A phylogenetic analysis of the Chamelaucium alliance (Myrtaceae)

2002 ◽  
Vol 15 (4) ◽  
pp. 535 ◽  
Author(s):  
N. Lam ◽  
P. G. Wilson ◽  
M. M. Heslewood ◽  
C. J. Quinn
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Sensu Stricto ◽  
Fruit Type ◽  
Generic Status ◽  
Matk Gene

Analysis of sequence data from the matK gene and the atpβ–rbcL intergenic spacer for 70 representatives of the Chamelaucium alliance sensu Briggs and Johnson (1979) provides strong support for the monophyly of the alliance, but there is no support for their concept of suballiances on the basis of fruit type: indehiscent fruit have arisen in multiple lineages. There is, however, strong support for Calytrix, Homalocalyx and Ochrosperma being the first lineages to diverge within the alliance. A number of genera within the alliance are not monophyletic in this analysis, namely Astartea, Babingtonia, Baeckea sensu lato, Darwinia and Hypocalymma. Monophyly of Baeckea sensu stricto, Euryomyrtus, Ochrosperma, Rinzia, Scholtzia and Triplarina is strongly supported. Several well-supported groups that may warrant generic status have been identified.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Borrelia Isolates in Northern Colorado Identified as Borrelia bissettii

2000 ◽  
Vol 38 (8) ◽  
pp. 3103-3105 ◽  
Author(s):  
Bradley S. Schneider ◽  
Nordin S. Zeidner ◽  
Thomas R. Burkot ◽  
Gary O. Maupin ◽  
Joseph Piesman
Keyword(s):  
Phylogenetic Analysis ◽  
Borrelia Burgdorferi ◽  
Intergenic Spacer ◽  
Sensu Stricto ◽  
Ribosomal Genes ◽  
Northern Colorado

Previous work described Borrelia burgdorferi sensu lato group DN127 as a new genospecies, Borrelia bissettii, and prompted the present study to identify the Borrelia spp. that exist in northern Colorado. To determine the genospecies present, we analyzed two specific intergenic spacer regions located between the 5S and 23S and the 16S and 23S ribosomal genes. Phylogenetic analysis of the derived sequences clearly demonstrated that these isolates, originating from rodents captured in the foothills of northern Colorado, diverged from B. burgdorferi sensu stricto by 5 to 5.5% and were members of the new genospecies B. bissettii.

Scytolyngbya timoleontis, gen. et sp. nov. (Leptolyngbyaceae, Cyanobacteria): a novel false branching Cyanobacteria from China

Phytotaxa ◽  
2015 ◽  
Vol 224 (1) ◽  
pp. 72 ◽  
Author(s):  
Gaofei Song ◽  
Yongguang Jiang ◽  
Renhui Li
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Type Species ◽  
Intergenic Spacer ◽  
Secondary Structures ◽  
Sensu Stricto ◽  
Polyphasic Approach ◽  
23S Rrna ◽  
Rrna Sequences ◽  
16S Rrna Sequences

A novel genus within Leptolyngbyaceae related to Leptolyngbya morphotypes, Scytolyngbya, gen. nov., is described based on a polyphasic approach in the present study. From a freshwater sample with filaments of oscillatorean cyanobacteria from a well in Hubei Province, China, Scytolyngbya (type species: Scytolyngbya timoleontis, sp. nov.) was found to possess richly and repeatedly false branches and thick sheaths, which distinguishs this genus from Leptolyngbya sensu stricto. Phylogenetic analysis based on 16S rRNA sequences showed that this species was clustered into the Leptolyngbyaceae and separated from the type species Leptolyngbya boryana. The secondary structures of 16S-23S rRNA intergenic spacer of Scytolyngbya timoleontis did not correspond to any previously described species in cyanobacteria.

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

2012 ◽  
Vol 25 (1) ◽  
pp. 1 ◽  
Author(s):  
Anna E. Syme ◽  
Daniel J. Murphy ◽  
Gareth D. Holmes ◽  
Stuart Gardner ◽  
Rachael Fowler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Molecular Data ◽  
Species Level ◽  
Internal Transcribed Spacer Region ◽  
Deep Coalescence ◽  
History Of ◽  
Levels Of Support

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

scholarly journals Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 170
Author(s):  
Ran Li ◽  
Zhiming Lei ◽  
Wenjuan Li ◽  
Wei Zhang ◽  
Changfa Zhou
Keyword(s):  
Gene Duplication ◽  
Trna Gene ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Gene Arrangement ◽  
Stem Loop ◽  
Gene Block ◽  
Intergenic Spacers

Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

scholarly journals Molecular-phylogenetic analysis of the Cystopteridaceae family from North Asia based on plastid DNA loci

2020 ◽  
Author(s):  
D.O. Ulko ◽  
◽  
I.I. Gureyeva ◽  
R.S. Romanets ◽  
A.A. Kuznetsov ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Plastid Dna ◽  
Monotypic Genus ◽  
Phylogenetic Studies ◽  
North Asia ◽  
Matk Gene ◽  
Molecular Phylogenetic ◽  
Gymnocarpium Dryopteris

The results of molecular phylogenetic studies based on the sequencing of matK gene and trnG-R intergenic spacer of the chloroplast DNA and analysis of the concatenated data of these loci of North Asian representatives of the Cystopteridaceae family are presented. In the genus Gymnocarpium, a dryopteris-clade was distinguished including species without glandular pubescence of fronds – Gymnocarpium dryopteris. Species having glandular pubescent fronds have formed the robertianum-clade (G. robertianum and G. fedtschenkoanum), and 2 subclades, including G. continentale, G. jessoense, and G. tenuipes. In the genus Cystopteris, the analysis confirmed the separation of C. montana from other Cystopteris species, and the separation of C. sudetica from the C. fragilis-complex. This advocate the recognition of monotypic genus Rhizomatopteris including Rh. montana (≡Cystopteris montana), and allows to recognize the section Khokhrjakovia (with C. sudetica) within the genus Cystopteris. This analysis did not allow to separate the species of the type subgenus Cystopteris (C. fragilis-complex) from each other.

scholarly journals Geum sunhangii (Rosaceae), a new species from Hubei Province, China

PhytoKeys ◽  
2020 ◽  
Vol 156 ◽  
pp. 113-124
Author(s):  
Zhen-Yu Lv ◽  
Dai-Gui Zhang ◽  
Xian-Han Huang ◽  
Heng-Chang Wang ◽  
Jing-Yuan Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Nature Reserve ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Hubei Province ◽  
Terminal Leaflet ◽  
National Nature Reserve ◽  
A New Species

Geum sunhangii – first discovered in Shennongjia National Nature Reserve, Hubei Province, China – is described as a new species of Rosaceae. Compared to all known Chinese Geum species, the new species differs by possessing jointed styles, imbricate petals and a reniform radical leaf terminal leaflet. Most significantly, the jointed style is curved at an obtuse or a right angle. In addition, the inclusion of this species within the genus Geum was supported by phylogenetic analysis using the sequence data of a nuclear ribosomal internal transcribed spacer (nrITS) and a chloroplast trnL–trnF intergenic spacer. The new species was found to be closely related to G. rivale and G. aleppicum.

A revision of Lissanthe (Styphelioideae: Ericaceae)

2003 ◽  
Vol 16 (5) ◽  
pp. 595 ◽  
Author(s):  
Darren M. Crayn ◽  
Elizabeth A. Brown ◽  
Jocelyn M. Powell
Keyword(s):  
New Species ◽  
Western Australia ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
New Combinations ◽  
Abaxial Surface ◽  
Distribution Maps ◽  
Two New Species ◽  
Matk Gene

A revision of the styphelioid genus Lissanthe recognises seven species and two subspecies: L. brevistyla A.R.Bean, L. sapida R.Br., L. strigosa (Sm.) R.Br. subsp. strigosa, L. strigosa subsp. subulata (R.Br.) J.M.Powell. New combinations are made for two species transferred from Leucopogon: Lissanthe rubicunda (F.Muell.) J.M.Powell, D.M.Crayn & E.A.Br. and Lissanthe pluriloculata (F.Muell.) J.M.Powell, D.M.Crayn & E.A.Br. Two new species from Western Australia, Lissanthe powelliae D.M.Crayn & E.A.Br. and L. scabra D.M.Crayn & E.A.Br. are described, and Lissanthe sapida is lectotypified. Keys, illustrations and distribution maps are provided for all taxa. Lissanthe as defined here is a strongly supported clade based on analyses of sequence data from two chloroplast loci, the atpB–rbcL intergenic spacer and the matK gene. Potential morphological synapomorphies for Lissanthe include flowers pedicellate above the bracteoles, styles hairy at least at the base, and leaves with an abaxial surface that is grooved longitudinally.

Corydalis ternatifolia belongs to C. sect. Asterostigmata, not C. sect. Incisae (Papaveraceae): Evidence from morphological and phylogenetic study

Phytotaxa ◽  
2018 ◽  
Vol 382 (2) ◽  
pp. 193
Author(s):  
XIAODONG XU ◽  
DONG WANG
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Taxonomic Position ◽  
Perennial Herb ◽  
Phylogenetic Study ◽  
Molecular Evidence ◽  
Morphological Comparison ◽  
Matk Gene

Corydalis ternatifolia (Papaveraceae), a perennial herb endemic to China, shares morphological similarities with both C. sect. Incisae and C. sect. Asterostigmata, rendering its taxonomic position controversial. In this study, we carried out a detailed morphological comparison of C. ternatifolia with the related species and conducted a phylogenetic analysis of C. ternatifolia and five species from C. sect. Incisae, three species from C. sect. Asterostigmata (including the type species of these two sections), and additional 21 species of Corydalis from 10 other sections. To reconstruct the phylogenetic relationships, sequences of the nuclear NADPH gene and chloroplast DNA (matK gene + trnG intron) were analyzed using Bayesian inference and maximum parsimony. The resulting four phylogenetic trees shared almost identical topology and resolved C. ternatifolia within C. sect. Asterostigmata with strong support. Our results suggested that C. ternatifolia belongs to the C. sect. Asterostigmata. This study has demonstrated that molecular evidence is effective in resolving the sectional placement of Corydalis species with elusive taxonomic position.

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