SSU rDNA phylogeny of cladoniiform lichens

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.     

Monophyly of the family Desmoscolecidae (Nematoda,Demoscolecida) and Its Phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].     

Relationships of the Insect-Pathogenic Order Entomophthorales (Zygomycota, Fungi) Based on Phylogenetic Analyses of Nuclear Small Subunit Ribosomal DNA Sequences (SSU rDNA)

We sequenced the nuclear small subunit of ribosomal DNA (SSU rDNA) from seven species within the insect-pathogenic order Entomophthorales. These sequences were aligned with other published SSU rDNA sequences and phylogenies were inferred using phenetic and cladistic methods. Based on three different phylogenetic methods the Entomophthorales (excludingBasidiobolus ranarum) is monophyletic;B. ranarumwas more closely related to chytrids from Chytridiales and Neocallimasticales than to Entomophthorales, as was proposed by Nagahamaet al.(Mycologia87:203–209, 1995). Nuclear characters (large nuclei containing conspicuous condensed chromatin and lack of a prominent nucleolus) were of predictive value for the monophyly of the family Entomophthoraceae. Conidial characters separate the Entomophthoraceae, which only includes obligate pathogens, into at least two lineages: one lineage with uninucleate conidia and another with multinucleate conidia. The two species ofConidiobolusstudied were paraphyletic in our analyses and only distantly related to each other. This information may prove to be important in the use of these fungi as biocontrol agents.     

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.     

Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.     

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.     

Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences

Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes.     

Phylogenetic relationships and generic affinity of Uncinula septata inferred from nuclear rDNA sequences

Based on 18S, 5.8S, and 28S rDNA sequences, the phylogenetic position of Uncinula septata within the Erysiphales has been inferred. Although appendages of the ascomata are uncinula like, i.e., unbranched with curved-coiled apices, U. septata is situated at the very base of the large Erysiphales cluster, far away from the pseudoidium clade (Erysiphe emend., including Microsphaera and Uncinula). Morphologically, U. septata differs from the species of Erysiphe sect. Uncinula (Uncinula) in having terminal, pluriseptate ascoma appendages, curved ascospores, and the absense of an anamorph. This species is a basal, tree-inhabiting powdery mildew with some additional ancestral characteristics, viz., uncinula-like appendages and 8-spored asci. The new genus Parauncinula with U. septata as the type species is proposed. Uncinula curvispora (U. septata var. curvispora) is tentatively maintained as a separate species, which is also assigned to Parauncinula.     

Phylogenetic relationships of rodent pinworms (genus Syphacia) in Japan inferred from 28S rDNA sequences

The 28S rDNA from nine species of the genus Syphacia collected in Japan was sequenced, and the phylogenetic relationship was inferred from multiple sequence alignment of 28S rDNA by the MAFFT program. Phylogenetic tree indicates that S. petrusewiczi, which was the only species belonging to the subgenus Seuratoxyuris, has diverged earlier than other rodent pinworms examined and was distantly separated from the others genetically. It was revealed that S. agraria and S. vandenbrueli, whose subgeneric status has not been specified, belonged to the subgenus Syphacia together with other 6 species. Syphacia montana from Clethrionomys, Eothenomys and Microtus was very closely related to S. obvelata from Mus, and that S. frederici from Apodemus and S. vandenbrueli from Micromys were comparatively closely related to the former two species. The phylogenetic relationship among the three species of Syphacia found in Japanese Apodemus was inconsistent with the biogeography of host rodents. The co-evolutionary relationship between pinworm species and their host rodents may not be so strict and host switching has probably occurred frequently during the course of evolution.     

The Phylogeny of the Families Lecanoraceae and Bacidiaceae (Lichenized Ascomycota) Inferred from Nuclear SSU rDNA Sequences

Abstract: The phylogeny of the families Lecanoraceae and Bacidiaceae (Lecanorales, Ascomycota) was investigated using 29 nuclear small subunit ribosomal DNA sequences, 9 of which were newly determined. The data set contained 368 variable characters, 234 of which were parsimony-informative. Phylogenetic estimations were performed with maximum parsimony and maximum likelihood optimality criteria. In the most parsimonious and most likely reconstructions, the Bacidiaceae sensu Hafellner 1988 forms a monophyletic group and the Lecanoraceae sensu Hafellner a paraphyletic group. The genera Tephromela and Scoliciosporum appear to belong outside these families. However, the hypothesis that the Lecanoraceae sensu Hafellner is monophyletic cannot be rejected, as indicated by a Kishino-Hasegawa test. Three hypotheses were rejected by Kishino-Hasegawa tests, viz. (1) that the Lecanoraceae and Bacidiaceae together form a monophyletic group; (2) that both the Lecanoraceae (incl. Scoliciosporum ) and Bacidiaceae (incl. Tephromela ) are monophyletic; and (3) that the ascus apex anatomy reflects phylogeny. The suborder Lecanorineae is paraphyletic unless the Stereocaulaceae and Cladoniaceae are included. One or both of the Bacidia and Lecanora types of ascus have probably evolved at least twice.     

从核rDNA序列探讨隙蛛亚科Coelotinae的分类地位

隙蛛亚科Coelotinae主要分布于东亚地区,其中我国的已有种类占到全世界种数的一半以上,因此对于我国隙蛛类蜘蛛的研究已经成为世界暗蛛科研究的重点之一。隙蛛亚科属于无筛器类群,于1893年,由Cambridge以隙蛛属为模式属而建立,归属于无筛器的漏斗蛛科。之后,虽然经历了数次修订     

Phylogenetic relationships of the Japanese minnows,Pseudorasbora (Cyprinidae), as inferred from mitochondrial 16S rRNA gene sequences

The phylogenetic relationships among threePseudorasbora fishes (Cyprinidae, Sarcocheiichthyinae) occurring in Japan (P. parva, P. pumila pumila andP. pumila subsp. sensu Nakamura [1963]) were inferred from nucleotide sequences of the mitochondrial 16S rRNA gene. The sequences. of 1240 bp, were determined and compared for 22 specimens from 2–8 populations for each taxon, with a singlePungtungia herzi specimen as an outgroup. A total of 171 sites (13.8%) were variable among the specimens, but only 0–2 sites within each population. The phylogenetic relationships estimated by neighbor-joining, maximum-parsimony and maximum-likelihood methods confirmed a sister relationship between the twoP. pumila subspecies, with a high level of confidence. However, their genetic distinction from each other (4.1±0.4SD % sequence difference on average) was at a level similar to that between them andP. parva (5.9±0.5%). The geographic distribution of the twoP. pumila subspecies, which are separated by the Fossa Magna region, suggests that the genetic divergence of the two subspecies originated from a vicariant process separating the freshwater ichthyofaunas of eastern and western Honshu.Pseudorasbora parva populations were divided into two genetic groups (1.8±0.2% sequence difference), one group comprising continental and part of the Japanese populations, and the other the remaining Japanese populations. This suggests that at least two genetically divergent lineages had been originally distributed in Japan, but a strong possibility remains that the present situation has resulted from artificial transplantation.     

Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences

The phylogeny of Oedogoniales was investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium, as a separated clade, was clustered within the clade of Oedogonium; whereas the genus Bulbochaete was in a comparatively divergent position to the other two genera. The relationship among the species of Oedogonium was discussed, focusing on ITS-2 phylogeny analyzed combining with some morphological characteristics. Our results showed that all the dioecious nannandrous taxa involved in this study were resolved into one clade, while all the monocious taxa were clustered into another clade as a sister group to the former. The report also suggests that the dioecious macrandrous taxa form a paraphyly and could be more basally situated than the dioecious nannandrous and the monoecious taxa by means of molecular phylogeny and morphotype investigations.     

Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences

The nuclear small subunit ribosomal DNA (18S rDNA) of 27 anostracans (Branchiopoda: Anostraca) belonging to 14 genera and eight out of nine traditionally recognized families has been sequenced and used for phylogenetic analysis. The 18S rDNA phylogeny shows that the anostracans are monophyletic. The taxa under examination form two clades of subordinal level and eight clades of family level. Two families the Polyartemiidae and Linderiellidae are suppressed and merged with the Chirocephalidae, of which together they form a subfamily. In contrast, the Parartemiinae are removed from the Branchipodidae, raised to family level (Parartemiidae) and cluster as a sister group to the Artemiidae in a clade defined here as the Artemiina (new suborder). A number of morphological traits support this new suborder. The Branchipodidae are separated into two families, the Branchipodidae and Tanymastigidae (new family). The relationship between Dendrocephalus and Thamnocephalus requires further study and needs the addition of Branchinella sequences to decide whether the Thamnocephalidae are monophyletic. Surprisingly, Polyartemiella hazeni and Polyartemia forcipata ("Family" Polyartemiidae), with 17 and 19 thoracic segments and pairs of trunk limb as opposed to all other anostracans with only 11 pairs, do not cluster but are separated by Linderiella santarosae ("Family" Linderiellidae), which has 11 pairs of trunk limbs. All appear to be part of the Chirocephalidae and share one morphological character: double pre-epipodites on at least part of their legs. That Linderiella is part of the Polyartemiinae suggests that multiplication of the number of limbs occurred once, but was lost again in Linderiella. Within Chirocephalidae, we found two further clades, the Eubranchipus-Pristicephalus clade and the Chirocephalus clade. Pristicephalus is reinstated as a genus.     

Phylogenetic relationships in the harmful dinoflagellate Cochlodinium polykrikoides (Gymnodiniales, Dinophyceae) inferred from LSU rDNA sequences

Phylogenetic relationships among chain-forming Cochlodinium species, including the harmful red tide forming dinoflagellate Cochlodinium polykrikoides, were investigated using specimens collected from coastal waters of Canada, Hong Kong, Japan, Korea, Malaysia, México, Philippines, Puerto Rico, and USA. The phylogenetic tree inferred from partial (D1–D6 regions) large subunit ribosomal RNA gene (LSU rDNA) sequences clearly differentiated between C. polykrikoides and a recently described species, Cochlodinium fulvescens. Two samples collected from the Pacific coasts of North America (British Columbia, Canada and California, USA) having typical morphological characters of C. fulvescens such as the sulcus located in the intermediate region of the cingulum, were closely related to C. fulvescens from western Japan in the phylogenetic tree. Cochlodinium polykrikoides formed a monophyletic group positioned as a sister group of the C. fulvescens clade with three well-supported sub-clades. These three clades were composed of (1) East Asian, including specimens collected from Hong Kong, western Japan, and southern Korea, (2) Philippines, from Manila Bay, Philippines and Omura Bay, Japan, and (3) American/Malaysian, from the Atlantic coasts of USA, the Pacific coast of México, Puerto Rico, and Borneo Island, Malaysia. Each of these clades is considered to be a so-called “ribotype” representing the population inhabiting each region, which is distinguished based on ribosomal RNA gene sequences in the species despite similarities in their morphological characters.     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。     

Phylogenetic relationships in Saxifragaceae sensu lato: A comparison of topologies based on 18S rDNA and rbcL sequences

Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.     

Systematic position of Asteropyrum (Ranunculaceae) inferred from chloroplast and nuclear sequences

Sequences of chloroplast gene rbcL and partial nuclear 26S rDNA were used to evaluate phylogenetic relationships of Asteropyrum. Four primary clades were recognized in Ranunculaceae, corresponding to subfamilies Hydrastidoideae, Coptidoideae, Thalictroideae, and Ranunculoideae. Our results place Asteropyrum in Ranunculoideae, sister to the tribe Actaeeae, which includes Beesia, Cimicifuga, and Eranthis. This is supported by chromosome characters, including chromosome size and basic number, and the stainability of prophase chromosomes and interphase nuclei. Our results do not support previous placements of Asteropyrum in either Coptidoideae or Thalictroideae. Considering its uniqueness in a few characters (e.g. simple peltate leaves, accumulating benzylisoquinoline alkaloids, vessel elements with only typical scalariform perforation plates), we recognize Asteropyrum as a monotypic tribe of Ranunculoideae, Asteropyreae W. T. Wang et C. Y. Chang.