Phylogenetic relationships of Chalara and allied species inferred from ribosomal DNA sequences

The phylogenetic relationships of Chalara and allied taxa are studied based on ribosomal DAN sequences. Partial 28S rDNA and 18S rDNA regions from 26 strains were sequenced in this study. These and related sequences from GenBank were analyzed using parsimony and Bayesian analyses. Most of the Chalara species clustered in a strongly supported monophyletic lineage representing Helotiales. However, a few Chalara species appeared closely related to Xylariales. The phylogenetic significance of morphological characters observed in Chalara species are evaluated based on our sequence analyses. Conidial septation, conidial width and conidiophore pigmentation are thought to be indicative in understanding their evolutionary relationships. Sterile setae, which traditionally have been used to delimitate Chaetochalara from Chalara, are phylogenetically insignificant.     

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 of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.     

Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences

Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.     

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.     

Phylogenetic relationships among Puccinellia and allied genera of Poaceae as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among accessions of Catabrosa P. Beauv., Phippsia (Trin.) R. Br., Sclerochloa P. Beauv., and Puccinellia Pari, resolved a monophyletic Puccinellia, with Sclerochloa as its sister group, Phippsia the sister of the Puccinellia + Sclerochloa clade, and Catabrosa situated more distantly. These results suggest that the taxonomic fusion of Phippsia and Puccinellia, which has been proposed in light of the existence of natural hybrids between them (currently recognized as the nothogenus × Pucciphippsia Tsvelev), would yield a grouping that would not be monophyletic unless Sclerochloa also was included. The set of restriction site characters that resolve these relationships provides minimal support for species groupings within Puccinellia, and the groupings that are resolved are inconsistent in some cases with species boundaries as determined by morphology and isozymes.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.     

Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences

Summary Phylogenetic trees among eukaryotic kingdoms were inferred for large- and small-subunit rRNAs by using a maximum-likelihood method developed by Felsenstein. Although Felsenstein's method assumes equal evolutionary rates for transitions and transversions, this is apparently not the case for these data. Therefore, only transversiontype substitutions were taken into account. The molecules used were large-subunit rRNAs fromXenopus laevis (Animalia), rice (Plantae),Saccharomyces cerevisiae (Fungi),Dictyostelium discoideum (Protista), andPhysarum polycephalum (Protista); and small-subunit rRNAs from maize (Plantae),S. cerevisiae, X. laevis, rat (Animalia), andD. discoideum. Only conservative regions of the nucleotide sequences were considered for this study. In the maximum-likelihood trees for both large- and small-subunit rRNAs, Animalia and Fungi were the most closely related eukaryotic kingdoms, and Plantae is the next most closely related kingdom, although other branching orders among Plantae, Animalia, and Fungi were not excluded by this work. These three eukaryotic kingdoms apparently shared a common ancestor after the divergence of the two species of Protista,D. discoideum andP. polycephalum. These two species of Protista do not form a clade, andP. polycephalum diverged first andD. discoideum second from the line leading to the common ancestor of Plantae, Animalia, and Fungi. The sequence data indicate that a drastic change occurred in the nucleotide sequences of rRNAs during the evolutionary separation between prokaryote and eukaryote.     

Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences

Sparassis species show extensive morphological variation, especially when materials from eastern Asia and Australia are compared with collections from North America and Europe. We have been studying the taxonomy of Sparassis from eastern Asia, North America, Australia and Europe, using both morphological and molecular data. DNA was extracted from 32 recent collections of Sparassis from Australia, Canada, China, Finland, France, Germany, Japan, Switzerland, Thailand, the United Kingdom and the United States. The report of a Sparassis taxon from Australia is the first report of this genus from the Southern Hemisphere. Sequences of nuclear and mitochondrial rDNA and the gene encoding RNA polymerase subunit II (RPB2) were used to examine relationships both within the genus Sparassis and between Sparassis species and other members of the polyporoid clade. Equally weighted parsimony analyses and Bayesian analyses were performed using independent datasets and combined datasets of sequences from different regions. Our results suggest that: (i) Polyporoid fungi producing a brown rot may form a clade; (ii) as suggested in a previous study, Sparassis and Phaeolus form a monophyletic group, which is united by the production of a brown rot, the presence of a bipolar mating system and the frequent habit of growing as a root and butt rot on living trees; (iii) at least seven lineages are within Sparassis, represented by S. spathulata, S. brevipes, S. crispa, S. radicata and three taxa that have not been described, which can be distinguished on the basis of fruiting body structure, presence or absence of clamp connections, presence or absence of cystidia and spore size.     

Phylogeny of Isatis (Brassicaceae) and allied genera based on ITS sequences of nuclear ribosomal DNA and morphological characters

Systematics of the genus Isatis (Brassicaceae) is difficult and controversial, and previous studies were based solely on morphological characters. Sequence variation of the internal transcribed spacer (ITS) regions and the 5.8S gene of nuclear ribosomal DNA (nrDNA) were analyzed using parsimony and Bayesian methods. Twenty-eight taxa of Isatis and related genera of the tribe Isatideae were sampled, including 20 Isatis species representing almost all major morphological lineages, all three species of Pachypterygium, two of nine species of Sameraria, and monospecific Boreava, Myagrum, and Tauscheria. Two well-supported clades were resolved in the ITS tree, and they demonstrate the artificiality of the present delimitation of the tribe. One clade includes I. emarginata, I. minima, I. trachycarpa, P. brevipes, P. multicaule, P. stocksii, and T. lasiocarpa. The second clade includes I. buschiana, the polymorphic I. cappadocica with five subspecies, I. gaubae, I. kotschyana, I. leuconeura, I. pachycarpa, I. takhtajanii, I. tinctoria, and S. armena. Pachypterygium is polyphyletic and, together with Boreava, Sameraria, and Tauscheria, all are nested within Isatis. This study is a continuation of our recent systematic survey based on seed-coat microsculpturing ( Moazzeni et al., 2007. Flora 202, 447–454) and reveals that fruit characters mapped onto the molecular tree show considerable convergence. The reliance on fruit characters alone in the delimitation of genera may well lead to erroneous phylogenetic results and thus to incorrect taxonomic conclusions.     

Phylogenetic relationships of freshwater bryozoans (Ectoprocta, Phylactolaemata) inferred from mitochondrial ribosomal DNA sequences

Most species of freshwater bryozoans (Ectoprocta: Phylactolaemata) have few morphological distinctions, and within phylactolaemates, the morphology of the statoblast has been used to determine evolutionary relationships. Here, two controversial phylogenies have been proposed for phylactolaemates with regard to the relationship of Lophopodidae to other families. Two plumatellid genera, Gelatinella and Hyalinella , are candidates for the ancestral type of lophopodids. In addition, the coexistence of spines on the surfaces of the statoblast has led to the suggestion that lophopodids are closely related to the family Cristatellidae. In this study, we analysed mitochondrial DNA sequences of the 12S and 16S rDNA genes of 10 phylactolaemate species. Our results suggest that plumatellids may not be a direct ancestral group of lophopodids and that cristatellids are not a sister group of lophopodids. Fredericella , which was previously thought to be an ancestral group, was revealed to be derived. In addition, our results suggest that Stephanella is the most basal phylactolaemate. Mapping morphological characteristics onto the sequence-based phylogenetic tree revealed convergent evolution of statoblast characters.     

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 of Polyporus and morphologically allied genera

Polyporus accommodates morphologically heterogeneous species and is divided into six infrageneric groups based on macromorphological characters. On the other hand allied genera have macro- and microscopic characters similar to those of Polyporus. The phylogenetic relationships of Polyporus and allied genera were established from sequences of RNA polymerase II second largest subunit (RPB2), nuclear ribosomal large subunit (nucLSU) and mitochondrial ATPase subunit 6 (ATP6). The molecular phylogenetic trees confirmed that Polyporus is a polyphyletic genus and recognized six major clades (1-6) containing species of Polyporus and several allied genera. Among the clades one contained three infrageneric groups of Polyporus and two allied genera, Datronia and Pseudofavolus while one other contained group Polyporellus and Lentinus. Five of the six major clades contained species belonging to a single infrageneric group, Favolus, Melanopus, Polyporellus or Polyporus. This suggests that morphological characters used to define these groups have phylogenetic significance and reveals the need for a taxonomic revision of Polyporus and its allied genera.     

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 of Australian strongyloid nematodes inferred from ribosomal DNA sequence data

The sequence of the second internal transcribed spacer of the ribosomal DNA was determined for the following strongyloid nematodes: Cylicocyclus insignis, Chabertia ovina, Oesophagostomum venulosum, Cloacina communis, Cloacina hydriformis, Labiostrongylus labiostrongylus, Parazoniolaimus collaris, Macropostrongylus macropostrongylus, Macropostrongylus yorkei, Rugopharynx australis, Rugopharynx rosemariae, Macropostrongyloides baylisi, Oesophagostomoides longispicularis and Paramacropostrongylus toraliformis, and compared with published sequences for species of Strongylus and for Hypodontus macropi. The resultant phylogenetic trees supported current hypotheses based on morphological evidence for the separation of the families Strongylidae and Chabertiidae, but did not support the separation of the endemic Australian genera as a distinctive clade within the Chabertiidae. The implications of this finding for the phylogenetic origins of the Australian strongyloids are discussed.     

Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences.

To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.     

Phylogeny of Steinernema travassos, 1927 (Cephalobina: Steinernematidae) inferred from ribosomal DNA sequences and morphological characters

Entomopathogenic nematodes in Steinernema, together with their symbiont bacteria Xenorhabdus, are obligate and lethal parasites of insects that can provide effective biological control of some important lepidopteran, dipteran, and coleopteran pests of commercial crops. Phylogenetic relationships among 21 Steinernema species were estimated using 28S ribosomal DNA (rDNA) sequences and morphological characters. Sequences of the rDNA internal transcribed spacers were obtained to provide additional molecular characters to resolve relationships among Steinernema carpocapsae, Steinernema scapterisci, Steinernema siamkavai, and Steinernema monticolum. Four equally parsimonious trees resulted from combined analysis of 28S sequences and 22 morphological characters. Clades inferred from analyses of molecular sequences and combined datasets were primarily reliably supported as assessed by bootstrap resampling, whereas those inferred from morphological data alone were not. Although partially consistent with some traditional expectations and previous phylogenetic studies, the hypotheses inferred from molecular evidence, and those from combined analysis of morphological and molecular data, provide a new and comprehensive framework for evaluating character evolution of steinernematids. Interpretation of morphological character evolution on 6 trees inferred from sequence data and combined evidence suggests that many structural features of these nematodes are highly homoplastic, and that some structures previously used to hypothesize relationships represent ancestral character states.     

Phylogenetic relationships of the monozoic tapeworms (Eucestoda: Caryophyllidea) inferred from morphological characters

Phylogenetic relationships of all genera of the order Caryophyllidea, possibly the earliest branching group of true tapeworms (Platyhelminthes: Eucestoda) and the only one that is monozoic, have been assessed for the first time. Results of this cladistic analysis, inferred from 30 unweighted morphological characters, are only partly congruent with the existing classification, which consists of four families based on the position of the inner longitudinal muscles in relation to the internal genital organs. Whereas all but five genera of the Caryophyllaeidae form a monophyletic clade, members of the Capingentidae are split, occurring within six unrelated groups. The Lytocestidae is also paraphyletic, as some genera appear in four unrelated clades. Archigetes appears in a derived clade, indicating that its direct (monoxenous) life-cycle involving only tubificid oligochaetes is secondarily derived and not plesiomorphic among the Eucestoda, as postulated by some authors.     

Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA

 Phylogenetic relationships of Coffea species were estimated from the sequences of the internal transcribed spacer (ITS 2) region of nuclear ribosomal DNA. The ITS 2 region of 37 accessions belonging to 26 Coffea taxa and to three Psilanthus species was directly sequenced from polymerase chain reaction (PCR)-amplified DNA fragments. The level of variation was high enough to make the ITS 2 a useful tool for phylogenetic reconstruction. However, an unusual level of intraspecific variation was observed leading to some difficulty in interpreting rDNA sequence divergences. Sequences were analysed using Wagner parsimony as well as the neighbour-joining distance method. Coffea taxa were divided into several major groups which present a strong geographical correspondence (i.e. Madagascar, East Africa, Central Africa and West Africa). This organisation is well supported by cytogenetic evidence. On the other hand, the results were in contradiction with the present classification of coffee-tree taxa into two genera, namely Coffea and Psilanthus. Furthermore, additivity of parental rDNA types was not observed in the allotetraploid species C. arabica. Received: 25 July 1996 / Accepted: 18 October 1996     

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.