Phylogenetic relationships of JapaneseAster (Asteraceae, Astereae) sensu lato based on chloroplast-DNA restriction site mutations

RFLPs of cpDNA were examined for 18 species ofAster, six species ofKalimeris, two species ofMiyamayomena and one species and one variety ofHeteropappus from Japan, using 16 restriction endonucleases. Approximately 275 restriction sites were surveyed, and a total of 74 restriction site mutations was detected, and 31 of these were phylogenetically informative. Sixteen most parsimonious trees constructed from Wagner parsimony analysis indicated the polyphyly ofKalimeris andMiyamayomena sensu Kitamura;K. miqueliana belongs to a different clade from the remaining species ofKalimeris, and two species ofMiyamayomena did not make a single clade. This result suggests that the shortening or loss of pappus have happened parallelly in different evolutionary lineages. We must be careful to assess the pappus character in taxonomy and phylogeny, and it is desirable to examine their phylogenetic relationships using a molecular data.     

Chloroplast DNA restriction site data support a narrowed interpretation ofEupatorium (Asteraceae)

Chloroplast DNA (cpDNA) restriction site analysis was used to assess relationships among samples of Eupatorieae from eastern North America. A total of 270 cpDNA variants was recorded from 35 species using 13 restriction enzymes. Phylogenetic analysis usingGalinsoga, Flaveria, andHelianthinae as outgroups indicated that samples ofAgeratina, Hofmeisteria, Mikania, andStevia, each of which have relatively high base chromosome numbers, formed an unresolved basal polytomy. The remaining samples examined formed a well-supported clade, within which there was a split betweenBrickellia, which hasx = 9, and a number of genera withx = 10. Within thex = 10 clade, there was an unresolved trichotomy, with one group ofAgeratum, Conoclinium, Fleischmannia, andCritonia, a second ofLiatris andTrilisa, and a third ofEupatorium s.s. Within theEupatorium s.s. clade there were three further clades, withE. sect.Verticillata diverging first, and a subsequent split between species originating from North America and those from Asia. The cpDNA restriction site data provided support for a relatively narrow interpretation ofEupatorium, and indicated that a high chromosome base number is plesiomorphic for Eupatorieae.     

A molecular systematic study ofCathaya, a relic genus of thePinaceae in China

The systematic position ofCathaya, a relic genus of thePinaceae, was discussed based on therbcL gene sequence. The sequence data were analysed with PAUP and MEGA programs. The great genetic distance value betweenCathaya and any other genus of thePinaceae showed thatCathaya was a distinct and isolated genus. The most parsimonious Fitch tree and neighbor-joining tree showed thatCathaya was distantly related to the clade comprisingAbies, Keteleeria, Pseudolarix andTsuga, and a sister group relationship betweenCathaya andPinus was weakly supported.Pseudotsuga is closely related toLarix. In theAbies-Keteleeria-Pseudolarix-Tsuga clade,Abies has a close relationship toKeteleeria whilePseudolarix is relatively closely related toTsuga.     

Systematic overview of Krigia (Asteraceae-Lactuceae)

Cytological and morphological variation among Krigia species is examined. Krigia exhibits a broad range of chromosome numbers including n = 4, 5, 6, 9, 10, 15, and 30. Section Krigia is characterized by reflexed phyllaries and a base chromosome number of x = 5, while section Cymbia is characterized by erect phyllaries and chromosome numbers of n = 4, 6, and 9. The micromorphological characteristics of achenes, pappus, styles, corolla, pollen, stomata, and trichomes are documented using scanning electron microscopy. Among these, the pappus shows the greatest diversity and three major types are identified: 1) a pappus of many bristles and scales, as in K. dandelion, K. montana, and K. biflora; 2) a pappus of five bristles and five scales, as in K. virginica and K. occidentalis; and 3) an absent or highly reduced pappus, as in the K. cespitosa complex and K. wrightii. Thirty-five cytological and morphological characters are subjected to phylogenetic analyses. The two sections, Krigia and Cymbia, form monophyletic lineages. Within section Krigia, the annual species, K. virginica, forms an independent clade, while the perennial species, K. dandelion, K. biflora, and K. montana, form a monophyletic clade. Krigia montana and K. biflora are identified as sister species and a hybrid between these has been identified. The hybrid is more similar morphologically to K. montana than K. biflora. Within section Cymbia, phylogenetic relationships among K. wrightii, K. occidentalis, and K. cespitosa are uncertain. Nine taxa of Krigia are herein recognized: K. dandelion, K. biflora, K. biflora var. viridis (comb. nov.), K. montana, K. virginica, K. wrightii (comb. nov.), K. occidentalis, K. cespitosa, and K. cespitosa f. gracilis (comb. nov.). Phylogenetic relationships among 12 taxa of Krigia species are compared using various combinations of morphology, chloroplast DNA, and nuclear ribosomal DNA data. Tree topologies from different combinations of data are largely congruent. The most resolved phylogenetic tree is obtained using the combined data from morphology, chloroplast DNA, and nuclear ribosomal DNA.     

Molecular phylogenetics of the tribeInuleae s. str.(Asteraceae), based on ITS sequences of nuclear ribosomal DNA

The sequences of the internal transcribed spacer (ITS) region of 18S–26S nrDNA for a sample of 16 taxa from theInuleae s. str. and two outgroup taxa are analysed cladistically with PAUP. A consensus tree of the four most parsimonious cladograms is presented. Three different tests of cladogram stability are conducted (Bremer support, parsimony jackknifing and bootstrapping); all tests indicate a high degree of support for the basal nodes of the tree. The ITS phylogeny of the tribe is compared with previous hypotheses based on morphological data. The position ofAnisopappus as sister group to the rest of the tribe is supported by the molecular data, but the proposed subdivision ofInuleae s. str. into a paleate grade group and an epaleate clade is not. The interpretation of the character evolution of, e.g. receptacular paleae and pappus features within the tribe is discussed.     

Phylogeny and biosystematics ofPseudomonotes (Dipterocarpaceae) based on molecular and morphological data

The placement of a recently discovered South American monotypic genus,Pseudomonotes tropenbosii, in subfam.Monotoideae (Dipterocarpaceae) extends the geographical range of the subfamily from Africa to the Neotropics. Although morphological and anatomical evidence suggest similarities betweenPseudomonotes andMonotes, the close alliance of these two genera was questionable due to their disjunct distribution and a lack of phylogenetic analysis. In the present study, we reconstructed the phylogeny ofPseudomonotes and other putatively related taxa usingrbcL sequence data. The analysis ofrbcL sequences of 20 taxa belonging to 15 genera and eight families recovered a single most parsimonious tree. The genusSarcolaena (Sarcolaenaceae) formed a clade sister to the monophyleticDipterocarpaceae clade.Monotes andPseudomonotes formed a strongly supported group, sister to the monophyletic clade withPakaraimaea and the remaining Asiatic dipterocarp species studied. The study strongly supports the placement ofPseudomonotes within subfam.Monotoideae of theDipterocarpaceae.     

Evolution of thedec-1 eggshell locus inDrosophila. I. Restriction site mapping and limited sequence comparison in themelanogaster species subgroup

Summary We have analyzed 18 kb of DNA in and upstream of thedefective chorion-1 (dec-1) locus of the eight known species of themelanogaster species subgroup ofDrosophila. The restriction maps ofD. simulans, D. mauritiana, D. sechellia, D. erecta, andD. orena are shown to have basically the restriction map ofD. melanogaster, whereas the maps ofD. teissieri andD. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65–200 bp) is found in a repeated sequence of the central transcribed region ofD. melanogaster, D. simulans, andD. erecta. Restriction site mapping indicated that thedec-1 gene is highly conserved in themelanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5 translated region. The 5 flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within themelanogaster species subgroup except that theerecta-orena pair is placed closer to themelanogaster complex than toD. teissieri andD. yakuba.     

6-Phosphogluconate Dehydrogenase (6PGD) Gene Duplication in Kalimeris (Asteraceae)

Abstract The genus Kalimeris with a diagnostic character of short or inconspicuous pappus consists of two sections, Asteromoea and Cordifolium. As a result of 6PGD isozyme analysis, sect, Asteromoea, including 2 × and poly-ploid taxa from 5 × to 8 ×, show similar cytosolic isozyme multiplicity and share a monomorphic locus. The data suggest that gene duplication of polyploid members was derived from a common ancestor. K. miqueliana, belonging to sect. Cordifolium. also possessed a gene duplication in 6PGD, though significant differences were detected in electrophoretic mobility between the sections. The occurrence of gene duplication in East Asian diploid Astereae leaves intact the validity of the allopolyploid-origin hypothesis of n= 9, which was rejected by Gottlieb (1981a) in American Astereae.     

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.     

Taxonomy and distribution ofPresbytis melalophos group in Sumatera,Indonesia

Taxonomy of thePresbytis melalophos group in Sumatera has been based solely on the distinction in the pelage coloration and has been a subject of controversy. In the present study, extensive field observations were undertaken. Three species, i. e.P. melalophos, P. thomasi, andP. femoralis, are recognized in Sumatera based on the cranial morphology, pelage coloration, and vocalization. Subspecies of each species are revised, a new classification is proposed, and a new subspecies,Presbytis melalophos bicolor, is described. A detailed distribution map of species and subspecies is presented. No sympatry occurs between the species. Finally, a cladistic analysis is presented for the three species, based on the cranial characters; the branching sequence is first between theP. melalophos clade and theP. femoralis- P. thomasi clade and second between theP. femoralis clade and theP. thomasi clade.     

A phylogenetic analysis ofPanax (Araliaceae): Integrating cpDNA restriction site and nuclear rDNA ITS sequence data

A phylogenetic analysis ofPanax was performed using restriction site variations of eight PCR-amplified chloroplast regions. Twenty populations were examined, representing 13 of the 14 species ofPanax. Aralia cordata was used as the outgroup. The 11 restriction endonucleases produced a total of 105 restriction sites and length variations from the large single-copy region of cpDNA. Forty restriction variations are polymorphic. The cpDNA tree is largely congruent with the nuclear ribosomal ITS phylogeny. Similar to the ITS tree, the cpDNA dataset suggests the following relationships: (1)P. trifolius from eastern North America is sister to the clade consisting of all otherPanax species; (2)P. ginseng andP. japonicus from eastern Asia form a clade withP. quinquefolius from eastern North America; (3) the HimalayanP. pseudoginseng is most closely related toP. stipuleanatus of southwestern China; and (4) the medicinally importantP. notoginseng forms a clade with the closely relatedP. bipinnatifidus, P. ginseng, P. japonicus, P. major, P. quinquefolius, P. sinensis, P. wangianus, andP. zingiberensis. Two biogeographic disjunctions are detectable withinPanax. One is the connection of the eastern North AmericanP. trifolius with the rest ofPanax species. The other is the more recent disjunction between the North AmericanP. quinquefolius and the eastern AsianP. ginseng andP. japonicus. The active orogenies caused by the collision of the Indian Plate with Asia may have facilitated the diversification ofPanax taxa in Asia in the late Tertiary.     

Evolution of flower shape inVeroniceae (Scrophulariaceae)

Floral evolution in the tribeVeroniceae was examined using phylogenetic analysis combining 24 adult morphology and chromosome number characters with 22 qualitative and quantitative floral development characters. Taxa sampled included nine species ofVeroniceae and as an outgroup one species each ofDigitaleae andVerbasceae. Veronica, Besseya, andSynthyris formed one clade, subtended byPseudolysimachion and then by theHebe group;Veronicastrum orWulfenia represent the basal-most branch of the tribe. The ancestral flowers of theVeroniceae may have been small with moderately short corolla tubes and lobes; long corolla tubes arose four times in the tribe and large corolla lobes twice.     

Taxonomy and phylogeny of the tribePlucheeae (Asteraceae)

The tribePlucheeae (Benth.)A. Anderb., has been analysed cladistically by means of a computerized parsimony program (Hennig 86), using theArctotideae as outgroup. The results of the analysis are presented in a consensus tree and one cladogram. Four major monophyletic subgroups can be recognized: TheColeocoma group (3 genera), thePterocaulon group (3 genera), theLaggera group (6 genera), and thePluchea group (12 genera). All recognized genera are described and most genera are supplied with taxonomical notes including comments on their taxonomic status. Genera such asBlumea, Pluchea, andEpaltes are demonstrated to be unnatural assemblages.Monarrhenus andTessaria are both closely related to thePluchea complex. The old generic nameLitogyne Harv. has been taken up for one species ofEpaltes, the genusRhodogeron is reduced to a synonym ofSachsia, and the following new combinations are made;Litogyne gariepina (DC.)A. Anderb., andSachsia coronopifolia (Griseb.)A. Anderb.     

Relationships in theAcanthaceae and related families as suggested by cladistic analysis ofrbcL nucleotide sequences

A parsimony analysis of DNA sequences of the chloroplast-encoded generbcL from twelve members of theAcanthaceae s.l., including members of the sometimes segregateThunbergioideae andNelsonioideae, and other families in theBignoniales sensuThorne (1992) is presented. The results largely agree with the classification of theAcanthaceae presented byBremekamp (1965) andThorne (1992) and supportNelsonioideae as a sister group to the rest of theAcanthaceae. Thunbergioideae are placed as a sister toAcanthaceae s.str.Acanthus andAphelandra, both representatives ofAcanthoideae, form a sister group toRuellioideae. An analysis of branch support found that many branches throughout theBignoniales are weakly upheld. This points to the need for further studies in the group using more sequences ofrbcL as well as other data. None of the families ofBignoniales as presently circumscribed (includingAcanthaceae s.l.) were strongly supported, although the larger clade containing the families of theBignoniales was robust.     

Four additive genes determining pappus part numbers inMicroseris annual hybrid C34 (Asteraceae/Lactuceae)

Microseris strain C34 is a hybrid between the Chilean speciesM. pygmaea (10 pappus parts) and the CalifornianM. bigelovii (5 pappus parts). The F1 specimen had from 5 to 10 pappus parts per achene with an average of 6. F2, F3 and F4 plants derived from this hybrid by spontaneous selfing show segregation for the average number of pappus parts. Four segregating unlinked genes could be demonstrated, each with an allele determining 5 pappus parts from thebigelovii parent, one with an allele determining 10 pappus parts, three with null alleles from thepygmaea parent. The expected average pappus part number is the arithmetic mean of the 5- and 10-determining factors. Considerable environmental and developmental influences, both random noise and systematic shifts, could be demonstrated to influence the phenotypic expression. The parallel hybrid strain B87 has two 10-alleles rather than one in itspygmaea genome. The evolution of the pappus part genes ofM. pygmaea from those of abigelovii-like ancestor seems to demand the concerted (non-independent) mutation of at least two genes.     

Phylogenetic relationships and generic delimitation of Eurasian Aster (Asteraceae: Astereae) inferred from ITS, ETS and trnL-F sequence data

Background and Aims

The classification and phylogeny of Eurasian (EA) Aster (Asterinae, Astereae, Asteraceae) remain poorly resolved. Some taxonomists adopt a broad definition of EA Aster, whereas others favour a narrow generic concept. The present study aims to delimit EA Aster sensu stricto (s.s.), elucidate the phylogenetic relationships of EA Aster s.s. and segregate genera.

Methods

The internal and external transcribed spacers of nuclear ribosomal DNA and the plastid DNA trnL-F region were used to reconstruct the phylogeny of EA Aster through maximum parsimony and Bayesian analyses.

Key Results

The analyses strongly support an Aster clade including the genera Sheareria, Rhynchospermum, Kalimeris (excluding Kalimeris longipetiolata), Heteropappus, Miyamayomena, Turczaninowia, Rhinactinidia, eastern Asian Doellingeria, Asterothamnus and Arctogeron. Many well-recognized species of Chinese Aster s.s. lie outside of the Aster clade.

Conclusions

The results reveal that EA Aster s.s. is both paraphyletic and polyphyletic. Sheareria, Rhynchospermum, Kalimeris (excluding K. longipetiolata), Heteropappus, Miyamayomena, Turczaninowia, Rhinactinidia, eastern Asian Doellingeria, Asterothamnus and Arctogeron should be included in Aster, whereas many species of Chinese Aster s.s. should be excluded. The recircumscribed Aster should be divided into two subgenera and nine sections. Kalimeris longipetiolata, Aster batangensis, A. ser. Albescentes, A. series Hersileoides, a two-species group composed of A. senecioides and A. fuscescens, and a six-species group including A. asteroides, should be elevated to generic level. With the Aster clade, they belong to the Australasian lineages. The generic status of Callistephus should be maintained. Whether Galatella (including Crinitina) and Tripolium should remain as genera or be merged into a single genus remains to be determined. In addition, the taxonomic status of A. auriculatus and the A. pycnophyllus–A. panduratus clade remains unresolved, and the systematic position of some segregates of EA Aster requires further study.     

New classification of liverworts based on molecular and morphological data

Complete sequences for the 18S-rRNA gene of 22 bryophytes (12 completely new) were determined and used to construct phylogenetic trees. The evaluation of sequence data according to the maximum parsimony principle (PAUP 3.1.1) and the neighbor-joining method (MEGA) results in similar phylogenetic trees in which theBryopsida appear as a sister group to theJungermanniopsida, and both together as a sister group to theMarchantiopsida. Among theMarchantiopsida, theSphaerocarpales diverge early as a separate clade. TheMetzgeriales andJungermanniales are monophyletic. They belong to one clade and cannot be separated by either method of evaluation.     

Implications ofrbcL sequence data for higher order relationships of theLoasaceae and the anomalous aquatic plantHydrostachys (Hydrostachyaceae)

Subclass and ordinal relationships ofLoasaceae, a small predominately New World family, are examined usingrbcL sequence data. Sequences were examined for eight of the fifteen genera of theLoasaceae and the morphologically anomalous aquatic genusHydrostachys (Hydrostachyaceae). Parsimony analyses of these sequences, combined with previously publishedrcbL data, indicate thatLoasaceae belong in theCornales, and are the sister group ofHydrangeaceae. This agrees with phylogenies based on chloroplast DNA inverted repeat restriction site, morphological and chemical data. TherbcL trees support the monophyly of theLoasaceae and most generic relationships correspond to current subfamily divisions. TherbcL phylogeny also provides the first suggestion thatHydrostachys is allied with theHydrangeaceae in theCornales.     

Chloroplast DNA restriction site mapping and the phylogeny ofRanunculus (Ranunculaceae)

A chloroplast DNA restriction site map forRanunculus sceleratus (Ranunculaceae) was constructed using 14 restriction endonucleases. The total size of the chloroplast genome is 152.4kb. No inversions were detected relative to the tobacco chloroplast DNA. Cladistic analyses of chloroplast DNA restriction site polymorphism were employed in order to elucidate the phylogeny among 76 species of the genusRanunculus in a wide sense and one species ofTrautvetteria. A total of 341 informative restriction site changes were detected. Parsimony jackknifing, bootstrapping and decay analysis were undertaken in order to evaluate the amount of support for the monophyletic groups. The results suggest that the analysed species ofRanunculus are divisible into two main clades. Only few of the traditional sections and subgenera ofRanunculus are monophyletic. The genusTrautvetteria is nested within a clade comprising, e.g.Ranunculus cymbalaria, R. andersonii, R. lapponicus andR. ficaria. SubgenusBatrachium lies within a larger clade containing, e.g.R. sceleratus andR. hyperboreus. Contractions of the inverted repeat due to parallel deletions of 200–300 bp close to the J_SB have occurred in many clades and the phylogenetic distribution of this size reduction was mapped among the species.     

Relationships, circumscription, and biogeography of Arcytophyllum (Rubiaceae) based on evidence from cpDNA

A cladistic analysis was performed using nucleotide sequence variation in therps16 intron and thetrmL-F region (plastid DNA).Arcytophyllum belongs in a subclade of the tribe Spermacoceae (s.l.) together with the American species presently classified in the generaHedyotis andHoustonia. This subclade is morphologically characterized by cymbiform seeds.Arcytophyllum is the sister group of all AmericanHedyotis andHoustonia and it is suggeste that these latter would be most conveniently treated as a single genus, the correct name of which would beHoustonia.Arcytophyllum should be circumscribed such that it excludesA. serpyllaceum, which is not a member of theArcytophyllum-Houstonia clade but more closely related toBouvardia. The phylogeny that was reconstructed suggests that the ancestral area of theArcytophyllum-Houstonia clade is the South American tectonic plate.