Phylogenetic relationships among diploid species of Symphyotrichum (Asteraceae: Astereae) based on two nuclear markers, ITS and GAPDH

The mostly North American subtribe Symphyotrichinae (Asteraceae: Astereae) comprises Canadanthus, Ampelaster, Psilactis, Almutaster, and Symphyotrichum. Intergeneric and interspecific relationships within the subtribe have been investigated in the past, particularly by Nesom [Nesom, G.L., 1994. Review of the taxonomy of Aster sensu lato (Asteraceae: Astereae), emphasizing the new world species, Phytologia 77, 141–297] and Semple [Semple, J.C., 2005. Classification of Symphyotrichum. Available from: <http://www.jcsemple.uwaterloo.ca/Symphyotrichumclassification.htm/>], using morphological and cytological approaches. Symphyotrichum is the largest and most complex genus within the subtribe and includes four subgenera: Symphyotrichum (x = 7, 8), Virgulus (x = 4, 5), Astropolium (x = 5), and Chapmaniani (x = 7). In this study we used two nuclear markers, the nrDNA internal transcribed spacer (ITS) and the low-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH), to resolve intergeneric and interspecific relationships within the subtribe at the diploid level, and to determine whether our phylogenies validate the classifications of Nesom or Semple. Our results confirm the distinct generic status of Canadanthus and Ampelaster, whereas Psilactis and Almutaster form a polytomy with Symphyotrichum. Within Symphyotrichum, subg. Virgulus is monophyletic based on ITS and appears polyphyletic based on GAPDH. Neither the ITS nor the GAPDH analyses support a distinct status for subg. Astropolium, which groups within subg. Symphyotrichum. In general, interspecific relationships within Symphyotrichum are unresolved. Lack of resolution may be interpreted as a case of recent and rapid evolutionary radiation.     

Phylogenetic relationships among the ciliate arthrodontous mosses: Evidence from chloroplast and nuclear DNA sequences

Parsimony and maximum likelihood analyses of combinedtrnL (UAA) 5 exon —trnF (GAA) andrps4 exon cpDNA, and 18S nrDNA sequences of 60 arthrodontous moss taxa indicate strong support for the monophyly of a clade containing theSplachnineae, Orthotrichineae, and diplolepideous alternate sub-orders. A clade including theSplachnineae, Meesiaceae andLeptobryum (Bryaceae) is similarly well supported and forms the sister group to a clade comprising theOrthotrichineae and the other diplolepideous alternate mosses. Within this latter clade a number of well supported lineages are identified, but relationships among these remain poorly resolved. These analyses indicate that the Splachnaceous and Orthotrichaceous peristomes have been independently derived from an ancestral perfect bryoid peristome.     

Phylogenetic relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast matK sequences

The phylogenetic relationships within the genus Betula (Betulaceae) were investigated using a part of the nuclear ADH gene and DNA sequences of the chloroplast matK gene with parts of its flanking regions. Two well-supported phylogenetic groups could be identified in the chloroplast DNA sequence: one containing the three American species B. lenta, B. alleghaniensis, and B. papyrifera and the other including all the other species studied. The ADH gene displayed more variation, and three main groups could be identified. In disagreement with the classical division of the genus Betula, B. schmidtii and B. nana grouped with the species in subgenus Betula, and B. ermanii grouped with species in subgenus Chamaebetula, including B. humilis and B. fruticosa. The ADH phylogeny suggests that several independent polyploidizations within the genus Betula could have taken place. The ADH and chloroplast phylogenies were in part incongruent due to the placement of B. papyrifera. The most likely reason for this seems to be cytoplasmic introgression.     

Phylogenetic relationships of Empetraceae inferred from sequences of chloroplast gene matK and nuclear ribosomal DNA ITS region

We used sequences of nrDNA ITS and chloroplast gene matK to evaluate the monophyly of Empetrum and Corema and to examine phylogenetic relationships of the Empetraceae. Sequences of these two DNA markers were obtained for 11 plant samples, representing species of Empetrum from both the Southern and Northern Hemispheres, species and subspecies of Corema, and the monotypic Ceratiola. Sequences of four species of Rhododendron were used for rooting purposes. Our results show that species of Empetrum form a clade sister to the clade containing both Corema and Ceratiola. These two clades are strongly supported in both the matK and ITS trees, suggesting that Ceratiola is more closely related to Corema than to Empetrum, and is not of a hybrid origin between the ancestors of the latter two genera. In the matK tree, Corema conradii is more closely related to Ceratiola than to Corema album and C. album subsp. azoricum, whereas in the ITS tree, Ceratiola is allied with Corema album and C. album subsp. azoricum. This suggests that C. conradii might be a hybrid between ancestral populations of Ceratiola and C. album. The monophyly of Empetrum rejects the hypothesis of its independent origin in the two Hemispheres. Our trees also suggest the fact that the modern amphitropical distribution of Empetrum is the result of long distance dispersal, not of the vicarious events.     

Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on noncoding nuclear and chloroplast DNA data

To examine relationships and test previous sectional delimitations within Fuchsia, this study used parsimony and maximum likelihood analyses with nuclear ITS and chloroplast trnL-F and rpl16 sequence data for 37 taxa representing all sections of Fuchsia and four outgroup taxa. Results support previous sectional delimitations, except for F. verrucosa, which is related to a Central American clade rather than to section Fuchsia and is described here as a new section Verrucosa. The basal relationships within Fuchsia are poorly resolved, suggesting an initial rapid diversification of the genus. Among the species sampled, there is strong support for a single South Pacific lineage, a southern South American/southern Brazilian lineage, a tropical Andean lineage, and one or two Central American and Mexican lineages. There is no clear support for an austral origin of the genus, as previously proposed, which is more consistent with Fuchsia's sister group relationship with the boreal Circaea. An ultrametric molecular clock analysis (all minimal dates) places the split between Fuchsia and Circaea at 41 million years ago (mya), with the diversification of the modern-day lineages of Fuchsia beginning at 31 mya. The South Pacific Fuchsia lineage branches off around 30 mya, consistent with fossil records from Australia and New Zealand. The large Andean section Fuchsia began to diversify around 22 mya, preceded by the divergence of the Caribbean F. triphylla at 25 mya. The Brazilian members of section Quelusia separated from the southern Andean F. magellanica around 13 mya, and the ancestor of the Tahitian F. cyrtandroides split off from the New Zealand species of section Skinnera approximately 8 mya.     

Phylogenetic relationships among Cucumis species based on the ribosomal internal transcribed spacer sequence and microsatellite markers

The phylogenetic relationships within the genus Cucumis (a total of 25 accessions belonging to 17 species) were studied using the nuclear ribosomal DNA internal transcribed spacer (ITS) region. The analysis included commercially important species such as melon (C. melo L.) and cucumber (C. sativus). Two additional cucurbit species, watermelon and zucchini, were also included as outgroups. The data obtained reflected the clustering of Cucumis species in four main groups, comprising accessions from cucumber, melon, C. metuliferus and the wild African species. Some of the species clustered in different positions from those reported in classifications previously described by other authors. The data obtained clearly identify a division between the 2n=2x = 14 species (C. sativus) and the 2n = 2x = 24 ones (C. melo and wild species). Within the wild species we identified a subgroup that included C. sagittatus and C. globosus. Oreosyce africana, also classified as Cucumis membranifolius, was shown to be nested within Cucumis. Three accessions previously classified as independent species were shown to be genotypes of Cucumis melo. A set of melon and cucumber SSRs were also used to analyse the Cucumis species and the results were compared with the ITS data. The differential amplification of the SSRs among the accessions made it possible to distinguish three main groups: melon, cucumber and the wild species, though with less detail than applying ITS. Some SSRs were shown to be specific for melon, but other SSRs were useful for producing PCR fragments in all species of the genus.We are grateful to NCRPIS, IPK in Gatersleben, Semillas Fitó S.A., Michel Pitrat and Fernando Nuez for providing seeds. We would also like to thank Vanessa Alfaro, Trinidad Martínez and Núria Galofré for their excellent technical assistance. This work was financed by project AGL2000-0360 of Spains Ministerio de Ciencia y Tecnología (MCYT). AJMs work was supported by a postdoctoral contract from Spains MCYT.     

Phylogenetic relationships among Fusarium species measured by DNA reassociation

Deoxyribonucleic acid of 11 Fusarium species (F. acuminatum, F. arthrosporioides, F. avenaceum, F. culmorum, F. graminearum, F. heterosporum, F. moniliforme, F. oxysporum, F. sambucinum, F. semitectum, F. solani) have been compared with respect to their physical characteristics (T_m, % G + C), homology values and nucleotide sequence divergence.A phylogenetic tree based on physical characteristics, homology values and differences in percentage divergence of Fusarium species DNAs has been constructed.     

Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA

The complete mitochondrial gene cytochrome b in combination with a nuclear gene, beta-fibrinogen intron 7, is sequenced for different groups of mostly granivorous species in the superfamily Passeroidea, with a focus on the estrildids and fringillids. From our study we can conclude that within the group of granivorous finches two clades can be distinguished, the estrildid weaver clade and the cardueline, fringillid, emberizid, passerine sparrow clade. In contrast to many other studies the passerine sparrows are not placed within the weavers estrildid clade which is in agreement with other recent studies (e.g., ). Our study also shows that the estrildids do form a monophyletic group, but there is a division based on geographic origin: an African group and an Asian-Australian group. Within the Fringillidae the Fringilla species are the sister group of the carduelines.     

Phylogenetic relationships among Thunnus species inferred from rDNA ITS1 sequence

Intra and interspecific nucleotide sequence variation of rDNA first internal transcribed spacer (ITS1) was analysed using all eight species of the genus Thunnus plus two out‐group species within the same family, skipjack tuna Katsuwonus pelamis and striped bonito Sarda orientalis . Intraspecific nucleotide sequence variation in ITS1, including intra‐genomic variation, was low, ranging from 0·003 to 0·014 [Kimura's two parameter distance (K2P)], whereas variation between species within the genus Thunnus ranged from 0·009 to 0·05. The Atlantic and Pacific northern bluefin tunas Thunnus thynnus thynnus and Thunnus thynnus orientalis , recently proposed to be distinct species, were found to share nearly identical ITS1 sequences (mean K2P = 0·006) well within the range of intraspecific variation. The northern bluefin tuna appeared to be a sister group to albacore Thunnus alalunga , with all other Thunnus species in a distinct clade. The ITS1 phylogeny was consistent with mtDNA phylogeny in clustering the three tropical Thunnus species ( T. albacares , T. atlanticus and T. tonggol ). Southern bluefin Thunnus maccoyii and bigeye Thunnus obesus tunas showed a closer affinity to this tropical tuna group than to the northern bluefin tuna and albacore. The molecular data supported mitochondrial introgression between species and contradicted morphological subdivision of the genus into two subgenera Neothunnus and Thunnus .     

Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences

Sequences of the nuclear ribosomal DNA internal transcribed spacer region 1 and the chloroplast-encoded genes maturase K and ribulose-1,5 biphosphate carboxylase large subunit were obtained from species of Ephedra (Ephedraceae) representing the geographic range and morphological diversity of the genus. Phylogenetic analyses of the DNA data indicate that relationships within the genus are better predicted by geographic region of origin than by ovulate cone characters. The sampled species with dry, winged (versus fleshy) ovulate cone bracts or single-seeded cones do not form monophyletic groups and therefore the previous classification systems of Ephedra based on these aspects of bract morphology appear to be largely unnatural. Three groups were identified among the Old World species studied, one comprising European and Mediterranean species and two including only Asian species. The sequence data suggest a possible early divergence of a New World clade of Ephedra from among the Old World groups. The South American species form a distinct clade apparently related to one of two groups of North American species, which accords with a frequent floristic pattern of close relationships between species groups in western South America and southwestern North America.     

Phylogenetic analyses of Septoria species based on the ITS and LSU-D2 regions of nuclear ribosomal DNA

The phylogenetic relationships of 17 selected Septoria spp. (eight with a known Mycosphaerella teleomorph), Phloeospora ulmi (teleomorph M. ulmi) and 18 additional taxa (10 with a Mycosphaerella teleomorph) were inferred from ITS and D2-LSU nrDNA sequences. In total, 10 anamorph genera associated with Mycosphaerella were represented. Intraspecific variation in ITS was limited in Septoria, with the exception of three strains that all were identified as S. rubi but originated from different Rubus spp. and probably belong to different species of Septoria. The results of D2 region sequencing confirmed Mycosphaerella sense lato (including Davidiella and Eruptio) as monophyletic. The cereal pathogen Septoria tritici, which is closely related to S. passerinii as found in ITS analysis, clusters with Ramularia spp. in the D2 analyses, distant from the other Septoria spp. The pathogens S. apiicola, S. linicola and S. populicola cluster in a major clade containing Phl. ulmi, and other Septoria spp. and Cercospora spp. Short branch lengths in this clade suggest a very recent evolution. Septoria castaneicola and S. pyricola also might represent relatively distant lineages. Both analyses of the regions indicated that Septoria is not monophyletic within Mycosphaerella and that conidiomatal structure (acervulus, pycnidium) has little value for predicting phylogenetic relatedness. As a consequence, the separation between the acervular Phloeospora and pycnidial Septoria is untenable. The loss of the teleomorph most likely has occurred several times in the evolutionary history of Mycosphaerella.     

Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation

Chloroplast DNA (cpDNA) restriction-site mutations in seven cultivated Prunus species were compared to establish the phylogenetic relationships among them. Mutations were detected in 3.2-kb and 2.1-kb amplified regions of variable cpDNA, cut with 21 and 10 restriction endonucleases, respectively, to reveal polymorphisms. Parsimony and cluster analyses were performed. The species pairs P. persica-P. dulcis, P. domestica-P. salicina, and P.cerasus-P. fruticosa were completely monophyletic. All of the species were grouped with conventional subgenus classifications. The subgenus Cerasus was the most diverged. Cerasus ancestors separated from the remainder of Prunus relatively early in the development of the genus. P. persica-P. dulcis, P. domestica-P. salicina and P. armeniaca formed a second monophyletic group. Prunophora species were less diverged than Amygdalus species. The results also suggest that the rate of mutation in Cerasus spp. chloroplast genomes is significantly greater than for the other subgenera sampled.     

Phylogenetic relationships among Japanese flowering cherries (Prunus subgenus Cerasus) based on nucleotide sequences of chloroplast DNA

Flowering cherries are classified into Prunus subgenus Cerasus (family Rosaceae). Nine species and some varieties originated in Japan were used in this study. Phylogenetic relationships among Japanese taxa were analyzed by four chloroplast regions using 46 individuals from 16 taxa. Eighteen haplotypes were distinguished. P. pendula f. ascendens and P. cerasoides formed a clade which is distantly related to other Japanese taxa. These two species were morphologically different from other taxa. All Japanese taxa except for P. pendula f. ascendens formed another clade. All taxa in this clade except for P. maximowiczii showed very similar sequences. However, these taxa could be identified by many morphological characters. Even now, based on previous work, it is thought that interspecific hybridization frequently occurs in flowering cherries. We conclude from the current study, Japanese flowering cherries have experienced complicated speciation arising from hybridization.     

Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

Background  

Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and particularly in the cytogenetic distinct subspecies group of Hapalemur griseus, 357 bp sequence of cytochrome b and 438 bp of 12S mitochondrial DNAs were analyzed on a sample of animals captured in areas extending from the north to the south-east of Madagascar. This sample covers all cytogenetically defined types recognized of the genus Hapalemur.     

Phylogenetic relationships among Portuguese rye based on isozyme, RAPD and ISSR markers

The phylogenetic relationships of 10 rye landraces and cultivars from the north of Portugal and from Brazil were analysed using 20 isozyme loci, and a total of 511 PCR markers (342 ISSRs and 169 RAPDs). The isozymes were analysed in at least 100 plants of each population/cultivar and, therefore, we have data about intra and inter population/cultivar genetic variability. However, the analyses with ISSRs and RAPDs were obtained using a mix of 25 plants of each population. Therefore, each population/cultivar was reduced to one tube and we have no data about intra genetic variability. As expected in a cross pollinated crop we found genetic diversity and a larger variation within than among the populations using isozymes. Somewhat unexpectedly, however, we found that the breeding cultivars have the same level of heterozygosity as the landraces. The phylogenetic relationships obtained using isozymes among the landraces, synthetic cultivar and the cultivars from breeding programs do not reflect their origin. Moreover, the cultivar from Brazil is not separated from the remaining populations/cultivars studied. However, the data observed using RAPDs and ISSRs are in agreement with their known origin. The populations maintained by the farmers in the north of Portugal are grouped in a cluster in the phenogram and the C902591 (from Brazil), the Alv?o (synthetic variety) and Larouco (a hybrid between Montalegre and Brazil) are in a different cluster. The ISSRs and RAPDs provide a rapid method for the production of polymorphic markers, which appear to correspond to known pedigree information.     

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.     

Phylogenetic relationships of four Puccinia species parasitic on Artemisia in Japan

Puccinia dioicae var. micropuncta and P. caricis-stipatae complete their life cycle by host-alternating between Artemisia (spermogonial-aecial stage) and Carex (uredinial-telial stage). These species are suggested to be biologically distinct by inoculation experiments and field observations. Two additional Puccinia ferruginosa and P. artemisiae-keiskeanae produce only telial stage on Artemisia. Similarities in the teliospore morphology and host relationship of the four Puccinia species suggest their close phylogenetic relationship. Nucleotide sequences of D1/D2 region and ITS2 regions with partial 5.8S rDNA were analyzed to depict possible phylogenetic relationships among the four Puccinia species. In D1/D2 analysis, both macrocyclic and microcyclic species were closely positioned in one clade, not permitting resolution of the phylogenetic relationship between the species. The DNA sequence of ITS2 including partial 5.8S rDNA was sufficiently variable to separate two macrocyclic species and P. artemisiae-keiskeanae; however, confident resolution of phylogenetic relationships of the three species was not possible. Nevertheless, the analysis suggested the derivation of P. artemisiae-keiskeanae from a macrocyclic, heteroecious ancestor that is most likely to be an ancestor of both P. caricis-stipatae and P. dioicae var. micropuncta. In contrast, three isolates of morphologically identifiable P. ferruginosa were variously positioned in the phylogenetic tree, suggesting that P. ferruginosa is not monophyletic.Contribution no. 192, Laboratory of Plant Parasitic Mycology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan