Aroideae). Canalization of traits of the spathe and spadix considered typical of Araceae evolved after the split of Gymnostachydoideae, Orontioideae, and Lemnoideae. An association with aquatic habitats is a plesiomorphic attribute in Araceae, occurring in the helophytic Orontioideae and free-floating Lemnoideae, but evolving independently in various derived aroid lineages including free-floating Pistia (Aroideae).     

基于叶绿体基因rbcL和psbA-trnH间区探讨石杉科植物系统关系

关于石杉科Huperziaceae植物的分类,一直存在一些争议。在旧的分类体系中石杉科植物被包含在一个混合的石松科Lycopodiaceae和多谱系的石松属Lycopodium中。本文利用叶绿体rbcL基因和psbA-trnH基因间区序列探讨石杉科植物的系统位置及石杉科内部的分类关系,用最大简约法和邻接法对自测序列结合由GenBank下载的rbcL及psbA-trnH基因间区序列进行系统发育分析。结果显示,石杉科与Phylloglossum属关系较近,与石松科关系较疏远。在石杉科中热带石杉属Huperzia植物和马尾杉属Phlegmariurus植物的关系要比它们与其他石杉属植物更近。所以,我们的rbcL基因数据不支持秦仁昌关于石杉科分为石杉属和马尾杉属的分类处理。但是,因为我们的psbA-trnH序列没有包括热带种类,对石杉属植物和马尾杉属植物的关系无验证。因此需要更多的样品和序列数据进一步探讨石杉科的演化关系。