rbcL sequences support exclusion ofRetzia,Desfontainia, andNicodemia from theGentianales

The taxonomic positions ofRetzia, Desfontainia, andNicodemia have been much discussed, and all three genera have been included inLoganiaceae (Gentianales). We have made a cladistic analysis ofrbcL gene sequences to determine the relationships of these taxa toGentianales. Four newrbcL sequences are presented; i.e., ofRetzia, Desfontainia, Diervilla (Caprifoliaceae), andEuthystachys (Stilbaceae). Our results show thatRetzia, Desfontainia, andNicodemia are not closely related toLoganiaceae or theGentianales. Retzia is most closely related toEuthystachys and is better included inStilbaceae. The positions ofDesfontainia andNicodemia are not settled, butDesfontainia shows affinity for theDipsacales s.l. andNicodemia for theLamiales s.l.     

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.     

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.     

Ovules and seeds ofDirachma socotrana (Dirachmaceae)

Dirachma has a bitegmic, crassinucellate and anatropous ovule with a single median provascular tegumentary bundle. The seed coat is characterized by an exotesta and an endotegmic pigment layer. Although the fruit ofDirachma superficially resembles that of theGeraniaceae s. str., the characters of ovule and seed do not support a relationship with that family. Also a relationship withBarbeyaceae, as suggested by recentrbcL studies, is not supported by seed anatomical characters. The true relationships ofDirachma are difficult to assess on the basis of ovule and seed characters alone. TheRhamnaceae may be a closer relative.     

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.     

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.     

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.     

Phylogenetic analysis ofUlmaceae

A phylogenetic analysis of theUlmaceae, Cannabaceae, Barbeyaceae, andBroussonetia of theMoraceae produced nine equally parsimonious trees with 127 steps. TheUlmoideae (Ulmaceae, sensuGrudzinskaya) are a monophyletic group and distinct from theCeltidoideae. The genusAmpelocera occupies an isolated taxonomic position among the celtidoids. The similarity ofAmpelocera to the fossil celtidoid flowerEoceltis of North America suggests thatAmpelocera posesses an archaic suite of characters, and occupies a primitive position among the celtidoids, theCannabaceae and theMoraceae. The relationships among the other celtidoid taxa,Cannabaceae, andBroussonetia are problematic. TheCannabaceae andBroussonetia of theMoraceae are nested within the celtidoids suggesting that this is a paraphyletic group. The close, but unresolved, relationship of the celtidoids to theMoraceae andCannabaceae observed in this analysis, and the appearance of the celtidoids in the fossil record prior to the ulmoids suggests that the evolutionary relationship of the ulmoids and celtidoids may be more distant than current taxonomic treatments reflect.     

Altered expression of the<Emphasis Type="Italic"> Arabidopsis</Emphasis> ortholog of<Emphasis Type="Italic"> DCL</Emphasis> affects normal plant development

The DCL (defective chloroplasts and leaves) gene of tomato (Lycopersicon esculentum Mill.) is required for chloroplast development, palisade cell morphogenesis, and embryogenesis. Previous work suggested that DCL protein is involved in 4.5S rRNA processing. The Arabidopsis thaliana (L.) Heynh. genome contains five sequences encoding for DCL-related proteins. In this paper, we investigate the function of AtDCL protein, which shows the highest amino acid sequence similarity with tomato DCL. AtDCL mRNA was expressed in all tissues examined and a fusion between AtDCL and green fluorescent protein (GFP) was sufficient to target GFP to plastids in vivo, consistent with the localization of AtDCL to chloroplasts. In an effort to clarify the function of AtDCL, transgenic plants with altered expression of this gene were constructed. Deregulation of AtDCL gene expression caused multiple phenotypes such as chlorosis, sterile flowers and abnormal cotyledon development, suggesting that this gene is required in different organs. The processing of the 4.5S rRNA was significantly altered in these transgenic plants, indicating that AtDCL is involved in plastid rRNA maturation. These results suggest that AtDCL is the Arabidopsis ortholog of tomato DCL, and indicate that plastid function is required for normal plant development.Abbreviations DCL Defective chloroplasts and leaves - GFP Green fluorescent protein     

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.     

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.     

Hectorella: A member of the betalain-suborderChenopodiineae of the orderCentrospermae

Roots ofHectorella caespitosa Hook. f. were induced to produce a red pigment which was shown to be a betalain and not an anthocyanin. These data indicate thatHectorella belongs to theChenopodiineae, the betalain suborder of theCentrospermae, and excludes alignment with the anthocyanin family theCaryophyllaceae.     

Phylogenetic utility of the nuclear rDNA ITS region in subfamilyIxoroideae (Rubiaceae): Comparisons with cpDNArbcL 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.     

Phylogenetic relationships in theCampanulales based onrbcL sequences

Phylogenetic relationships within the angiosperm orderCampanulales were investigated by comparative sequencing of the chloroplast generbcL. CompleterbcL sequences were obtained for ten species in six families within the order. These data were analyzed along with previously publishedrbcL sequences from other taxa (for a total of 117 species) within the subclassAsteridae and outgroups, producing 32 equally parsimonious trees. A subset consisting of 44 of these taxa was then chosen and more rigorous analyses performed, resulting in four equally parsimonious trees. Results indicate that two major clades roughly corresponding to traditionally circumscribedAsterales andCampanulales exist as sister taxa. In particular, therbcL trees indicate thatSphenoclea is not a member ofCampanulales orAsterales, thatPentaphragma is more closely allied toAsterales thanCampanulales, that theCyphiaceae are not monophyletic, thatCampanulaceae andLobeliaceae are not sister taxa, and thatStylidiaceae are correctly placed withinCampanulales.     

Thehermit transposable element of the Australian sheep blowfly,Lucilia cuprina, belongs to thehAT family of transposable elements

We report the cloning ofhermit, a member of thehAT family of transposable elements from the genome of the Australian sheep blowfly,Lucilia cuprina. Hermit is 2716 bp long and is 49% homologous to the autonomoushobo element,HFL1, at the nucleic acid level.Hermit has 15 bp terminal inverted repeats that share 10 bp with the terminal inverted repeats ofHFL1. Conceptual translation reveals a 583 residue open reading frame (ORF) that is 64% similar and 42% identical to theHFL1 ORF. However, the sequence of thehermit element contains two frameshifts within the putative ORF, indication thathermit is an inactive element. Analysis ofL. cuprina strains from within and outside Australia suggested thathermit is present as a single copy in all the genomes analysed.     

The phylogenetic relationships ofByblis andRoridula (Byblidaceae-Roridulaceae) inferred from partial 18S ribosomal RNA sequences

The phylogenetic relationships of the angiosperm generaByblis andRoridula have been the subject of ongoing taxonomic controversy. Twenty-eight taxa of varying degrees of alleged relationship, including 3 members of theWinteraceae (as an outgroup), were investigated using partial sequences of 18S rRNA (small subunit) and also compared against the morphological data set fromHufford's (1992) cladistic treatment of 80 members of theRosidae-Asteridae. The morphological analysis placed the two genera in a clade with theSarraceniaceae in theCorniflorae-Asterid group as a sister taxon to anEricales-Hydrangeales clade. The 18S rRNA analysis supports the recently publishedrbcL DNA analysis ofAlbert & al. (1992), withRoridula joined to taxa in the lowerRosidae, butByblis joining instead to members of theAsteridae near theSolanaceae. Comparisons for congruence between the three analyses placeByblis in the higher Asterid group near theSolanaceae, andRoridula possibly nearer theSarraceniaceae andEricales. These results imply that the traditional morphological characters used to relate the two genera are possibly the result of convergence towards similar ecological and life-history strategies rather than synapomorphies.     

Therps16 intron and the phylogeny of theRubioideae (Rubiaceae)

The phylogeny of the subfamilyRubioideae (Rubiaceae) was estimated from sequence variation in therps16 intron (cpDNA) in 143 ingroup and 5 outgroup taxa. The analysis largely confirms a recent one based onrbcL sequences, but branch support is often much stronger. Three of the traditional subfamilies are supported,Rubioideae, Cinchonoideae s. str., andIxoroideae s. l. while there is no support forAntirheoideae. TheRubioideae are the sister group of all otherRubiaceae and comprise the tribesAnthospermeae, Coccocypseleae, Cruckshanksieae, Coussareeae, Gaertnereae, Hedyotideae, Knoxieae, Morindeae, Ophiorrhizeae, Paederieae, Pauridiantheae, Perameae, Psychotrieae, Rubieae, Spermacoceae, Theligoneae, andUrophylleae. TheHamelieae andHillieae belong to theCinchonoideae. Rachicallis andSiemensia should be transferred from theHedyotideae to theCinchonoideae. ThePauridiantheae, Urophylleae, Ophiorrhizeae, andRaritebe form the basalmost subclade of theRubioideae. The second basalmost clade consists of the generaLasianthus andPerama. The third basalmost clade consists of the tribesCoussareeae, Coccocypseleae andCruckshanksieae, and the generaDeclieuxia andHindsia. The tribesKnoxieae, Anthospermeae, Argostemmateae, Paederieae, Theligoneae, Rubieae, Hedyotideae, andSpermacoceae are members of one clade. TheKnoxieae are monophyletic ifOtiophora, Otomeria, andPentas are included. The tribeAnthospermeae is supported as monophyletic, but its subtribes are not. ThePaederieae, together withTheligonum, form a paraphyletic grade basal to theRubieae. TheHedyotideae, includingSchismatoclada, form a grade at the base of theSpermacoceae. TheGaertnereae are monophyletic and distinct from thePsychotrieae. TheMorindeae are monophyletic and includeDamnacanthus andMitchella. Schradera is the sister group of theMorindeae. ThePsychotrieae are monophyletic when theGaertnereae, Lasianthus, andDeclieuxia are excluded. The recognition of a subtribeHydnophytineae leaves the rest of thePsychotrieae paraphyletic.Psychotria is paraphyletic with respect to all other genera of the tribe. Approximately 50 genera are here classified for the first time based on molecular data.     

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.