Home About us Contact
|
Home About us Contact | ||
|
|
||
Phylogenetic Study (phylogenetic + study)
Selected AbstractsPhylogenetic study on Shiraia bambusicola by rDNA sequence analysesJOURNAL OF BASIC MICROBIOLOGY, Issue 5 2004Tian-Fan Cheng In this study, 18S rDNA and ITS-5.8S rDNA regions of four Shiraia bambusicola isolates collected from different species of bamboos were amplified by PCR with universal primer pairs NS1/NS8 and ITS5/ITS4, respectively, and sequenced. Phylogenetic analyses were conducted on three selected datasets of rDNA sequences. Maximum parsimony, distance and maximum likelihood criteria were used to infer trees. Morphological characteristics were also observed. The positioning of Shiraia in the order Pleosporales was well supported by bootstrap, which agreed with the placement by Amano (1980) according to their morphology. We did not find significant inter-hostal differences among these four isolates from different species of bamboos. From the results of analyses and comparison of their rDNA sequences, we conclude that Shiraia should be classified into Pleosporales as Amano (1980) proposed and suggest that it might be positioned in the family Phaeosphaeriaceae. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Phylogenetic study of benthic, spine-bearing prorocentroids, including Prorocentrum fukuyoi sp. nov.PHYCOLOGICAL RESEARCH, Issue 2 2007Shauna Murray SUMMARY Species of prorocentroid dinoflagellates are common in marine benthic sediment and epibenthic habitats, as well as in planktonic habitats. Marine planktonic prorocentroids typically possess a small spine in the apical region. In this study, we describe a new, potentially widely distributed benthic species of Prorocentrum, P. fukuyoi sp. nov., from tidal sand habitats in several sites in Australia and from central Japan. This species was found to possess an apical spine or flange and was sister species to P. emarginatum. We analyzed the phylogeny of the group including this new species, based on large subunit (LSU) rDNA sequences. The genus contained a high level of divergence in LSU rDNA, in some cases among sister taxa. P. fukuyoi and P. emarginatum were found to be most closely related to a clade of generally planktonic taxa. Several morphological features may constitute more informative synapomorphies than habitat in distinguishing clades of prorocentroid species. [source] Sensilla on the External Genitalia of the Carabid Beetle, Carabus (Ohomopterus) dehaanii dehaanii Chaudoir (Coleoptera, Carabidae)ENTOMOLOGICAL RESEARCH, Issue 3 2004Lark KIM ABSTRACT Sensilla on the male and female external genitalia of the carabid beetle, Carabus (Ohomopterus) dehaanii dehaanii Chaudoir, were investigated with scanning electron microscopy. The investigation for female genitalia was conducted on the coxites and styli. As a result, 4 types of sensilla were distinguished. In male, a total of 6 types of sensilla were identified on the aedeagus. The external morphology and distribution pattern of each type of the sensilla in both sexes were described. Results are expected to provide a ground work for future research on the phylogenetic study of the genus Carabus and the comparative ultrastructure or behavior in the carabid beetle. [source] A phylogenetic study of human respiratory syncytial viruses group A and B strains isolated in two cities in Japan from 1980,2002JOURNAL OF MEDICAL VIROLOGY, Issue 2 2005Yuki Kuroiwa Abstract The circulation pattern and genetic evolution of respiratory syncytial virus (RSV) in Japan were examined based on 109 RSV field strains isolated over 20 seasons (1980,2002) in two cities, Sapporo and Tokyo. The second hypervariable region of the large glycoprotein (G) gene was amplified by RT-PCR and the products sequenced directly. The nucleotide sequences were compared to those representatives of RSV genotypes identified previously. Japanese group A and B isolates clustered into five and four genotypes defined previously, respectively. Another one group A and one group B genotypes, which could not be assigned to previous genotypes, were also identified. Although different genotypes usually co-circulated in each season, the isolates in proximate seasons from two communities were usually located in the same branches. Moreover, the strains with genotypes defined previously were usually isolated at the same time as each reference strain of Western countries. Several mutant group B strains with 1,20 longer amino acid G proteins were newly identified in Sapporo. These findings suggest that Japanese RSV strains underwent geographical and also temporal clustering while participating in RSV genetic evolution in a global setting. In addition, Japanese strains, especially group B, might have evolved individually in each community, sometimes changing the length of the G protein. J. Med. Virol. 76:241,247, 2005. © 2005 Wiley-Liss, Inc. [source] Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizationsMOLECULAR ECOLOGY, Issue 4 2005JENNIFER L. TRUSTY Abstract A molecular phylogenetic study of Bystropogon L'Hèr. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution. [source] Labyrinthula terrestris: a new pathogen of cool-season turfgrassesMOLECULAR PLANT PATHOLOGY, Issue 6 2007MARY W. OLSEN ABSTRACT A new disease of turfgrass known as rapid blight is caused by Labyrinthula terrestris, a newly described member of the Labyrinthulids. This unusual group of microorganisms previously has been found in marine systems, and L. terrestris is the only member of the genus Labyrinthula known to be a pathogen of terrestrial plants. Members of this genus are defined by the formation of ectoplasmic networks in which the unicellular somatic cells move or ,glide'. Infections of cool-season turfgrasses occur most commonly when they are irrigated with suboptimal irrigation water with elevated salinity. Disease has been observed in 11 states in the United States and in the United Kingdom. A phylogenetic study indicates that isolates from turfgrass in the United States fall firmly within a clade containing other Labyrinthula spp. and that they came from a common lineage. Its rapid emergence as a turfgrass pathogen may coincide with increased use of relatively high-salinity water or reclaimed water for irrigation. L. terrestris is a potential problem in susceptible turfgrass varieties wherever soil salinity is allowed to accumulate as a result of poor soil structure or suboptimal quality irrigation water is used for irrigation. [source] Phylogenetic analysis and species identification of popular shrimp species in southeast China using the first internally transcribed spacer of ribosomal DNAAQUACULTURE RESEARCH, Issue 11 2009Zhigang Wu Abstract The ribosomal DNA internally transcribed spacer 1 (ITS1) was investigated in the search for an appropriate genetic marker that was suitable for phylogenetic study and species identification of eight major exported shrimp species in southeast China. Using the selected primers, the amplified ITS1 sequences exhibited a high degree of length polymorphisms, ranging from 448 bp in Metapenaeopsis dalei to 1491 bp in Macrobrachium nipponense. Many microsatellite loci were found at the 5, end and in the middle region of ITS1, which seemed to be associated with intragenomic sequence variation among samples of the same species. This variation might obscure the phylogenetic relationship between some shrimp populations, but the separation of five Penaeus species was well supported. In combination with polymerase chain reaction-restriction fragment length polymerism methods analysis, ITS1 sequences from shrimp species belonging to different families and genera could also be easily discernable. The results suggested that ITS1 was highly variable among different shrimp groups and could be an appropriate marker for species identification and molecular systematic studies. [source] Phylogenetic patterns of diversification in a clade of Neotropical frogs (Anura: Aromobatidae: Mannophryne)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009JESÚS MANZANILLA We used partial sequences of mitochondrial 16S and cytochrome oxidase I genes to perform a phylogenetic study of collared frogs (Anura: Aromobatidae: Mannophryne), a genus endemic to Venezuela and the islands of Trinidad and Tobago. We analysed 1.2 kb from 13 of the 15 described species of Mannophryne. Maximum parsimony, maximum likelihood and Bayesian analyses support the monophyly of Mannophryne. Mannophryne consists of three deeply differentiated clades that split from each other in a relatively short period of time. The diversification of Mannophryne occurred well before the glacial-interglacial periods of the Quaternary. Our data support the taxonomic validity of M. olmonae, a species endemic to Tobago Island. Mannophryne olmonae is more closely related to the continental species Mannophryne riveroi than to the Trinidad island endemic Mannophryne trinitatis. As in most tropical clades of frogs, molecular evidence indicates that species richness in Mannophryne is largely underestimated and, consequently, current priorities for conservation are inadequate. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 185,199. [source] Amphistemon and Thamnoldenlandia, two new genera of Rubiaceae (Spermacoceae) endemic to MadagascarBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2010INGE GROENINCKX Amphistemon and Thamnoldenlandia are described as two new genera of Rubiaceae endemic to Madagascar. The two novelties belong to the predominantly herbaceous tribe Spermacoceae. Amphistemon is unique within the tribe in having its stamens inserted at two levels in the corolla tube. The genus includes two species: the subshrub A. humbertii and the geoxylic herb A. rakotonasolianus. Thamnoldenlandia includes only one species, T. ambovombensis, which differs from most other Spermacoceae in being a medium-sized shrub with winged seeds. We present a detailed description of Amphistemon and Thamnoldenlandia, including observations of pollen and seeds. A molecular phylogenetic study based on atpB - rbcL, petD, rps16 and trnL - trnF sequences demonstrates that the two new genera belong to the Hedyotis,Oldenlandia complex of tribe Spermacoceae. Amphistemon and Thamnoldenlandia are sister taxa and share a common ancestor with the Madagascan endemic genus Astiella. A second, but not closely related, Madagascan clade includes the endemic genera Lathraeocarpa and Gomphocalyx and the Afro-Madagascan genus Phylohydrax. This indicates that the Madagascan endemic members of Spermacoceae are the result of at least two independent colonization events, most likely by long-distance dispersal from the African mainland. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163, 447,472. [source] Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence dataBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2002NINA RØNSTED A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria. Aragoa is sister to genus Plantago. Plantago subgenus Littorella is sister to the other subgenera of Plantago. The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans. Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni, endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 139, 323,338. [source] | ||||||||||||||||||||||