A search for the phylogenetic position of the seven-son flower (Heptacodium, Dipsacales): Combining molecular and morphological evidence

A first report on the problematic phylogenetic position ofHeptacodium (2 spp.; China) using molecular data from chloroplast DNA is presented. Amplification of ORF2280 homolog region was executed in a number of representative taxa in order to determine ifHeptacodium shows similar structural rearrangements as other Dipsacales. DNA sequences ofndhF were generated to clarify the phylogenetic position ofHeptacodium among Caprifoliaceae (s.l.). Six outgroup taxa and fifteen representatives of Dipsacales were sampled and more than 2100 basepairs ofndhF sequence were used in a cladistic analysis. Parsimony analysis produced two shortest trees and showedHeptacodium as sister to all members of Caprifoliaceae (s.str.), although weakly supported. Additionally, trees were constructed withndhF data supplemented with availablerbcL sequences and a morphological data set. Results of all analyses support an unresolved basal position forHeptacodium among Caprifoliaceae (s.l.), which in part explains the difficulty experienced previously in classifying the genus.     

Phylogeny of the tribe Antirrhineae (Scrophulariaceae) based on morphological andndhF sequence data

Phylogenetic relationships within the tribe Antirrhineae (Scrophulariaceae) are analysed and discussed on the basis of parsimony analyses of morphological andndhF gene sequence data. The results indicate that the tribe Antirrhineae consists of four major groups of genera, theAnarrhinum clade, theGambelia clade, theMaurandya clade, and theAntirrhinum clade. TheAnarrhinum clade, consisting of the Old World bee-pollinated generaAnarrhinum andKickxia, is sister to the rest of the tribe. TheGambelia clade consists of the New World generaGambelia andGalvezia, which are very closely related and pollinated by hummingbirds. TheMaurandya clade consists of one subclade includingMaurandya and a number of related bee- or hummingbird-pollinated New World genera and another subclade with the Old World bee-pollinated generaAsarina andCymbalaria. TheAntirrhinum clade consists mainly of bee-pollinated Old World genera, such asAntirrhinum, Linaria, Chaenorhinum, and their segregates, but also includes the New World generaMohavea andHowelliella, of which the latter is known to be partly pollinated by hummingbirds. It is concluded that hummingbirdpollination has evolved independently within Antirrhineae at least three times from bee-pollinated ancestors.     

Phylogenetic relationships of theJuglandaceae

A cladistic analysis of molecular data from the chloroplast generbcL was used to examine the taxonomic relationships of the walnut family (Juglandaceae). In addition, chemical and morphological data from a previous study byHufford (1992) were incorporated, expanded, and analyzed independently and in combination with the molecular data. The results of these analyses suggest that theJuglandaceae are more closely related to theFagaceae, Betulaceae, Casuarinaceae, andUrticaceae and their relatives (sensuCronquist 1981) than they are to theAnacardiaceae (sensuThorne 1983). However, sequence data fromrbcL also suggest a relationship between the higherHamamelidae and certain families in theRosidae sensuCronquist 1981 (such asRosaceae andRhamnaceae), an outcome which would add credence to the widely accepted view of the polyphyletic nature of theHamamelidae.     

Phylogenetic reconstruction of the genusBrachypodium P. Beauv. (Poaceae) from combined sequences of chloroplastndhF gene and nuclear ITS

A phylogenetic reconstruction of eight species of the genusBrachypodium P. Beauv. (Poaceae) has been obtained combining sequence data from the chloroplastndhF gene and the nuclear ITS, and using five representatives of tribes Triticeae (Secale), Poeae (Lolium), Meliceae (Melica, Glyceria) and Oryzeae (Oryza) as out-groups. Similar numbers of informative substitutions for the ingroup species were provided by both the 3 region of the chloroplastndhF gene and the nuclear ITS region. The Mediterranean annualBrachypodium distachyon appears to be the basal lineage, followed by the divergence of the New World non-rhizomatousB. mexicanum, which antedates the separation of a core of six European and Eurosiberian rhizomatous perennials (Brachypodium arbuscula, B. retusum, B. rupestre, B. phoenicoides, B. pinnatum, andB. sylvaticum). The evolutionary reconstruction based on sequences of the chloroplast and the nuclear genomes is congruent with topologies obtained from analysis of RAPD data.     

Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: Evidence fromrbcL nucleotide sequences

Nucleotide sequences fromrbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship betweenLophosoria andDicksonia, and also betweenHymenophyllopsis andCyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships ofLophosoria are consistent with most (but not all) recent treatments. However,Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes ofHymenophyllopsis are needed to test these hypotheses of relationship.     

Phylogenetic Diversity of New Zealand Gelidiales as Revealed by rbcL Sequence Data

Diversity and phylogenetic relationships of New Zealand representatives of the red algal order Gelidiales have been examined using rbcL sequence data. Extensive field collections have been made from throughout the New Zealand region. Six genera have been reported previously from New Zealand (Capreolia, Gelidium, Pterocladia, Pterocladiella, Pterocladiastrum, Ptilophora). This research has revealed species with very restricted local distributions, as well as the discovery of several undescribed, cryptic taxa. The common and widespread Gelidium caulacantheum is confirmed to be more closely related to Capreolia than to other species of Gelidium. The generic concept of Capreolia, based on life history characters, will need to be modified to accommodate additional species possessing “Gelidium” life histories. A species endemic to New Zealand, Gelidium ceramoides, has been found to differ significantly from all other members of the Gelidiales and requires reclassification in another genus and order. Examination of field collections and herbarium specimens in addition to molecular sequence data have led us to conclude that specimens previously placed in the genera Ptilophora and Pterocladiastrum belong within Pterocladia lucida.     

Phylogeny inLabiatae s. l., inferred from cpDNA sequences

Sequences ofrbcL andndhF were analysed independently and in combination to resolve phylogenetic relationships inLabiatae s. l. Monophyly ofLabiatae s. l was supported by all three analyses.Congea tomentosa (Symphoremataceae) is nested withinLabiatae s. l. in therbcL analysis, but emerges as the sister group ofLabiatae s. l. in thendhF and combined analyses. Four noteworthy clades ofLabiate s. l. also are supported by all analyses corresponding to subfamiliesNepetoideae, Lamioideae, Pogostemonoideae andScutellarioideae. Monophyly of subfamiliesChloanthoideae andViticoideae is not supported. A clade comprisingTeucrioideae plusAjuga is supported byndhF and the combined analysis.     

Sorghum laxiflorum and S. macrospermum, the Australian native species most closely related to the cultivated S. bicolor based on ITS1 and ndhF sequence analysis of 25 Sorghum species

Australian species make up seventeen of the worlds twenty-five recognised species of Sorghum, with the genus separated into five sections: Eu-sorghum, Chaetosorghum, Heterosorghum, Para-sorghum and Stiposorghum. Whereas the genetic relationships within section Eu-sorghum are well known, little is known about the genetic relationships and crossabilities outside the primary genepool. We made a detailed investigation of phylogenetic relationships within Sorghum to identify wild species most closely related to cultivated sorghum (with outgroups Zea mays and Saccharum officinarum). The ribosomal ITS1 gene of ten species and the chloroplast ndhF gene from nineteen species were sequenced. Independent and combined analyses of the ITS1 and ndhF data sets were undertaken. The Eu-sorghum species were resolved into a strongly supported lineage by all three analyses, and included the Australian natives S. laxiflorum and S. macrospermum in the ITS1 and combined analyses. All remaining sorghum species were resolved into a second well-supported lineage in the combined analyses, although some internal relationships within this second lineage remain unresolved. We identified S. laxiflorum and S. macrospermum as the Australian species most closely related to cultivated sorghum. Our data support a reduction in the number of subgeneric sections from five to three: Eu-sorghum (unchanged); a combined Chaetosorghum/Heterosorghum to reflect the very close relationship between these two species; and a combined Para-sorghum/Stiposorghum section, thereby removing the unclear taxonomic and genetic boundaries between these species.     

Phylogenetic analysis ofEremosyne pectinata (Saxifragaceae s. l.) based onrbcL sequence data

Earlier analyses ofrbcL sequences clarified phylogenetic relationships of 16 of 17 subfamilies ofSaxifragaceae s. l. This study investigates the affinities of the monotypicEremosynoideae, the only subfamily ofSaxifragaceae s. l. not examined previously forrbcL sequence variation. Our analyses suggest thatEremosyne is only distantly related to core members ofSaxifragaceae s. l. (i.e.Saxifragoideae = Saxifragaceae s. str.); it is allied instead with members ofAsteridae. A particularly close relationship is indicated betweenEremosyne andEscallonia, another traditional member ofSaxifragaceae s. l. that also appears as part ofAsteridae. Inclusion ofEremosyne withinAsteridae is in agreement with embryology, as well as with 18S rDNA sequence data.     

Molecular evidence for naturalness of genera in the tribe Antirrhineae (Scrophulariaceae) and three independent evolutionary lineages from the New World and the Old

The tribe Antirrhineae consists of 29 genera distributed in the New World and the Old. Phylogenetic analyses of ITS and ndhF sequences served to recognize six main lineages: Anarrhinum group (Anarrhinum, Kickxia); Linaria group (Linaria); Maurandya group (Cymbalaria, Asarina, Maurandella, Rhodochiton, Lophospermum); Schweinfurthia group (Pseudorontium, Schweinfurthia); Antirrhinum group (Antirrhinum, Pseudomisopates, Misopates, Acanthorrhinum, Howeliella, Neogarrhinum, Sairocarpus, Mohavea, Galvezia); Chaenorrhinum group (Chaenorrhinum, Albraunia, Holzneria). Parsimony (cladistics), distance-based (Neighbor-Joining), and Bayesian inference reveal that: (1) the tribe is a natural group; (2) genera such as Linaria, Schweinfurthia, Kickxia, and Antirrhinum also form natural groups; (3) three Antirrhineae lineages containing genera from the New and Old World are the result of three intercontinental disjunctions displaying similar levels of ITS-sequence divergence and differentiation times (Oligocene-Miocene); (4) evolution of flower shapes is not congruent with primitiveness of personate flowers; (5) both polyploidy and dysploidy appear to be responsible for most variation in chromosome number in the six main lineages. Nuclear and chloroplast evidence also supports the split of American and Mediterranean species of Antirrhinum into different genera, a result that should be contemplated in the interest of a more natural (monophyletic) taxonomy. Nucleotide additivity causes poor resolution in the ITS analysis of 22 species of Mediterranean Antirrhinum and lead us to interpret extensive hybridization in the Iberian Peninsula.This research was supported by the Spanish Dirección General de Investigación Científica y Técnica (DGICYT) through the project Flora Iberica (PS91-0070-C03-01). We thank Jorge Martínez and Emilio Cano for his assistance in the lab, Rafael Rubio and Omar Fiz for helping on the Bayesian inferences, the curators/collection managers of BCF, E, JACA, MA, SALA, SALAF, SEV, TARI, VAL for loans and access to specimens, and two anonymous reviewers for improving the quality of this publication.     

Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data

Phylogenetic analysis of noncoding trnL plastid DNA sequences and morphological data for 43 species of Zygophylloideae, representing most of the morphological and geographical variation in the subfamily, indicates that the currently recognised genera Augea (monotypic, southern Africa), Tetraena (monotypic, China), and Fagonia (c. 30 species, widespread), are embedded in Zygophyllum (c. 150 species, widespread). A generic classification based on six monophyletic and morphologically distinctive entities is proposed: Roepera with c. 60 species in Australia and southern Africa, Zygophyllum with c. 50 species in Asia, Tetraena with c. 40 species in Africa and Asia, Augea with a single species in southern Africa, Melocarpum with two species in the Horn of Africa region, and Fagonia with c. 30 species in both the Old and the New World. Scanning electron microscopy studies of testa structure provided important characters for the delimitation of some genera. New combinations (61) are made in Roepera, a resurrected genus originally described from Australia, one new name is proposed in Zygophyllum, 35 new combinations are made in Tetraena, and two new combinations are made in Melocarpum (previously Zygophyllum sect. Melocarpum).     

Reinstatement of Lophocoleaceae (Jungermanniopsida) based on chloroplast gene rbcL data: exploring the importance of female involucres for the systematics of Jungermanniales

Maximum likelihood analysis of 113 rbcL sequences leads to a well resolved phylogeny of Jungermanniales. All species with perigynia or marsupia are found in one clade, whereas species with coelocaules are placed in several lineages. The broadly circumscribed Geocalycaceae (including Lophocoleaceae) of most recent authors are resolved as polyphyletic. Geocalycaceae genera which develop female involucres without involvement of stem tissue (Chiloscyphus, Heteroscyphus, Leptoscyphus, Physotheca) form a robust clade which is placed sister to Plagiochilaceae whereas the genera with involucres originating at least partly from stem tissue (Geocalycaceae s.str., Geocalyx, Harpanthus, Saccogyna) are nested within the paraphyletic Jungermanniaceae. This topology leads to the exclusion of the strictly perianth-bearing species from Geocalycaceae and the reinstatement of Lophocoleaceae. Campanocolea is nested within Chiloscyphus. Physotheca and Chiloscyphus breutelii are placed within an unsupported clade with several accessions of Leptoscyphus. Heteroscyphus forms a paraphyletic grade at the base of Chiloscyphus.     

Phylogenetic relationships in gnetophyta deduced fromrbcL gene sequences

Part of the large subunit of the ribulose-1,5-bisphosphate carboxylase gene (rbcL) was sequenced (1333 base pairs) from three species of gymnosperms:Ephedra sinica Gnetum parvifolium, Welwitschia mirabilis. Phylogenetic trees inferred from the neighbor joining, Wagner parsimony and maximum likelihood methods showed thatGnetum andWelwitschia were more closely related to each other than either is toEphedra within Gnetophyta, and the result supports previous cladistical analysis of morphological data.     

Molecules and morphology: Congruence of data inColumnea (Gesneriaceae)

The cladistic analysis and comparison of molecular and morphological data has been the source of much recent debate. In this study, independent analyses of molecular and morphological data fromColumnea L. sects.Pentadenia andStygnanthe (Gesneriaceae) are compared. Comparative methods include consensus, visually comparing trees from independent analyses and combined data analysis. Consensus methods provided little resolution. Comparison of trees obtained from the independent analyses revealed some differences although the trees are highly similar. However, a combined analysis found that the level of incongruence between the two data sets was low. The tree resulting from the combined data has aspects of both the morphological and molecular trees despite the larger number of molecular characters. In addition, the combined data tree has greater resolution than either of the two data sets singly, indicating that the two types of data are congruent, and complementary to each other.     

Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data

Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

The phylogeny of the austral grass subfamily Danthonioideae: Evidence from multiple data sets

The grass subfamily Danthonioideae is one of the smaller in the family. We utilize DNA sequence data from three chloroplast regions (trnL, rpoC2 and rbcL) and one nuclear region (Internal Transcribed Spacer; ITS) both singly and in combination to elucidate the relationships of the genera in the subfamily. The topology retrieved by the ITS region is not congruent with that of the plastid data, but this conflict is not strongly supported. Nine well-supported clades are retrieved by all data sets. The relationships at the base of the subfamily are clearly established, comprising a series of three clades of Merxmuellera species. The earliest diverging clade probably does not belong in Danthonioideae. The other two clades are centered in the tropical African mountains and Cape mountains respectively. A clade of predominantly North and South American Danthonia species as well as D. archboldii from New Guinea is retrieved, but the African and Asian species of Danthonia are related to African species of Merxmuellera, thus rendering Danthonia polyphyletic. The relationships of the Danthonia clade remain equivocal, as do those of the two Cortaderia clades, the Pseudopentameris and Rytidosperma clades. Paseka Mafa was tragically killed in a vehicle accident in July 2001. This paper includes information he collected during the course of his MSc in Systematics and Biodiversity Science at the University of Cape Town.