Phylogenetic relationships within Chamaecrista sect. Xerocalyx (Leguminosae, Caesalpinioideae) inferred from the cpDNA trnE-trnT intergenic spacer and nrDNA ITS sequences

Chamaecrista belongs to subtribe Cassiinae (Caesalpinioideae), and it comprises over 330 species, divided into six sections. The section Xerocalyx has been subjected to a profound taxonomic shuffling over the years. Therefore, we conducted a phylogenetic analysis using a cpDNA trnE-trnT intergenic spacer and nrDNA ITS/5.8S sequences from Cassiinae taxa, in an attempt to elucidate the relationships within this section from Chamaecrista. The tree topology was congruent between the two data sets studied in which the monophyly of the genus Chamaecrista was strongly supported. Our analyses reinforce that new sectional boundaries must be defined in the Chamaecrista genus, especially the inclusion of sections Caliciopsis and Xerocalyx in sect. Chamaecrista, considered here paraphyletic. The section Xerocalyx was strongly supported as monophyletic; however, the current data did not show C. ramosa (microphyllous) and C. desvauxii (macrophyllous) and their respective varieties in distinct clades, suggesting that speciation events are still ongoing in these specimens.     

Phylogenetic relationships and biogeography of the genus Chondrostoma inferred from mitochondrial DNA sequences

A phylogeny of the species of the nase genus Chondrostoma was constructed from a complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise the current systematics of this group, and to infer a biogeographical model of the Mediterranean area during the Cenozoic period. We confirmed the monophyly of the genus Chondrostoma, and defined seven different lineages within it: Polylepis, Arcasii, Lemmingii, Toxostoma, Nasus, C. genei, and C. soetta. The separation of main lineages within Chondrostoma occurred in the Middle-Upper Miocene, approximately 11 million years ago, while the greatest species radiation took place in the Pliocene close to the time the current drainages system were created. It is unlikely that this genus experienced an extensive dispersal during the Messinian, in the Lago-Mare Phase. Given the level of current knowledge, a biogeographical model constructed on the basis of vicariant events seems more realistic than does a dispersalist model.     

A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences

The systematics of the mainly yellow flowered Gagea species complex (Liliaceae) has long been considered difficult because only a few phenotypic features within this genus and as a result of hypothesized interspecific hybridisation. A molecular phylogenetic study of seven Gagea species (G. bohemica, G. lutea, G. minima, G. pomeranica, G. pratenis, G. spathacea and G. villosa) from Germany has been undertaken, based on plastid DNA sequences (trnL(UAA)-trnF(GAA), psbA-trnH) and on the nuclear ribosomal internal transcribed spacer (ITS). Sequence divergence within the Gagea species ranges up to 15.5% for psbA-trnH, 22.0% for trnL-trnF and 23.7% for ITS (ITS1 + 5.8S rRNA + ITS2). Two subspecies of Gagea bohemica: G. bohemica subsp. saxatilis and G. bohemica subsp. bohemica are characterized by trnL-trnF data and morphological features. Analysis of the ITS region shows that G. pomeranica represents a hybrid of G. pratensis and G. lutea. Lloydia serotina was initially used as an outgroup species, but it was placed within the investigated Gagea species in the psbA-trnH and the trnL-trnF phylogenetic tree.     

Molecular phylogeny ofNothofagus (Nothofagaceae) based on theatpB-rbcL intergenic spacer of the chloroplast DNA

The genusNothofagus is distributed in the Southern Hemisphere from South America to Oceania, and its distribution has been assumed to be formed by continental drift by means of Gondwana break-up during the Mesozoic era. The phylogeny of the genus was elucidated by the sequences ofatpB-rbcL intergenic spacer of cpDNA for the better understanding of its evolution and biogeography. The phylogeny ofNothofagus corresponded completely to the pollen morphology which recognizes four pollen types in extant species, and agrees well with the taxonomic system of Hill and Read (1991) although there, the subgenusNothofagus showed in unresolved polytomy. The topology of the phylogenetic tree reveals that subgenusLophozonia was derived first, and thenFuscospora, Nothofagus andBrassospora. Species from South America and New Zealand were assigned to each cluster according to their pollen morphology. Therefore, diversification ofNothofagus should have already proceeded at the subgenus level before the completion of Gondwana break-up Tropical species distributed in New Guinea and New Caledonia whose evolutionary history has been controversial were revealed to be a derived group. All five New Caledonian species formed a monophyletic group with very few sequence divergences in the intergenic spacer of cpDNA, thus showing rapid adaptive radiation in the island. Evolutionary trends of several morphological traits ofNothofagus are discussed. The evolution of valve number of cupules, number of nuts per cupule, and habit of leaf-fall (evergreen or deciduous) which are diversified in the genus, were revealed as having occurred several times as the result of convergence.     

Phylogenetic relationships ofPolemoniaceae inferred from 18S ribosomal DNA sequences

Cladistic analyses of chloroplast DNA disagree with current classifications by placingPolemoniaceae near sympetalous families with two staminal whorls, includingFouquieriaceae andDiapensiaceae, rather than near sympetalous families with a single staminal whorl, such asHydrophyllaceae andConvolvulaceae. To explore further the affinities ofPolemoniaceae, we sequenced 18S ribosomal DNA for eight genera ofPolemoniaceae and 31 families representing a broadly definedAsteridae. The distribution of variation in these sequences suggest some sites are hypervariable and multiple hits at these sites have obscured much of the hierarchical structure present in the data. Nevertheless, parsimony, least-squares minimum evolution, and maximum likelihood methods all support a monophyleticPolemoniaceae that is placed nearFouquieriaceae, Diapensiaceae and related ericalean families.     

Phylogenetic relationships in the Crassulaceae inferred from chloroplast DNA restriction-site variation

A restriction-site analysis of chloroplast DNA from 44 species, representing 19 genera and all six subfamilies of the Crassulaceae was conducted using 12 restriction endonucleases. A total of 969 variable sites was detected, 608 of which were phylogenetically informative and used in parsimony analysis. Estimated values of nucleotide sequence divergence were used to construct a distance tree by the neighbor-joining method. Maximum sequence divergence in the family was ~7%. Different tree inference methods yielded only moderately different topologies. The amount of support for the monophyletic groups obtained in the Wagner parsimony analysis was evaluated by bootstrap and decay analysis. There is very strong support for a basal division of the family, which separates the monophyletic subfamily Crassuloideae from all other taxa. Four of the six traditionally recognized subfamilies are indicated to be polyphyletic. These include the Cotyledonoideae, Sempervivoideae, Sedoideae, and Echeverioideae. The Kalanchoideae and the genera Cotyledon and Adromischus exhibit low levels of cpDNA sequence divergence relative to one another, suggesting a relatively recent radiation. The genera Sedum and Rosularia are indicated to be polyphyletic. Sedum comprises sister taxa of most of the other genera of the family.     

Phylogenetic relationships in the genus Leonardoxa (Leguminosae: Caesalpinioideae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences

The African genus LEONARDOXA: (Leguminosae: Caesalpinioideae) comprises two Congolean species and a group of four mostly allopatric subspecies principally located in Cameroon and clustered together in the L. africana complex. LEONARDOXA: provides a good opportunity to investigate the evolutionary history of ant-plant mutualisms, as it exhibits various grades of ant-plant interactions from diffuse to obligate and symbiotic associations. We present in this paper the first molecular phylogenetic study of this genus. We sequenced both the chloroplast DNA trnL intron (677 aligned base pairs [bp]) and trnL-trnF intergene spacer (598 aligned bp). Inferred phylogenetic relationships suggested first that the genus is paraphyletic. The L. africana complex is clearly separated from the two Congolean species, and the integrity of the genus is thus in question. In the L. africana complex, our data showed a lack of congruence between clades suggested by morphological and chloroplast characters. This, and the low level of molecular divergence found between subspecies, suggests gene flow and introgressive events in the L. africana complex.     

Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences

SSU rDNA was sequenced from the lichenized fungiBunodophoron scrobiculatum andLeifidium tenerum (Sphaerophoraceae), andStereocaulon ramulosum andPilophorus acicularis (Stereocaulaceae) and analysed by maximum parsimony with 44 homologous ascomycete sequences in a cladistic study. A small insertion (c. 60 nt.) was found in the sequence ofLeifidium tenerum. Sphaerophoraceae constitutes a strongly supported monophyletic group which groups together withLecanora dispersa and theStereocaulaceae. Together withPorpidia crustulata, this larger group is a sistergroup to thePeltigerineae. This analysis thus supports theLecanorales as monophyletic, includingSphaerophoraceae and thePeltigerineae, but does not provide strong support for this monophyly. The analysis also suggests that the prototunicate ascus in theSphaerophoraceae is a reversion to the plesiomorphic state. Based on morphological, anatomical and chemical reasons,Sphaerophoraceae is proposed to belong to one of the groups presently included in the paraphyletic suborderCladoniineae within theLecanorales.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

Phylogenetic relationships ofMicrosphaera andErysiphe sectionErysiphe (powdery mildews) inferred from the rDNA ITS sequences

The genusMicrosphaera has been considered to be derived from sectionErysiphe of the genusErysiphe by a single event. Cleistothecial appendages are the most distinct difference between the two genera and have an important role for overwintering. To understand the phylogenetic relationship betweenErysiphe sectionErysiphe andMicrosphaera more precisely, phylogenetic trees were constructed using the nucleotide sequences of the rDNA ITS region from 11Erysiphe (sectionErysiphe) and 16Microsphaera taxa. The phylogenetic trees indicated the close relationship between the two genera. However, the generaErysiphe (sectionErysiphe) andMicrosphaera did not group into separate monophyletic lineages; instead, they formed several small clusters that were mixed together. This result suggests that the differentiations of the genera occurred two or more times independently. This also supports the idea that appendage morphology does not always accurately reflect the phylogeny of the powdery mildews because the morphology of appendages may evolve convergently under the selection pressure of their particular biotopes (host plants). Contribution No. 144 from the Laboratory of Plant Pathology, Mie University.     

The phylogenetic relationships of Cynoglottis (Boraginaceae- Boragineae) inferred from ITS, 5.8S and trnL sequences

A molecular phylogenetic analysis of Cynoglottis was performed to evaluate previous hypotheses based on non-molecular evidence concerning the position of this genus within Boraginaceae tribe Boragineae. ITS-5.8S and trnL_UAA sequences from the nuclear and chloroplast non-coding genomes were obtained for four Cynoglottis taxa and selected members of the related genera Anchusa, Anchusella, Gastrocotyle, Brunnera and Pentaglottis. Cynoglottis is monophyletic, but neither trnL nor ITS support a close relationship with Brunnera, unlike previously supposed on morphological grounds. Brunnera is, instead, related to the southwestern European monotypic genus Pentaglottis, with which it forms a basal clade. ITS-5.8S sequences show that Anchusa thessala, a southeastern European annual species of Anchusa subg. Buglossellum, is sister to Cynoglottis and that the two taxa form a clade which also includes the Balkan endemic Gastrocotyle macedonica. Species of Anchusa subg. Anchusa form a separate lineage with high bootstrap support, suggesting that this heterogeneous genus is paraphyletic with respect to Cynoglottis. ITS sequences also discriminate between the Balkan-Apenninic diploid C. barrelieri and the Anatolian tetraploid C. chetikiana, albeit with low support. The molecular results are discussed in the light of karyological, morphological and chorological aspects.This work has been supported by M.I.U.R. 40% 2003 and the University of Firenze.     

The genomic relationships among six wild perennial species of the genus Glycine subgenus Glycine Willd.

Summary Based on meiotic chromosome behavior in intra- and interspecific hybrids, genome symbols were assigned to the following diploid (2n=40) Glycine species: G. canescens = AA; G. clandestina- Intermediate pod (Ip)=A ₁ A ₁; G. clandestina-Short pod (Sp)=BB; G. latifolia = B ₁ B ₁; G. tabacina = B ₂ B ₂; G. cyrtoloba = CC; and G. tomentella = DD. Genome symbol GG was reserved for the soybean, G. max. At metaphaseI, loose chromosome associations were observed in completely sterile interspecific hybrids whose parents differed in their genomes, suggesting some chromosome homologies among species. Although G. clandestina-Sp, G. latifolia and G. tabacina are morphologically distinct species, they differ only by a paracentric inversion. Similar observations were recorded for G. canescens and G. clandestina-Ip. Evidence is presented that demonstrates that G. tabacina (2n=80) and G. tomentella (2n=78, 80) are allotetraploid species complexes. Hybrid weakness, sterility, seedling lethality and seed inviability were found in intra- and interspecific hybrids.This research was supported in part by the Illinois Agricultural Experiment Station and the U.S. Department of Agriculture (Special grant 82-CRSR-2-2007). Travel grants to collect Glycine germplasm were received from the Rockefeller Foundation, the Illinois Soybean Program Operating Board, the National Science Foundation (INT76-14753) and the International Board for Plant Genetic Resources     

Phylogenetic relationships of the genera Arthroderma and Nannizzia inferred from mitochondrial DNA analysis

The phylogenetic relationship of the genera Arthroderma and Nannizzia, was investigated by mitochondrial DNA analysis based on the restriction-fragment-length polymorphisms. Phylogenetic trees made on ten species. A. benhamiae, A. insingulare, A. quadrifidum, A. simii, A. vanbreuseghemii, N. fulva, N. grubyia, N. gypsea, N. incurvata and N. otae showed no definite distinctions between the genera Arthroderma and Nannizzia. These results support the conclusion of Weitzman et al. that the genera Arthroderma and Nannizzia are congeneric.     

Phylogenetic relationships among Pneumocystis from Asian macaques inferred from mitochondrial rRNA sequences

The presence of Pneumocystis organisms was detected by nested-PCR at mitochondrial large subunit (mtLSU) rRNA gene in 23 respiratory samples from Asian macaques representing two species: Macaca mulatta and M. fascicularis. A very high level of sequence heterogeneity was detected with 18 original sequence types. Two genetic groups of Pneumocystis could be distinguished from the samples. Within each group, the extent of genetic divergence was low (2.5+/-1.4% in group 1 and 2.3+/-1.7% in group 2). Genetic divergences were systematically higher when macaque-derived sequence types were compared with Pneumocystis mtLSU sequences from other primate species (from 5.3+/-2.7% to 19.3+/-3.0%). The two macaque-derived groups may be considered as distinct Pneumocystis species. Surprisingly, these Pneumocystis species were recovered from both M. mulatta and M. fascicularis suggesting that host-species restriction may not systematically occur in the genus Pneumocystis. Alternatively, these observations question about the species concept in macaques.     

Structure of the intergenic spacer region from the ribosomal RNA gene family of white spruce (Picea glauca)

Five genomic clones containing ribosomal DNA repeats from the gymnosperm white spruce (Picea glauca) have been isolated and characterized by restriction enzyme analysis. No nucleotide variation or length variation was detected within the region encoding the ribosomal RNAs. Four clones which contained the intergenic spacer (IGS) region from different rDNA repeats were further characterized to reveal the sub-repeat structure within the IGS. The sub-repeats were unusually long, ranging from 540 to 990 bp but in all other respects the structure of the IGS was very similar to the organization of the IGS from wheat, Drosophila and Xenopus.     

Identification ofArmillaria species from hokkaido by analysis of the intergenic spacer (IGS) region of ribosomal DNA using PCR-RFLP

The intergenic spacer (IGS) region, which is located between the 3′ end of 26S ribosomal DNA (rDNA) and the 5′ end of 5S rDNA, of sixArmillaria species from Hokkaido was investigated using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Restriction with onlyAlu I could distinguishA. mellea subsp.nipponica from the other species. WithAlu I andDde I,A. ostoyae andA. gallica could be distinguished from the other species. Digestion withAlu I resulted in two patterns (types A and B) ofA. singula and three patterns (types A, B, and C) ofA. jezoensis. One pattern (type B) of the former species and two patterns (types B and C) of the latter species were each different from those of the other species.Armillaria sinapina gave only oneAlu I digestion pattern, which was identical to that ofA. jezoensis (type A) andA. singula (type A). However, by digestion withDde I,A. singula (type A) could be distinguished fromA. jezoensis (type A) andA. sinapina.