Birgitta Bremer

A parsimony analysis of the Asteridae sensu lato based on rbcL sequences

A parsimony analysis of 156 representative sequences of the Asteridae sensu lato and 28 outgroup sequences was conducted using a two-tiered approach. First, an analysis of the entire group, including 105 sequences, examined relationships among major lineages within the Asteridae s.l.; subsequently, several clades within the larger group were examined individually in greater detail by including more sequences for the group in question. The search strategy was designed to discover multiple islands of equal parsimony using the heuristic search routine in PAUP. In the broad search and in each more detailed search of subclades, multiple islands were found that imply substantially different relationships

Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: 1) including all positions; 2) including only first and second codon positions; 3) including only third positions; and 4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognizes 1400 groups on the basis of allrbcL positions. These include major taxa such as green plants, land plants, flowering plants, monocots and eudicots. We include appendices of supported angiosperm families, as well as larger groups.

More characters or more taxa for a robust phylogeny--case study from the coffee family (Rubiaceae).

Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage of supported nodes within a tree is positively correlated with the number of characters, and negatively correlated with the number of taxa. The morphological analyses are based on few characters and weakly supported trees are expected. The percentage of supported nodes is also dependent on the kind of data analyzed. In analyses of Rubiaceae based on the same number of characters, RFLP data give trees with higher percentage of supported nodes than rbcL and morphological data. We also discuss the support values for particular nodes at the familial and subfamilial levels. Two new data sets of ndhF and rbcL sequences of Rubiaceae are analyzed and together with earlier studies of the family we can conclude that the monophyly of the Rubiaceae is supported and within the family there are three well supported, but not easily characterized, large subfamilies, Rubioideae, Cinchonoideae s.s. and Ixoroideae s.l. There are also a few genera (Luculia and Coptosapelta) unclassified to subfamily.

REORGANIZATION OF THE GENUS PSYCHOTRIA AND TRIBE PSYCHOTRIEAE (RUBIACEAE) INFERRED FROM ITS AND RBCL SEQUENCE DATA

Psychotria is one of the largest genera of angiosperms as currently delimited, with approximately 1650 species estimated worldwide. A molecular phylogenetic study was undertaken using ITS and rbcL ...

Phylogenetic relationships within the Gentianales based on NDHF and RBCL sequences, with particular reference to the Loganiaceae

Phylogenetic relationships in the Gentianales with focus on Loganiaceae sensu lato are evaluated using parsimony analyses of nucleotide sequence data from the plastid genes rbcL and ndhF. Inter- and intrafamilial relationships in the Gentianales, which consist of the families Apocynaceae (including Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae, are studied and receive increased support from the combination of rbcL and ndhF data, which indicate that the family Rubiaceae forms the sister group to the successively nested Gentianaceae, Apocynaceae, and Loganiaceae, all of which are well supported. The family Gelsemiaceae forms a distinct, supported group sister to Apocynaceae. The Loganiaceae sensu stricto form a strongly supported group consisting of 13 genera: Antonia, Bonyunia, Gardneria, Geniostoma, Labordia, Logania, Mitrasacme, Mitreola, Neuburgia, Norrisia, Spigelia, Strychnos, and Usteria. These genera form two well-supported lineages. Several members of Loganiaceae sensu Leeuwenberg and Leenhouts, i.e., Androya, Peltanthera, Plocosperma, Polypremum, and Sanango are clearly not members of the Gentianales. The earlier exclusion of Buddlejaceae (including Buddleja, Emorya, Gomphostigma, and Nicodemia) as well as the reclassification of the genera Nuxia and Retzia to Stilbaceae of the Lamiales are all well supported.

Genet Dynamics of the Clonal Plant Rubus Saxatilis

Populations of Rubus saxatilis were investigated between 1988 and 1991 in a study area (c. 2.5 km 2 ) in central Sweden. Different phases in the life cycle were studied: flowering, pollination, fruit-set, fruit-removal and seedling recruitment. Identification of genets was made by use of RAPD (random amplified polymorphic DNA). Information concerning these life-cycle phases were then used to infer processes in the population dynamics of R. saxatilis. A path analysis suggested a strong effect of fruit-set on total patch fruit production. Fruit-set varied between 6.6% and 8.3% (yearly averages) and was influenced by distance to nearest flowering conspecific patch (...)

THE FAMILIAL AND SUBFAMILIAL RELATIONSHIPS OF APOCYNACEAE AND ASCLEPIADACEAE EVALUATED WITH RBCL DATA

Sequence data for therbcL gene from twenty-four taxa of the familiesApocynaceae andAsclepiadaceae were cladistically analysed in order to evaluate the existing familial and subfamilial classification. The taxa sampled represent all described subfamilies and a majority of the described tribes. The cladistic analysis shows that theAsclepiadaceae are nested within theApocynaceae. An amalgamation of the two families is therefore recommended. The subfamilial classification is also in need of revision: the subfamiliesPlumerioideae andApocynoideae of the current classifications are paraphyletic, as are many of the tribes. Potential subfamily candidates and characters traditionally used in the classification are discussed.

Phylogenetic utility of the nuclear rDNA ITS region in subfamily Ixoroideae (Rubiaceae): comparisons with cpDNA rbcL sequence data

ITS of the nrDNA were sequenced for 21 taxa inIxoroideae and outgroups (Rubiaceae) and compared with sequences of the cp-generbcL. Separate and combined analyses were performed. ITS-variation was extensive and, because of alignment ambiguities, some sites were excluded from the analyses. Several topologies from therbcL analysis that conflicted with earlier classifications are corroborated by the ITS data: 1)Posoqueria should be excluded fromGardenieae. 2) The disputed genusBertiera, previously inGardenieae, is basal in an extendedCoffeeae, includingTricalysia. 3)Ixora should be excluded fromPavetteae. 4)Vangueria, (Antirheoideae), belongs toIxoroideae. This affiliation ofAntirheoideae tribes withIxoroideae is also shown by new ITS andrbcL data forAlberta. Incongruities found between the two data sets may be caused by density of taxon sampling, different evolutionary rates, phylogenetic sorting, homoplasy caused by functional constraints, or sampling of non-orthologous ITS types.

Phylogeny of theAsterales sensu lato based onrbcL sequences with particular reference to theGoodeniaceae

TherbcL gene of 25 taxa was sequenced and analyzed cladistically in order to define more precisely the orderAsterales s.l. and to reconstruct the phylogeny ofGoodeniaceae. The cladistic analyses show that theAsterales comprise the familiesAbrophyllaceae, Alseuosmiaceae, Argophyllaceae, Asteraceae, Calyceraceae, Campanulaceae s.l.,Donatiaceae, Goodeniaceae (includingBrunoniaceae),Menyanthaceae, Pentaphragmataceae, andStylidiaceae. Abrophyllaceae, Alseuosmiaceae, Brunoniaceae, andDonatiaceae have previously not been studied in this respect. Within theGoodeniaceae, four groups supported by therbcL data can be distinguished: the genusLechenaultia, theAnthotium-Dampiera-group, the genusBrunonia, and a group formed by the remaining genera, theScaevola-Goodenia-group.

Phylogeny of the Asteridae s. str. based on rbcL sequences, with particular reference to the Dipsacales

TherbcL gene of 15 taxa was sequenced and analyzed cladistically together with a large sample of genera representing all main clades of the subclassAsteridae in order to determine more precisely the delimitation of the orderDipsacales and to elucidate the phylogeny of the families within the order. The cladistic analyses show that the Dipsacales comprise the familiesCaprifoliaceae, Morinaceae, Dipsacaceae, andValerianaceae includingTriplostegia. The results also provide a basis for the exclusion of a number of taxa previously placed in theDipsacales, such asDesfontainia, Columellia andAdoxaceae s. l. (includingSambucus andViburnum). Ever since the orderDipsacales was first suggested byDumortier (1829) and the similarCaprifoliales byLindley (1833, 1836), there has been confusion concerning the circumscription of the order, the relations between the included families, their circumscriptions, and the position of the order in a larger context.