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Dinoflagellate Phylogeny as Inferred from Heat Shock Protein 90 and Ribosomal Gene Sequences  [PDF]
Mona Hoppenrath,Brian S. Leander
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013220
Abstract: Interrelationships among dinoflagellates in molecular phylogenies are largely unresolved, especially in the deepest branches. Ribosomal DNA (rDNA) sequences provide phylogenetic signals only at the tips of the dinoflagellate tree. Two reasons for the poor resolution of deep dinoflagellate relationships using rDNA sequences are (1) most sites are relatively conserved and (2) there are different evolutionary rates among sites in different lineages. Therefore, alternative molecular markers are required to address the deeper phylogenetic relationships among dinoflagellates. Preliminary evidence indicates that the heat shock protein 90 gene (Hsp90) will provide an informative marker, mainly because this gene is relatively long and appears to have relatively uniform rates of evolution in different lineages.
A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences
Guido W. Grimm,Susanne S. Renner,Alexandros Stamatakis,Vera Hemleben
Evolutionary Bioinformatics , 2006,
Abstract: The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.
Phylogeny of Metagentiana and related genera (Gentianaceae) inferred from nuclear ribosomal ITS sequences
用nrDNA ITS序列探讨狭蕊龙胆属及其近缘属(龙胆科)的系统发育

CHEN Sheng-Yun,CHEN Shi-Long,XIA Tao,WANG Yu-Jin,
陈生云
,陈世龙,夏涛,王玉金

植物分类学报 , 2005,
Abstract: The infrageneric phylogeny of Metagentiana, a newly erected genus in the Gentianaceae, was constructed based on the analysis of the nucleotide sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA of 10 representative species of this genus and 22 species of Gentiana, Tripterospermum and Crawfurdia. The analysis indicates that the genus Metagentiana is polyphyletic, because all sampled species of Tripterospermum and Crawfurdia are clearly embedded within Metagentiana. The species of Tripterospermum and Crawfurdia also did not cluster respectively as two monophyletic clades. These results do not merit status of three separate genera. However, these three genera clustered together as a monophyletic clade sister to Gentiana, which is in agreement with the previous conclusions on the separation of Metagentiana from Gentiana and its closer relationship to Tripterospermum and Crawfurdia based on studies of gross morphology, floral anatomy, chromosomes, palynology and embryology. The ITS sequences do not provide sufficient information to make a robust estimation of the phylogenetic relationships among dysploid cytotypes of x=17, 21 and 23, within the Metagentiana, Tripterospermum and Crawfurdia complex, but the preliminary results seem to indicate their reticulate and paralleling evolution.
Phylogeny of Metagentiana and related genera (Gentianaceae) inferred from nuclear ribosomal ITS sequences
用nrDNA ITS序列探讨狭蕊龙胆属及其近缘属 (龙胆科)的系统发育

CHEN Sheng-Yun,CHEN Shi-Long,XIA Tao,WANG Yu-Jin,
陈生云
,陈世龙,夏涛,王玉金

中国科学院研究生院学报 , 2005,
Abstract: The infrageneric phylogeny of Metagentiana, a newly erected genus in the Gentianaceae, was constructed based on the analysis of the nucleotide sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA of 10 representative species of this genus and 22 species of Gentiana, Tripterospermum and Crawfurdia. The analysis indicates that the genus Metagentiana is polyphyletic, because all sampled species of Tripterospermum and Crawfurdia are clearly embedded within Metagentiana. The species of Tripterospermum and Crawfurdia also did not cluster respectively as two monophyletic clades. These results do not merit status of three separate genera. However, these three genera clustered together as a monophyletic clade sister to Gentiana, which is in agreement with the previous conclusions on the separation of Metagentiana from Gentiana and its closer relationship to Tripterospermum and Crawfurdia based on studies of gross morphology, floral anatomy, chromosomes, palynology and embryology. The ITS sequences do not provide sufficient information to make a robust estimation of the phylogenetic relationships among dysploid cytotypes of x=17, 21 and 23, within the Metagentiana, Tripterospermum and Crawfurdia complex, but the preliminary results seem to indicate their reticulate and paralleling evolution.
A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences  [PDF]
Nan Song,Ai-Ping Liang,Cui-Ping Bu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0048778
Abstract: Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadom?orpha),Heteroptera),and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Hanno Teeling, Frank Gloeckner
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-66
Abstract: RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs.Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign is a first step in this direction and may be particularly interesting to scientists involved in whole genome sequencing of representatives of new or sparsely studied eubacterial phyla. RibAlign is available at http://www.megx.net/ribalign webciteAnalysis of 16S ribosomal rRNA (rRNA) sequences is currently the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. There are various reasons that have made the 16S rRNA gene the first choice as a phylogenetic marker, such as the presence of positions with different evolutionary rates, its universal occurrence within prokaryotes, its reasonable information content, a length that was suitable for complete sequencing when the technique started, knowledge about its secondary structure that helps with alignments and finally the presence of a comprehensive database of more than hundred thousand sequences [1]. With ARB [2], there is also a well-curated 16S rRNA database with a curated alignment and a program suite for phylogenetic reconstructions available that has gained broad acceptance among s
Eumalacostracan phylogeny and total evidence: limitations of the usual suspects
Ronald A Jenner, Ciara Dhubhghaill, Matteo P Ferla, Matthew A Wills
BMC Evolutionary Biology , 2009, DOI: 10.1186/1471-2148-9-21
Abstract: We combined evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) with a newly synthesized morphological dataset. We tested the homogeneity of data partitions, both in terms of character congruence and the topological congruence of inferred trees. We also performed Bayesian and parsimony analyses on separate and combined partitions, and tested the contribution of each partition. We tested for potential long-branch attraction (LBA) using taxon deletion experiments, and with relative rate tests. Additionally we searched for molecular polytomies (spurious clades). Lastly, we investigated the phylogenetic stability of taxa, and assessed their impact on inferred relationships over the whole tree. We detected significant conflict between data partitions, especially between morphology and molecules. We found significant rate heterogeneity between species for both the 18S rRNA and combined datasets, introducing the possibility of LBA. As a test case, we showed that LBA probably affected the position of Spelaeogriphacea in the combined molecular evidence analysis. We also demonstrated that several clades, including the previously reported and surprising clade of Amphipoda plus Spelaeogriphacea, are 'supported' by zero length branches. Furthermore we showed that different sets of taxa have the greatest impact upon the relationships within molecular versus morphological trees.Rate heterogeneity and conflict between data partitions mean that existing molecular and morphological evidence is unable to resolve a well-supported eumalacostracan phylogeny. We believe that it will be necessary to look beyond the most commonly utilized sources of data (nuclear ribosomal and mitochondrial sequences) to obtain a robust tree in the future.Attempts to infer the phylogeny of eumalacostracans have been high on the agenda of systematic zoology at least " [s]ince the awakening in natural science which followed the publica
Phylogeny of the Aconitum delavayi complex (Ranunculaceae ) based on evidence from nuclear ribosomal ITS sequences
紫乌头复合体nrDNA的ITS序列与系统发育分析

ZHANG Fu-Min,GE Song,CHEN Wen-Li,
张富民
,葛颂,陈文俐

中国科学院研究生院学报 , 2003,
Abstract: Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nr DNA) we re used to investigate the phylogeny of the Aconitum delavayi complex that was found mainly in Hengduan Mountains, SW China. Based on maximum parsimony and neighbor -joining
Ribosomal proteins expression and phylogeny in alpaca (Lama pacos) skin  [PDF]
Junming Bai, Ruiwen Fan, Shanshan Yang, Yuankai Ji, Jianshan Xie, Chang-Sheng Dong
Advances in Bioscience and Biotechnology (ABB) , 2012, DOI: 10.4236/abb.2012.33032
Abstract: Ribosomal proteins (RP) has been reported as a central player in the translation system, and are required for the growth and maintenance of all cell kinds. RP genes form a family of homologous proteins that express in the stable pattern and were used for phylogenetic analysis. Here we constructed a cDNA library of alpaca skin and 13,800 clones were sequenced. In the cDNA library, RP genes from skin cDNA library of alpaca were identified. Then 8 RP genes were selected at random and built the phylogenetic trees from the DNA sequences by using parsimony or maximum likelihood methods for molecular and evolutionary analysis of ribosomal proteins. The results showed that the 42 RP genes of alpaca have been expressed in alpaca skin. They were highly conserved. The phylogeny inferred from all these methods suggested that the evolutionary distances of alpaca RP genes were closer to rat.
Phylogeny of 12 species of genusGlycine Willd. reconstructed with internal transcribed region in nuclear ribosomal DNA
Dongwei Hui,Shouyi Chen,Bingchang Zhuang
Science China Life Sciences , 1997, DOI: 10.1007/BF02882041
Abstract: The ITS-Is of 24 accessions belong to 10 species of subgenusGlycine, and 2 species of subgenusSoja of genusGlycine were amplified, cloned and sequenced. According to the homology of the sequences, the phylogeny of the 24 accessions were reconstructed. The reconstructed dendrogram showed that there were some divergent genomic types found in the previously classified species, such asG. tomentella, G. canescens andG. tabacina, and they might be some cryptic species by morphologic analysis.
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