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.     

Chloroplast DNA study of the generaAmbrosia s.l. andHymenoclea (Asteraceae): Systematic implications

The relationship ofAmbrosia (ragweed) andFranseria has long been debated. Their treatment as separate genera has been repeatedly challenged. In this study, chloroplast DNA restriction site variation was examined for species from bothAmbrosia andFranseria as well as taxa from the closely related genusHymenoclea. The chloroplast genomes of members of these three genera were examined using 21 restriction endonucleases and the restriction mutations were used to construct phylogenetic trees. Wagner and Dollo parsimony as well as weighted parsimony were employed to compare the different phylogenies. The results support a close relationship betweenAmbrosia andFranseria, but indicate that the two groups are well separated. Compared toFranseria, Ambrosia is a much more strongly supported group, and the results indicate thatHymenoclea is closer toFranseria than toAmbrosia. The cpDNA phylogeny was used as a framework to examine evolutionary trends in morphology and secondary chemistry.     

Molecular systematics of the Old World Astragalus (Fabaceae) as inferred from nrDNA ITS sequence data

This study represents a nuclear rDNA ITS-based phylogenetic analyses of a greater sampling of the Old WorldAstragalus compared to our previous work (212 vs. 134 taxa). Phylogenetic relationships among 212 species (213 accessions) of the Old WorldAstragalus, including newly segregated monotypic genusPodlechiella, the two aneuploid New WorldAstragalus, and five related genera, were inferred from analyses of nuclear rDNA ITS sequences using maximum parsimony. A total of 658 nucleotide sites and four binary characters for indels were analyzed. The results of phylogenetic analyses suggest sect.Phyllolobium, comprising mostly the Chinese species, is placed outside of the so-calledAstragalus s. str. and is a well-supported monophyletic group. The monotypic annual segregate genusThlaspidium (≡Astragalus sect.Thlaspidium, A. thlaspi), is clearly nested withinAstragalus s. str. Among the many sections analyzed here, only sects.Cenanthrum, Caraganella, Eremophysa, Incani, Laxiflori, andLotidium are strongly supported as monophyletic. Our analysis, in agreement with previous studies, shows that the North American euploidAstragalus species are scattered throughout the Old World groups of the genus.     

Phylogeny ofRubiaceae-Rubieae inferred from the sequence of a cpDNA intergene region

A phylogenetic analysis of 25 species, representing eight genera of theRubieae tribe (Rubiaceae), has been made using the DNA sequence of the chloroplastatp B-rbc L intergene region. Six tropical genera from other tribes ofRubiaceae have been used as outgroups. Whatever the method of analysis (distance, parsimony or maximum likelihood), five groups are clearly separated and described as informal clades. Their relative relationships are not clearly resolved by the parsimony analysis, resulting in eight equally parsimonious trees, 327 steps long, with a consistency index (CI) of 0.749 (excluding uninformative sites). TheRubieae tribe appears monophyletic from the data available. Some new and partly unexpected phylogenetic relationships are suggested. The genusRubia forms a separate clade and appears to be the relatively advanced sister group of the remaining taxa. TheSherardia clade also includes the generaCrucianella andPhuopsis. Galium sect.Aparinoides appears closely attached to theAsperula sect.Glabella clade. The remaining taxa ofGalium are paraphyletic:Galium sect.Platygalium (in theCruciata clade) is linked to the advanced generaCruciata andValantia; the more apomorphic groups ofGalium form theGalium sect.Galium clade, including the perennial sectionsGalium, Leiogalium, andLeptogalium as well as the annual (and possibly polyphyletic) sect.Kolgyda.     

A MOLECULAR APPROACH TO THE CIRCUMSCRIPTION AND EVALUATION OF SOME GENERA SEGREGATED FROMPARMELIAS. LAT.

New sequences have been produced of the ITS rDNA region of twenty-nine species ofParmeliaceae, and analysed by neighbour-joining maximum likelihood distance analysis, and maximum parsimony analysis. Twelve monophyletic groups have been identified, most of which correspond to proposed generic segregated fromParmelias. lat.ParmeliaandParmelina,Melanelia, andPuncteliaappear as independent monophyletic groups; the type species of the two latter genera were, however, not included in the analysis. The parsimony analysis does not supportXanthoparmeliaas a monophyletic group separate fromNeofuscelia, andRimelia reticulatais nested withinParmotrema. Parmelinopsis horrescensis more closely related toHypotrachyna revolutathan toParmelina. Genetic distance values suggest thatFlavoparmelia caperatais closer toParmotremathan to other taxa included, and thatPlatismatia glaucaandHypogymnia tubulosaare closer toParmelias. lat. than to thePhysciaceae. However, there is no conclusive support for any of the latter groupings in the parsimony analysis. We conclude that the ITS region contains valuable information for studying generic delimitations within the familyParmeliaceae, but our study suggests that this region will not conclusively resolve within-family relationships in this group.     

Restriction enzyme analysis of the chloroplast and nuclear 45s ribosomal DNA ofAllium sectionsCepa andPhyllodolon (Alliaceae)

Estimates of the phylogenetic relationships among cultivated and wildAllium species would benefit from identification of molecular characters. Restriction enzyme analysis of the chloroplast DNA (cpDNA) of the bulb onion (Allium cepa), Japanese bunching onion (A. fistulosum), wildAllium species in sect.Cepa andPhyllodolon, and the outgroupsA. ampeloprasum andA. tuberosum detected 39 polymorphisms.Allium cepa andA. vavilovii were identical for all characters. Cladistic analysis generated three most-parsimoniousWagner trees of 44 steps differing only in a zero-length branch.Allium fistulosum andA. altaicum (sect.Phyllodolon) comprised a monophyletic lineage separated from theA. cepa andA. vavilovii of sect.Cepa. The unresolved node was composed ofA. galanthum, A. roylei, and the lineage containingA. cepa, A. vavilovii, A. fistulosum, andA. altaicum. The clade containingA. altaicum, A. cepa, A. fistulosum, A. galanthum, A. roylei, andA. vavilovii remained resolved for strict consensus ofWagner trees of 48 steps or less.Allium pskemense andA. oschaninii were increasingly distant.Allium oschaninii has been proposed as the progenitor of the bulb onion, but was more closely related to the common progenitor of all species in sect.Cepa andPhyllodolon. Phylogenies estimated from cpDNA characters usingDollo parsimony resulted in a single most-parsimonious tree of 46 steps and agreed with phylogenies based onWagner parsimony. Polymorphic restriction enzyme sites in the 45s ribosomal DNA were not used to estimate phylogenies because of uncertain homologies, but are useful for identifying interspecific hybrids. The maternal phylogenies estimated in this study help to distinguish wildAllium species closely related to the bulb onion. Although not in agreement with classifications based on morphology, the phylogenies closely reflected crossability among species in sect.Cepa andPhyllodolon.     

Chloroplast DNA variation and phylogeny of theRanunculaceae

Restriction site mapping of chloroplast DNA from 31 species representing 26 genera of theRanunculaceae was performed using eleven restriction endonucleases. The chloroplast genome varies in length from approximately 152 to 160 kb. Length variants are frequent in theRanunculaceae and range from usually less than 300 bp to rarely 1.5 kb. The inverted repeat is extended into the large single copy (LSC) region by 4–4.5 kb inAnemone, Clematis, Clematopsis, Hepatica, Knowltonia, andPulsatilla. Several inversions are present in the LSC-region of the cpDNA in all these genera and inAdonis. The frequency of restriction site mutations varies within the chloroplast genome in theRanunculaceae between 4 and 32 mutations per kilobase, and is lowest in the inverted repeat and the regions containing the ATPase-genes and the genespsaA, psaB, psbA, rpoB, andrbcL. A total of 547 phylogenetically informative restriction sites was utilized in cladistic analyses of the family using Wagner, Dollo, and weighted parsimony. These three parsimony analyses result in different tree topologies. Four, six, and one equally most parsimonious trees were obtained with Wagner, Dollo, and weighted parsimony, respectively. The amount of support for the monophyletic groups was evaluated using bootstrapping and decay analysis. All three parsimony methods suggest thatHydrastis is the sister group to the remainder of theRanunculaceae, and that theAnemone-Clematis group, which shares several derived cpDNA rearrangements, is monophyletic. Only a few of the traditional groups in theRanunculaceae are supported by cpDNA restriction side data. Only Dollo parsimony provides support for the hypothesis thatThalictroideae andRanunculoideae are monophyletic.     

Morphological and molecular comparisons ofCampsis grandiflora andC. radicans (Bignoniaceae), an eastern Asian and eastern North American vicariad species pair

Morphological and molecular comparisons were made forCampsis grandiflora (Thunb.)K. Schumann (Bignoniaceae) from eastern Asia andC. radicans (L.)Seemann from eastern North America. Chloroplast DNA (cpDNA) variation was surveyed with 20 restriction endonucleases. The cpDNA divergence between the two vicariad species was 2.44%, which is the highest reported among North Temperate disjunct taxa and one of the highest reported for infrageneric taxa. Detailed morphological comparisons also suggest a high level of divergence. Cluster analyses based on 22 morphological characters and 39 OTUs revealed two distinct groups corresponding with the two species. The average taxonomic distance between the two species was 1.806. Analyses of variance (ANOVA) revealed that 12 of the 18 quantitative characters differed significantly ( 0.01) betweenC. grandiflora andC. radicans. Divergence time based on cpDNA data was estimated as 24.4 million years. The Bering land bridge hypothesis was favored over the North Atlantic land bridge hypothesis based on the estimated divergence time and the geological history of the North Temperate region. The high levels of morphological and cpDNA divergence are not consistent with morphological stasis, which has been proposed as a common mode of evolution for North Temperate disjunct taxa.     

Allonia decandra: Floral remains of the tribeHamamelideae (Hamamelidaceae) from Campanian strata of southeastern USA

A single flower, detached anthers with in situ pollen grains, and isolated seeds from Campanian strata (Upper Cretaceous) of Georgia, southeastern USA, document the presence of plants assignable toHamamelidaceae in the Upper Cretaceous. The fossil flower is actinomorphic, pentacyclic and pentamerous. Irregular sepals are preserved as lobes of the floral cup, and petals are narrow, with parallel margins. The androecium has two whorls of functional stamens. Anthers are tetrasporangiate, dehisce through two valves, and have strongly elongate connective protrusions which converge over the center of the flower. The organizational and architectural features of the fossil document its affinity within subtribeLoropetalinae (Hamamelideae, Hamamelidoideae). Cladistic phylogenetic analyses using parsimony were conducted to explore the relationships between the fossil flower and extant genera of the tribeHamamelideae. The strict consensus of the four most parsimonious trees showsHamamelideae andLoropetalinae as well-supported monophyletic taxa. The fossil flower is clearly included within theLoropetalinae, and is placed as sister taxon to the southeastern Asian genusMaingaya. The occurrence of fossils assignable toLoropetalinae during the Campanian documents the existence ofHamamelidaceae with a level of floral organization and character evolution equivalent to that of extant genera, early in the evolutionary history of the family.     

Interspecific hybridization inRibes

The genusRibes, 2n=16, consisting of over 150 shrubby species has been divided byRehder into 15 sections grouped into four subgenera. Data on interspecies crosses within and between these sections and subgenera made by previous workers and at East Malling are tabulated and discussed.Species within a section are morphologically similar and will usually cross, forming fertile hybrids; 33 such hybrids in 6 of the 15 sections are known. Inter-sectional and inter-subgeneric crosses between more unlike species often fail, but matur flowering plants have been obtained from crosses involving the following combinations: –Symphocalyx x Calobotrya, Symphocalyx x Eucoreosma, Calobotrya x Eucoreosma, Eucoreosma x Heritiera, Eucoreosma x Ribesia, Eugrossularia x Robsonia, Euberisia x Eugrossularia, Symphocalyx x Eugrossularia, Calobotrya x Eugrossularia, Eucoreosma x Eugrossularia, andRibesia x Eugrossularia. Of these, only the combinationsEugrossularia x Robsonia andCalobotrya x Eucoreosma show any fertility.On the basis of these results, it is suggested that a more natural classification ofRibes would be to retainRehder's subgeneraBerisia, Grossularia andGrossularioides, while creating from his sevenRibesia sections, six new subgenera, viz.Microsperma, Symphocalyx, Calobotrya (comprising the sectionsCalobotrya andEucoreosma), Cerophyllum, Heritiera, andRibesia. With this classification, in the light of present knowledge, all intra-sectional hybrids are fertile, intra-subgeneric hybrids at least partially fertile, and such inter-subgeneric hybrids as can be raised are sterile.     

Spatial distribution of cpDNA and mtDNA haplotypes in a hybrid zone betweenPinus pumila andP. parviflora var.pentaphylla (Pinaceae)

Pinus species exhibit paternal chloroplast inheritance and maternal mitochondrial inheritance. This independent inheritance of two cytoplasmic genomes provides an exceptional environment for discriminating female (seeds) and male (pollen) components of gene flow across hybridizing species. We obtained mitochondrial genetic markers diagnostic toP. parviflora var.pentaphylla andP. pumila by PCR amplification of the intron ofnad1 on mtDNA, and examined the spatial-distribution pattern of the mtDNA haplotypes in a hybrid zone betweenP. parviflora var.pentaphylla andP. pumila in the Tanigawa Mountains of Japan. These data, in conjunction with previous information on cpDNA haplotypes and needle morphology, revealed contrastive patterns of introgression of two cytoplasmic genomes. CpDNA introgression has occurred uni-directionally fromP. parviflora var.pentaphylla toP. pumila. Conversely, mtDNA introgression has occurred in the opposite direction, fromP. pumila toP. parviflora var.pentaphylla. Levels of introgression are roughly equivalent for cpDNA and mtDNA. The contrastive spatial distribution pattern of cpDNA and mtDNA haplotypes could be caused by differential movement of seeds and pollen for interspecific genetic exchange.     

Ribosomal DNA evidence for the diversification of Tropaeolum sect. Chilensia (Tropaeolaceae)

Maximum parsimony and Bayesian likelihood analysis of ribosomal DNA internal transcribed spacer (ITS) sequences from 55 samples representing 25 species, subspecies, and/or hybrids of Tropaeolum sect. Chilensia yielded a tree with a large proportion of well-supported nodes at the interspecific and intersubspecific level. However, the tree shows samples from two species, T.azureum and T. brachyceras, arising in two different positions. Samples representing subspecies of T. hookerianum and T. leptophyllum suggest that these species are polyphyletic. The data corroborate evidence for hybridization between T. brachyceras and T. tricolor. Consideration of interfertility data, past and present Chilean ecology, and empirical evidence for the behavior of phenotypic and genotypic characters in known hybrids suggest a high likelihood that reticulate evolution has played a role in the diversification of T. sect. Chilensia. This reticulate evolution may explain the discordance between the ITS tree and the conventional taxonomy. High divergence in ITS sequences between T. sect. Chilensia and other members of Tropaeolum prohibits reliable outgroup-rooting, but midpoint rooting places the root at a partition comprising taxa whose distribution conforms to a relictual eastern-western South American disjunction described for other taxa. Within the Chilean taxa, the analysis suggests that biogeographic diversification has been from the mesophytic southern habitats northward to central mediterranean and northern arid zones.     

The phylogeny ofPapaver s. l. (Papaveraceae): Polyphyly or monophyly?

An RFLP analysis of the chloroplast genetrnK of 32 species of the generaPapaver, Roemeria, Stylomecon, andMeconopsis leads to the following conclusions: (1) AsianMeconopsis consists of two distinct clades and is paraphyletic in relation toPapaver, Roemeria, Stylomecon, and the W EuropeanMeconopsis cambrica. (2) Sister group relationships ofRoemeria toPapaver sect.Argemonidium and ofStylomecon toPapaver californicum are well-supported. (3)Meconopsis cambrica is nested withinPapaver (incl.Roemeria andStylomecon). The consideration of morphology, geographical distribution and ecology leads to the conclusion thatM. cambrica is best regarded as a member ofMeconopsis, and thatPapaver arose polyphyletically from within a paraphyleticMeconopsis in response to Tertiary climatic aridification. — The removal ofM. cambrica from the taxon matrix is discussed. It is concluded that this experiment illuminates the importance of critical taxon sampling, and shows that at least potentially the assessment of taxa as mono-, para-, or polyphyletic may characterize their present status only and need not reflect their phylogenetic history.     

Evolution alpiner Populationen vonEuphrasia (Scrophulariaceae): Chromosomenzählungen an diploiden und polyploiden Sippen aus den Ostalpen

Chromosome counts are reported for several E. Alpine taxa ofEuphrasia sect.Euphrasia. First records of diploidy for small-flowered taxa are 2n = 22 forE. inopinata andE. sinuata, related toE. minima (4 x). Aberrant E. AlpineE. hirtella is 2 x, just as the typical W. Alpine populations of this species. Tetraploidy, 2n = 44, has been found inE. pumila, close toE. stricta (also 4 x). The limitation of ploidy levels within sect.Euphrasia to 2 x and 4 x on the chromosome base number x = 11 is confirmed.

     

Phylogenetic relationships and infrageneric classification of Epidendrum subgenus Amphiglottium (Laeliinae, Orchidaceae)

Epidendrum L. is the largest genus of Orchidaceae in the Neotropical region; it has an impressive morphological diversification, which imposes difficulties in delimitation of both infrageneric and interspecific boundaries. In this study, we review infrageneric boundaries within the subgenus Amphiglottium and try to contribute to the understanding of morphological diversification and taxa delimitation within this group. We tested the monophyly of the subgenus Amphiglottium sect. Amphiglottium, expanding previous phylogenetic investigations and reevaluated previous infrageneric classifications proposed. Sequence data from the trnL-trnF region were analyzed with both parsimony and maximum likelihood criteria. AFLP markers were also obtained and analyzed with phylogenetic and principal coordinate analyses. Additionally, we obtained chromosome numbers for representative species within the group. The results strengthen the monophyly of the subgenus Amphiglottium but do not support the current classification system proposed by previous authors. Only section Tuberculata comprises a well-supported monophyletic group, with sections Carinata and Integra not supported. Instead of morphology, biogeographical and ecological patterns are reflected in the phylogenetic signal in this group. This study also confirms the large variability of chromosome numbers for the subgenus Amphiglottium (numbers ranging from 2n = 24 to 2n = 240), suggesting that polyploidy and hybridization are probably important mechanisms of speciation within the group.     

Phenetic studies in Nuphar Sm. (Nymphaeaceae):variation in sect. Nuphar

Previous taxonomic assessments of the hydrophytic genus Nuphar Sm. (Nymphaeaceae) have inadequately considered the range of morphological variation existing in the genus. A comprehensive statistical analysis of morphological features among the recognized taxa of Nuphar is presented here, first using 10 fruit characters to delimit the separation of two infrageneric groups of taxa, and secondly using 31 characters to quantify the morphological variation found within sect. Nuphar. Results from combined phenetic analyses provided empirical support for recognition of two infrageneric groups of species in the genus (largely by fruit, stigmatic disk margin, neck, and stigmatic disk size) and for separation of taxa within sect. Nuphar (by leaf size, and fruit disk and neck size). Statistical analyses demonstrate that extensive variation in ranges of character states exists among sect. Nuphar taxa. However, a suite of qualitative and quantitative characters can be used to recognize five species and three subspecies within this predominantly Old World assemblage.     

Intergeneric relationships ofLolium,Festuca, andVulpia (Poaceae) and their phylogeny

Morphological and seed protein analyses of 26 species of the generaLolium, Festuca andVulpia confirmed their close systematic affinities. Six inflorescence characters readily differentiatedFestuca fromLolium. Protein similarities betweenFestuca of sect.Bovinae and cross-pollinated species ofLolium, coupled with cytogenetic and crossability data, substantiate that they should be united into one genus.Vulpia had phenetic similarities with sect.Scariosae, Montanae andOvinae ofFestuca. Lolium, Festuca, andVulpia are most likely derived from a common ancestral form which was close toFestuca pratensis andLolium perenne.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

Phylogenetic relationships of Serpulidae (Annelida: Polychaeta) based on 18S rDNA sequence data, and implications for opercular evolution

Phylogenetic relationships of (19) serpulid taxa (including Spirorbinae) were reconstructed based on 18S rRNA gene sequence data. Maximum likelihood, Bayesian inference, and maximum parsimony methods were used in phylogenetic reconstruction. Regardless of the method used, monophyly of Serpulidae is confirmed and four monophyletic, well-supported major clades are recovered: the Spirorbinae and three groups hitherto referred to as the Protula-, Serpula-, and Pomatoceros-group. Contrary to the taxonomic literature and the hypothesis of opercular evolution, the Protula-clade contains non-operculate (Protula, Salmacina) and operculate taxa both with pinnulate and non-pinnulate peduncle (Filograna vs. Vermiliopsis), and most likely is the sister group to Spirorbinae. Operculate Serpulinae and poorly or non-operculate Filograninae are paraphyletic. It is likely that lack of opercula in some serpulid genera is not a plesiomorphic character state, but reflects a special adaptation.     

Systematics ofNama (Hydrophyllaceae): Flavonoids and phyletic position of sect.Arachnoidea and sect.Cinerascentia

Eight flavonoids, four 6-oxygenated flavones, two methyl ethers of luteolin, apigenin 6,8-C-diglucoside and quercetin 3-O-glucoside, were isolated fromNama lobbii andN. rothrockii, sole members of sects.Arachnoidea andCinerascentia, respectively. Both taxa diverge markedly from other namas in morphology and chromosome number and their placement inNama has been questioned. The occurrence of 6-oxygenated flavones in these taxa adds to their already distinctive nature. Flavonoid evidence argues that both are more closely allied toEriodictyon than either is toNama.