Phylogenetic relationships ofPseudopanax species (Araliaceae) inferred from parsimony analysis of rDNA sequence data and morphology

Sequence data from internal transcribed spacer (ITS) regions of rDNA and data from morphology, cytology and wood anatomy are used to study phylogenetic relationships inPseudopanax. The molecular and non-molecular data are analysed as independent data sets and in combination using parsimony. Results supported the conclusion that the genusPseudopanax is polyphyletic.Pseudopanax species emerge in two major monophyletic groups. The Anomalus group containsPseudopanax anomalus, P. edgerleyi, andP. simplex; these species share a common ancestor withCheirodendron trigynum and more distantly withPseudopanax gunnii. The second major group consists of two smaller groups: the Arboreus group, includingPseudopanax arboreus, P. colensoi, P. kermadecensis, P. laetus, andP. macintyrei, and the Crassifolius/Discolor group, includingP. chathamicus, P. crassifolius, P. discolor, P. ferox, P. gilliesii, P. lessonii, andP. linearis. Meryta species are close relatives of thePseudopanax Arboreus and Crassifolius/Discolor groups.     

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 of the Physciaceae inferred from rDNA sequence data and selected phenotypic characters

The monophyletic origin of the ascomycete family Physciaceae, its position within the Lecanorales and the phylogenetic structure within the family were investigated using nuclear rDNA sequence analyses. The common origin of the Caliciaceae and Physciaceae as previously shown (Wedin et al 2000) was confirmed. Further it could be shown that the Caliciaceae are nested within the Physciaceae. A unique region in loop 37 of the SSU rRNA secondary structure model was identified, which characterizes the Physciaceae/Caliciaceae. The SSU rDNA sequence data did not support a particular relationship with any other Lecanoralean family. Analyses of ITS rDNA sequences revealed a bifurcation of the Physciaceae/Caliciaceae clade, which was found to be congruent with the distribution of certain morphological characters. The congruence with the ITS phylogeny demonstrated the phylogenetic significance of ascus type, hypothecium pigmentation, ascospore characters and excipulum type. Fine-structure details of ascospores and the structure of excipula were found to be important in the recognition of convergences in these traits. Other previously used characters, i.e., growth habit, certain ascospore types or structure of the upper cortex, were found to be of multiple origins within the Physciaceae. All monophyletic lineages of noncrustose growth habit exhibit uniform ascospore types, indicating a higher evolutionary age of ascospore types than foliose growth habit. The taxonomic segregation of the Physciaceae into the Physciaceae and Caliciaceae is proposed here.     

Higher-level phylogenetic relationships of Homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions.

Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among these clades. A dataset of 93 species that represent all eight previously recognized clades was assembled, with 3800 bp of sequence data from nuclear and mitochondrial large and small subunit rDNAs for each taxon. Parsimony and maximum-likelihood analyses support the monophyly of the eight major clades recognized by Hibbett and Thorn. Most groups are strongly supported in bootstrapped parsimony analyses, but the polyporoid clade remains weakly supported. For the first time, the sister-group relationship of the euagarics clade and bolete clade is strongly supported, and the Hygrophoraceae is strongly supported as the sister group of the rest of the euagarics clade. Nevertheless, the backbone of the homobasidiomycete phylogeny, and the internal structure of several clades, remain poorly resolved.     

Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences

The phylogenetic relationships of nine species of freshwater sponges, representing the families Spongillidae, Lubomirskiidae, and Metaniidae, were inferred from analyses of 18S rDNA, cytochrome oxidase subunit I (COI) mtDNA, and internal transcribed spacer 2 (ITS2) rDNA sequences. These species form a strongly supported monophyletic group within the Demospongiae, with the lithistid Vetulina stalactites as the sister taxon. Within the freshwater sponge clade, the basal taxon is not resolved. Depending upon the method of analysis and sequence, the metaniid species, Corvomeyenia sp., or the spongillid species, Trochospongilla pennsylvanica , emerges as the basal species. Among the remaining freshwater sponge species, the spongillids, Spongilla lacustris and Eunapius fragilis , form a sister group to a clade comprised of the spongillid species, Clypeatula cooperensis , Ephydatia fluviatilis , and Ephydatia muelleri , and the lubomirskiid species, Baikalospongia bacillifera and Lubomisrkia baicalensis . C. cooperensis is the sister taxon of E. fluvialitis , and E. muelleri is the sister taxon of ( B. bacillifera + L. baicalensis ). The family Spongillidae and the genus Ephydatia are thus paraphyletic with respect to the lubomirskiid species; Ephydatia is also paraphyletic to C. cooperensis . We suggest that C. cooperensis be transferred to the genus Ephydatia and that the family Lubomirskiidae be subsumed into the Spongillidae.     

Phylogenetic relationships among diploid Aegilops species inferred from 5S rDNA units

Relationships among the currently recognized 11 diploid species within the genus Aegilops have been investigated. Sequence similarity analysis, based upon 363 sequenced 5S rDNA clones from 44 accessions plus 15 sequences retrieved from GenBank, depicted two unit classes labeled the long AE1 and short AE1. Several different analytical methods were applied to infer relationships within haplomes, between haplomes and among the species, including maximum parsimony and maximum likelihood analyses of consensus sequences, “total evidence” phylogeny analysis and “matrix representation with parsimony” analysis. None were able to depict suites of markers or unit classes that could discern among the seven haplomes as is observed among established haplomes in other genera within the tribe Triticeae; however, most species could be separated when displayed on gene trees. These results suggest that the haplomes currently recognized are so refined that they may be relegated as sub-haplomes or haplome variants. Amblyopyrum shares the same 5S rDNA unit classes with the diploid Aegilops species suggesting that it belongs within the latter. Comparisons of the Aegilops sequences with those of Triticum showed that the long AE1 unit class of Ae. tauschii shared the clade with the equivalent long D1 unit class, i.e., the putative D haplome donor, but the short AE1 unit class did not. The long AE1 unit class but not the short, of Ae. speltoides and Ae. searsii both share the clade with the previously identified long {S1 and long G1 unit classes meaning that both Aegilops species can be equally considered putative B haplome donors to tetraploid Triticum species. The semiconserved nature of the nontranscribed spacer in Aegilops and in Triticeae in general is discussed in view that it may have originated by processes of incomplete gene conversion or biased gene conversion or birth-and-death evolution.     

Two new Pythium species from China based on the morphology and DNA sequence data

In an investigation of Pythium species in lawn grassland of south China, two new species, Pythium breve and P. baisense, were identified based on morphological characteristics and DNA sequence data. These two new species differ morphologically from the other Pythium species by the oogonia encompassed by many antheridia and with 1?C3 antheridia on the wavy and curved stalks. Furthermore, P. baisense with complexly lobed antheridial stalks differs from P. breve with antheridial stalks entwining the hyphae nearby the oogonia with several turns. Results of phylogenetic analyses showed that these two new species were clearly separated from morphologically similar Pythium species based on the internal transcribed spacer region (ITS1, 5.8S, ITS2) and cytochrome c oxidase subunit I (COXI) gene sequences using maximum parsimony and Bayesian methods. These two new species are described and illustrated in detail.     

Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology

Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.     

Phylogenetic relationships of Palaeacanthocephala (Acanthocephala) inferred from SSU and LSU rDNA gene sequences

The Palaeacanthocephala is traditionally represented by 2 orders, Echinorhynchida and Polymorphida, with 10 and 3 families, respectively. To test the monophyly of the class, these 2 orders, and certain families, phylogenies were inferred using nuclear small-subunit (SSU) and large-subunit (LSU) ribosomal DNA sequences obtained for 29 species representing 10 families, 2 other classes of acanthocephalans, and 3 rotifer outgroups. Phylogenetic relationships were inferred by analyzing combined SSU and LSU sequences using maximum parsimony (MP) and maximum likelihood (ML) methods. Parsimony and ML trees inferred from combined analysis of these rDNA data strongly supported monophyly of Palaeacanthocephala and provided good resolution among species. Neither Polymorphida nor Echinorhynchida was monophyletic. Gorgorhynchoides bullocki (Echinorhynchida) was nested within the 6 species representing Polymorphida, and this clade was nested within species representing Echinorhynchida. Three of 4 palaeacanthocephalan families that could be evaluated were not monophyletic, and this finding was strongly supported. These results indicate that the family level classification of palaeacanthocephalans, which is mainly based on combinations of shared characters (not shared derived characters), needs to be reevaluated with respect to comprehensively sampled phylogenetic hypotheses.     

Phylogenetic relationships of Coreanomecon (Papaveraceae: Chelidonioideae) inferred from seed morphology and nrITS sequence data

The phylogenetic position of the Coreanomecon, a monotypic genus endemic to Korea, has been controversial for a long time. Coreanomecon has variously been placed in its own genus or combined with Hylomecon or Chelidonium. The main purpose of this study was to examine the phylogenetic position of Coreanomecon in relation to genera of the subfamily Chelidonioideae using seed morphology and molecular data. The seed morphology of 10 genera of Chelidonioideae was examined using microtome sections and scanning electron microscopy. The shape and size of exotestal cells varied between genera. The exotestal cells were tangentially elongated in Chelidonium majus, Stylophorum diphyllum and Hylomecon vernalis, whereas the cells were sub‐orbicular and broad in Coreanomecon hylomeconoides. The endotesta was represented by thick palisade‐like cells that contain small rectangular crystals near their outer walls. The mesotesta was totally collapsed in Co. hylomeconoides but wholly or partly persistent in Ch. majus and H. vernalis. The seed surface of Co. hylomeconoides was well ornamented with a unique echinate seed surface, whereas other genera showed plain and reticulate seed surfaces. A phylogenetic analysis of the genera including Coreanomecon was conducted with nuclear ribosomal internal transcribed spacer (nrITS) sequences using genetic distance, maximum parsimony, maximum likelihood and Bayesian inference methods. The results confirm that Co. hylomeconoides is separated from both Hylomecon species and is a sister group to Chelidonium majus and Stylophorum diphyllum with robust bootstrap support. In addition to differences in the absence of cauline leaves and rhizomes, the presence of a hairy stem and leaves, and 12‐pericolpate pollen, seed characters and molecular data strongly support the recognition of Coreanomecon as an independent genus, distinct from Hylomecon and Chelidonium.     

Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18S rDNA and rbcL sequence data

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.     

Two new species of powdery mildew fungi from Japan

The following two new species of powdery mildew fungi were found onStephania cephalantha (Menispermaceae) andViburnum opulus var.calvescens (Caprifoliaceae) in Japan:

1. Erysiphe stephaniae onS. cephalantha has smaller cleistothecia and more asci present in the cleistothecium, which include remarkably larger ascospores, thanErysiphe pisi, which has been previously described on the same host plant from Taiwan.
2. Microsphaera shinanoensis onV. opulus var.calvescens is easily distinguishable fromMicrosphaera alni, hitherto known on this plant, and otherMicrosphaera fungi onViburnum plants by the shape of its appendages and the numbers of its asci and ascospores.

     

Phylogenetic relationships of Italian Bellevalia species (Asparagaceae), inferred from morphology,karyology and molecular systematics

The seven Bellevalia species and subspecies known from Italy, representing about 10% of the genus and three out of six sections, were studied. An integrated morphological, karyological and molecular approach was used to infer phylogenetic and systematic relationships among them. B. romana (the generitype) is the most distinctive species on karyotype asymmetry grounds. B. boissieri and B.dubia, usually considered as subspecies of one species (the latter endemic to Sicily), deserve specific status based on biparental nrDNA markers (internal transcribed spacer, ITS), since they do not form a single clade. The allotetraploid endemic B. pelagica, morphologically similar to B. romana, is sister to the latter under parsimony, both in morphological and ITS trees; it is also related with B. dubia, based on karyotype asymmetry and a uniparental cpDNA marker (trnL^(UAA)–trnF^(GAA) IGS (intergenic spacer)). A second allotetraploid endemic, B. webbiana, is closely related, on morphological, karyological and molecular grounds, with B. boissieri and B. ciliata, and also with B. trifoliata, three species that might all involved in its origin. B. sect. Conicae Feinbr. and sect. Nutantes Feinbr. are here typified, the former (type: B. ciliata) is most likely a synonym of the latter (type: B. trifoliata).     

Evolutionary relationships among species of Puccinia and Uromyces (Pucciniaceae,Uredinales) inferred from partial protein coding gene phylogenies

The two rust genera with the largest number of species are Puccinia Pers. ex Pers. and Uromyces (Link) Unger in the family Pucciniaceae (Uredinales). The hosts of these pathogens include representatives from almost all major angiosperm orders. Despite their ecological and economic importance, the status of Puccinia and Uromyces as distinct genera has been disputed, and little is known about relationships within and among these groups. Here we present phylogenetic analyses based on sequence data from the translation elongation factor 1α gene for over 60 species in the family Pucciniaceae. In particular, we investigate evolutionary relationships between Puccinia and Uromyces. A relatively smaller phylogeny using the beta-tubulin 1 gene was generated to test support for this phylogeny. Two main phylogenetic clades were identified and indicate at least two radiations within the Pucciniaceae. As expected neither Puccinia s. lat. nor Uromyces s. lat. are supported as monophyletic groups by either of the protein coding genes. However, both Puccinia sensu stricto (type P. graminis), and Uromyces sensu stricto (type U. appendiculatus) constitute distinct clades. In general, members of Uromyces spp. occurred scattered throughout the phylogeny suggesting that they represent more recent radiations. Several host families are found in both of the two main clades while two families, Poaceae and Cyperaceae, are separated, with one in each of the two main clades.     

Basal relationships of Coleoptera inferred from 18S rDNA sequences

The basal relationships of the hyperdiverse insect order Coleoptera (beetles) have proven difficult to resolve. Examination of beetle suborder relationships using 18S ribosomal DNA reveals a previously unproposed relationship among the four major lineages: [(Archostemata(Myxophaga(Adephaga, Polyphaga)))]. Adding representatives of most other insect orders results in a non-monophyletic Coleoptera. However, constraining Coleoptera and its suborders to be monophyletic, in analyses of beetle and outgroup sequences, also results in the above beetle relationships, with the root placed between Archostemata and the remaining suborders.