Capillolejeunea from the East African Islands does not deserve generic recognition and is proposed as a synonym of Drepanolejeunea (Lejeuneaceae, Hepaticae) based on studies of fertile material. The new combination, Drepanolejeunea mascarena comb. nov., is proposed. Detailed description and illustrations of Drepanolejeunea mascarena are provided.

Phylogenetic relationships within the moss family Bryaceae were studied using chloroplast DNA sequences (atpB-rbcL, rpl16 intron, rps4, and trnL-trnF region) and anatomical and morphological data. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian methods indicate that the genera Brachymenium, Bryum, and Rhodobryum are not monophyletic. A clade including Acidodontium, Anomobryum, Brachymenium acuminatum, Bryum species, Haplodontium, Mielichhoferia himalayana, and Plagiobryum is robustly supported in all analyses. The sections Brachymenium, Globosa, and Leptostomopsis of Brachymenium occur in a basal grade also including Bryum billarderi and Rhodobryum. The total evidence analysis supports Acidodontium as a monophyletic genus. In general, the results are congruent with previous molecular analyses. Features of the reduced peristome are homoplastic within the Bryaceae, and it is obvious that circumscriptions of taxa based on sporophytic characters alone may unite taxa that are distantly related. The rosulate growth condition is homoplastic within the family, which suggests that the genus Rosulabryum is not monophyletic. Based on present phylogenetic evidence, no morphological synapomorphies can be detected for the Bryaceae.

ISSR (Inter-Simple Sequence Repeat) fingerprint data and nrITS sequences confirm the presence of Anacolia menziesii in Europe. The species is more variable genetically in North America than in Europe. The data show only minor differentiation between the North American and European populations of A. menziesii. Anacolia webbii is morphologically and genetically very similar to Anacolia menziesii, but can be separated from Anacolia menziesii with high confidence based on the ITS and ISSR data. Long distance dispersal is the most likely explanation for the disjunction of Anacolia menziesii between North America and Europe.

Anogramma is a genus of eight putative species with small annual sporophytes and potentially perennating gametophytes. Phylogenetic relationships within the genus as well as its relationships with other putatively taenitidoid genera and with traditionally cheilanthoid Cosentinia vellea have been poorly resolved and are investigated here. Maximum parsimony, maximum likelihood, and Bayesian inference analyses of rbcL sequences were used to test 1) the monophyly of Anogramma, 2) support for the proposed specific distinctness of A. guatemalensis and A. caespitosa from A. leptophylla, and 3) the asserted close (sister) relationship between Anogramma and Pityrogramma, as well as to infer the phylogenetic relationships among these genera. Results reveal that Anogramma in the traditional sense is polyphyletic. Anogramma guatemalensis and A. caespitosa nest within A. leptophylla. Pityrogramma is not sister to Anogramma as a whole but only to A. chaerophylla and A. novogaliciana. Anogramma osteniana is deeply separated from its traditional congeners and the new combination Jamesonia osteniana (Dutra) Gastony is made. Cosentinia vellea should not be subsumed within Cheilanthes but instead should be considered a taenitidoid genus closely related to A. leptophylla and A. lorentzii. Neighbor joining analysis of Amplified Fragment Length Polymorphism data sets inferred relationships among the A. leptophylla accessions, embedding A. guatemalensis and A. caespitosa in respective New World and Old World clades of A. leptophylla.

Some species of Annonaceae have been reported to have a spiral arrangement of branches on their orthotropic axes while other species have a distichous arrangement of branches, but the systematic distribution of this morphological difference in the family has not been studied. Growth architecture was surveyed for 48 genera and 100 species of Annonaceae using original observations of living plants and reports from the literature. The spiral branching pattern was found in all species of 27 genera examined, while distichous branching architecture characterized the other 21 genera. Architecture pattern is correlated with a difference in the orientation of the apical meristem of the primary shoot: in plants with spiral architecture the apex is erect; in plants with distichous architecture the apex is horizontal or drooping. The architecture data show remarkable congruence with recent infra-familial phylogenies constructed on the basis of rbcL and trnL-trnF sequence data, supporting several rearrangements of genera in the classification of this family, and may be more widely useful in the systematics of Annonaceae.

We investigated phylogenetic relationships within Erythronium using DNA sequences from the chloroplast gene matK and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. Erythronium, Amana, and Tulipa form a strongly supported clade that appears to be of Asian origin. Erythronium is widely distributed in the Northern Hemisphere, and consists of three well supported and geographically distinct clades occurring in western North America, eastern North America, and Eurasia. ITS analyses suggest that the Eurasian and eastern North American clades form a monophyletic group that separated into two lineages following divergence from the western North American clade. Although the three clades are each characterized by distinct morphological features, convergence both among and within geographic areas is seen in several characters. The western North American clade exhibits greater morphological and molecular diversity than either of the other two clades, and many of its species hybridize, suggesting both recent and ongoing speciation. The geographic distribution of Erythronium suggests initial diversification in Tertiary mixed mesophytic forest, followed by fragmentation of the range during the late Tertiary or early Pleistocene and subsequent radiation in western North America.

All published information on Globba (Zingiberaceae) in Sumatra is summarized and augmented by our own data obtained by revision of herbarium materials and observations in the field. Sixteen species and five varieties of Globba are reported from Sumatra, including one new species, which belongs to sect. Globba, G. multifolia sp. nov. The difference between G. multifolia and allied species is discussed. A key to the species of Globba in Sumatra is provided.

The phylogenetic relationships of Pachycereus (Cactaceae) species and relatives from subtribe Pachycereinae were studied using DNA sequence data. The plastid rpl16 intron, trnL intron, trnL-F intergenic spacer, and nuclear rDNA internal transcribed spacer region (ITS) were sequenced for 30 species, representing the four genera of subtribe Pachycereinae (Carnegiea, Cephalocereus, Neobuxbaumia, and Pachycereus) as well as three additional outgroup genera from subtribe Stenocereinae. Phylogenetic analyses support neither the monophyly of Pachycereus as currently circumscribed nor Pachycereinae unless Stenocereus aragonii and S. eichlamii are included within it. However, these results suggest that the subtribe can be divided into three major clades. The first includes Pachycereus hollianus and P. lepidanthus, which is sister to a large clade combining species from the Pachycereus and Cephalocereus groups. Within this large clade Cephalocereus and Neobuxbaumia together with Pachycereus fulviceps are sister to the remaining species of Pachycereus as well as Stenocereus aragonii, S. eichlamii, and Carnegiea gigantea. Our results suggest that Pachycereus is paraphyletic and that several other genera (Backebergia, Lemaireocereus, Lophocereus, and Pseudomitrocereus) may be resurrected to accommodate these new phylogenetic insights. A number of morphological and anatomical characters support these relationships, indicating that future analyses combining both molecular and morphological characters will be particularly useful in resolving relationships within this group of columnar cacti.

A phylogenetic analysis of exemplars of Acacieae, Ingeae, and some Mimoseae, based on trnK, matK, psbA-trnH, and trnL/trnF sequence data, is presented. The results support other recent studies in showing that neither the Ingeae nor Acacieae is monophyletic. Some subgenera of Acacia, specifically subgenera Acacia and Phyllodineae, are monophyletic, but subg. Acacia is in a basal polychotomy with various members of Mimoseae and a large clade with the other members of Ingeae and Acacieae. Acacia subg. Phyllodineae is sister group to members of the Ingeae. Both the Ingeae and Acacia subg. Aculeiferum are paraphyletic.

The nuclear gene encoding the chloroplast-expressed isozyme of glutamine synthetase (ncpGS) is single copy in diploid angiosperms but is duplicated in species of Glycine, a paleopolyploid genus. The two Glycine paralogues are sister to one another in phylogenetic analyses, a pattern that suggests that this ncpGS duplication occurred subsequent to the divergence of Glycine from extant Glycininae. This pattern does not support an allopolyploid hypothesis in which genomes from close relatives of extant genera combined to form the polyploid, 2n = 40 genome of Glycine, nor with an ancient gene duplication shared with other Glycininae. Rather, it is consistent with autopolyploidy or with a simple gene duplication. Teramnus ncpGS was the closest relative of the two Glycine paralogues, supporting a sister-group relationship between these two genera. In contrast, ncpGS results suggested that Sinodolichos, a genus that has been suggested as a possible congener of Glycine, is more closely related to Pseueminia and Pseudovigna. Both paralogues of ncpGS identify known genome groups among species of Glycine subg. Glycine, but neither strongly resolves relationships among these groups. Incongruence between the two paralogues in the placement of G. falcata mirrors incongruence between the chloroplast genome and other nuclear genes for this species.

Despite being the model organism for plant molecular genetic studies, little is known about the origins and evolutionary history of extant natural populations of Arabidopsis thaliana. We have analysed phylogenetic relationships between worldwide populations of Arabidopsis using polymorphic chloroplast microsatellites. These highly variable markers have revealed previously undetected levels of cytoplasmic variation and confirm previous hypotheses of a recent and rapid expansion of the species from its centre of origin. Furthermore, the results seem to verify previous nuclear analyses that call into question the true origin of several individual Arabidopsis ecotypes.

To clarify relationships among western North American members of the genus Draba, we produced a molecular phylogeny using nucleotide sequences from both internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS). Sequence data from 17 Draba taxa and two outgroups were subjected to both parsimony and maximum likelihood analyses. The phylogenetic results support previously proposed informal groupings for the sampled species. Western North American Draba are divided into two well-supported clades: 1) all taxa with a chromosome number based on x = 8, and 2) taxa whose chromosome base numbers appear to be aneuploid, deviating from x = 8. The resulting phylogenetic framework also reveals the taxonomic limitations of flower color, chromosome base number, and growth habit for predicting relationships within the genus.

Achimenes is a genus in the Gesneriaceae, subfamily Gesnerioideae, tribe Gloxinieae that shows remarkable variation in floral form and possibly floral pollination syndrome. This includes flowers that are salverform, tubular, or infundibuliform, white, yellow, pink, purple, and red, and with or without corolla spurs. Previous classifications of Achimenes have relied heavily on floral form as a measure of relationship. This study explores phylogenetic relationships in Achimenes and addresses questions of proper supraspecific classification, evolution of floral forms and pollination syndromes, the origins of floral spurs, chromosome evolution, and biogeographic patterns using nrDNA ITS and cpDNA trnL-F spacer sequences analyzed using maximum parsimony and maximum likelihood methodologies. Phylogenetic hypotheses support the non-monophyly of most of the supraspecific classification units currently recognized in Achimenes, multiple origins of each of the pollination syndromes and the major morphological characteristics used to define these syndromes, multiple origins of floral spurs, multiple tetraploid events, and sympatric distributions of many closely related species.

Tribe Anthocercideae (Solanaceae) is an Australian endemic group comprising 31 species in seven genera. Recent phylogenetic work has placed the Anthocercideae sister to Nicotiana. Two chloroplast DNA regions, ndhF and trnL/F, were analyzed and the phylogeny was used to test the tribe's monophyly, discover relationships within the tribe, and make inferences on character evolution and biogeography. The relationship between Nicotiana, Symonanthus, and the rest of tribe Anthocercideae is unresolved. Anthocercis, Anthotroche, Grammosolen, and Symonanthus are found to be monophyletic, while Cyphanthera and Duboisia are not (Crenidium is monotypic). Several characters were inferred to be derived within the Anthocercideae, including unilocular stamens with semicircular slits, ebracteolate flowers, and baccate fruits. Ancient colonization occurred in southwestern Australia followed by several radiation events eastward.

Phylogenetic analyses of internal transcribed spacer (ITS), external transcribed spacer (ETS), and 5.8S gene sequences of 18S–26S nuclear rDNA from all 23 genera of Cichorieae with centers of diversity in North America (and Picrosia from South America) show that all but three of the genera (Glyptopleura, Krigia, and Phalacroseris) belong to a series of seven clades that are well supported by bootstrap values >90%. Phalacroseris, endemic to California, with a single species (P. bolanderi), is sister to a well-supported (>95% bootstrap) clade that includes all other principally North American genera (plus Picrosia). The seven clades with major support and their component genera are: 1) the Lygodesmia Clade: Chaetadelpha, Lygodesmia, and Shinnersoseris; 2) the Pinaropappus Clade: Marshalljohnstonia and Pinaropappus; 3) the Pyrrhopappus Clade: Picrosia and Pyrrhopappus; 4) the Microseris Clade: Agoseris, Microseris, Nothocalais, Stebbinsoseris, and Uropappus; 5) the Stephanomeria Clade: Munzothamnus, Pleiacanthus, Prenanthella, Rafinesquia, and Stephanomeria; 6) the Malacothrix 1 Clade: Atrichoseris and various species of Malacothrix; and 7) the Malacothrix 2 Clade: Anisocoma, Calycoseris, and various other species of Malacothrix. The rDNA sequence data provide < 80% bootstrap support for other, larger groups that combine two or more of the seven major clades, except for one uniting all 24 ingroup genera and one uniting the Lygodesmia Clade and Pyrrhopappus Clade. The present analysis shows that Malacothrix, a genus of 22 species, is not monophyletic. None of the clades corresponds precisely to a suprageneric taxon of Cichorieae proposed previously, although taxa constituting each clade belong to a common subtribe or subgroup in classifications by Bremer, Jeffrey, and Stebbins, with two to three exceptions. As a group, the 24 genera represent a single, major radiation of Cichorieae based in North America.

The genus Dahlia presently consists of 35 species, primarily from Mexico. Species are usually placed in four sections: Pseudodendron, Epiphytum, Entemophyllon, and Dahlia, based largely on morphological characters, supplemented with cytological, geographical, and biochemical data. Combined molecular sequence data from both the internal and external transcribed spacer regions (ITS and ETS), located within the nuclear ribosomal gene repeat unit, are used to infer a phylogeny of the genus. Section Entemophyllon forms a very well-defined clade based on these data. Dahlia merckii and D. tubulata are positioned between sect. Entemophyllon the remaining taxa. Sections Pseudodendron and Epiphytum are closely allied with each other and a few species from sect. Dahlia to form the variable root clade (VRC), which incorporates all species with unusual underground structures, along with some species exhibiting the more typical tuberous type. The remaining species of sect. Dahlia form a well-defined clade, the core Dahlia clade (CDC).