Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

2006 ◽  
Vol 84 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Ihsan A. Al-Shehbaz ◽  
Connie A. Sauder
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
New Combinations ◽  
Arabidopsis Lyrata ◽  
Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

Evolutionary relationships in Oxytropis species, as estimated from the nuclear ribosomal internal transcribed spacer (ITS) sequences point to multiple expansions into the Arctic

Botany ◽  
2012 ◽  
Vol 90 (8) ◽  
pp. 770-779 ◽  
Author(s):  
Annie Archambault ◽  
Martina V. Strömvik
Keyword(s):  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Its Sequences ◽  
The Arctic ◽  
Evolutionary Relationships ◽  
Data Set ◽  
The North ◽  
North American Arctic

Species of the genus Oxytropis are distributed in the northern hemisphere, especially in alpine and arctic areas. Although comprehensive taxonomic treatments exist for local floras, an understanding of the evolutionary relationships is lacking for the genus as a whole. To determine if different ancestral Oxytropis species colonized the North American Arctic separately, as suggested by taxonomy, we sequenced the nuclear ribosomal internal transcribed spacer (ITS) region from 16 Oxytropis specimens, including four species that were used in a previous transcriptome study. In addition, 81 other Oxytropis ITS sequences were retrieved from public sequence databases and included in the analysis. The whole data set was analyzed using phylogenetic trees and statistical parsimony networks. Results show that all Oxytropis ITS sequences are very similar. Furthermore, at least six lineages evolved from different temperate ancestors to colonize the North American Arctic. This pattern is believed to be typical of the arctic flora. Additionally, the sequence relationship analyses confirm that the subgenus Phacoxytropis may be ancestral in Oxytropis.

On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 730-743 ◽  
Author(s):  
Malika L. Ainouche ◽  
Randall J. Bayer
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Direct Sequencing ◽  
Diploid Species ◽  
Pcr Amplification ◽  
Nuclear Ribosomal Dna ◽  
Species Introduction ◽  
Bromus Hordeaceus ◽  
Allotetraploid Species

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid–diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli–henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli–henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the tetraploid Bromus adoensis are sister taxa within section Bromus; they belong in a weakly differentiated clade with the diploids Bromus brachystachys, Bromus japonicus, Bromus squarrosus, Bromus arvensis, and Bromus intermedius.Key words: Bromus, allopolyploidy, ITS, ribosomal DNA, phylogeny.

scholarly journals (269) Taxonomic Relationship of Korean Native Aster, Based on Internal Transcribed Spacer (ITS) Sequences of Nuclear Ribosomal DNA

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1017A-1017
Author(s):  
Su-Young Hong ◽  
Kwang-Soo Cho ◽  
Ki-Oug Yoo ◽  
Jong-Taek Suh ◽  
Dong-Lim Yoo
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Its Region ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Its2 Region ◽  
Base Pairs ◽  
Total Length

There are 25 species of aster in Korea. There is a controversy about the taxonomical classification of Aster. The genus Aster was classified into four genera, Aster, Gymnaster, Kalimeris, and Heteropappus, by morphological characters. In order to clarify the phylogenetic position of aster, the nucleotide sequence of the nuclear ribosomal DNA internal transcribed spacer (ITS) region was compared among 11 taxa in Korean native aster. The size of ITS1 and ITS2 ranged from 283 to 286 bp and from 251 to 257 bp, respectively. The size of 5.8S region was 164 bp in 11 taxa. The total length of ITS1, 5.8S and ITS2, A. tripolium was shown to be the shortest length, 701 bp; and A. scaber was shown to be the longest length, 706 bp. The G+C content of ITS1 ranged from 47.9% to 51.2% and ITS2 ranged from 52.2% to 55.1%. The range of each taxon was narrow. The total length of the character matrix was 708 characters. Among them, total indel showed 9; in the ITS1 region indel showed 6 it was 67%; and in the ITS2 region, indel showed 3. Most of the indels showed deletion or insertion of only one base pair, but in A. spathulifolius deleted two base pairs and in A. tripolium deleted five base pairs. But in A. yomena, A. hayatae, A. koraiensis, and A. hispidus, the indel was not detected. Phylogenetic trees did not even make a difference inter-genus, but A. yomena and A. koraiensis called genus Kalimeris and genus Gymnaster, respectively; these constituted a clade. A. hispidus called genus Heteropappus was placed as a sister group to the clade of A. ageratoides and A. glehni.

Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal DNA internal transcribed spacers

1997 ◽  
Vol 75 (4) ◽  
pp. 519-532 ◽  
Author(s):  
Y. J. Liu ◽  
S. O. Rogers ◽  
Y. J. Liu ◽  
J. F. Ammirati
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Herbarium Specimens ◽  
Data Reorganization ◽  
Taxonomic Groups

The genus Cortinarius Fr. (Cortinariaceae, Agaricales) is divided into four or more subgenera. Dermocybe (Fr.) Sacc. has been recognized as either a subgenus of Cortinarius or a separate genus, distinguished in part by the presence of various anthraquinonic pigments. Nucleotide sequences of ribosomal DNA 5.8S and internal transcribed spacers were used to investigate the phylogenetic relationships among species of Dermocybe and selected taxa from subgenera of Cortinarius. Sequence data from 47 herbarium specimens representing 31 taxa (28 species plus 3 varieties) of Dermocybe and Cortinarius were analyzed using parsimony, maximum likelihood, and neighbor joining. In general, molecular data support the morphological groupings of the taxa, although they more closely correspond to biochemical (anthraquinone and other) analyses. Phylogenetic trees showed that, while the sections Dermocybe and Malicoriae are monophyletic, and the concolorous or almost concolorous red species (section Sanguineae, such as D. sanguinea and relatives) together formed a coherent clade, the subgenus Dermocybe sensu lato itself is polyphyletic. Cortinarius californicus clusters with taxa in Cortinarius, subgenus Telamonia, section Armillati. Dermocybe olivaceopicta is more closely related to other subgenera of Cortinarius than to Dermocybe. Within the genus Cortinarius, certain of the subgenera may actually represent coherent genera. Of the subgenera examined, Telamonia, Phlegmacium, and possibly Sericeocybe appear to represent well defined taxonomic groupings. However, current assignments of taxa within Leprocybe and Myxacium were inconsistent with the molecular data. Reorganization of some taxa and taxonomic groups is suggested. Key words: Dermocybe, Cortinarius, molecular phylogeny, rDNA, ITS1, ITS2.

PHYLOGENY AND SPECIES RELATIONSHIPS IN JASIONE (CAMPANULACEAE) WITH EMPHASIS ON THE ‘MONTANA-COMPLEX’

2005 ◽  
Vol 62 (1-2) ◽  
pp. 29-51 ◽  
Author(s):  
S. PÉREZ-ESPONA ◽  
F. SALES ◽  
I. HEDGE ◽  
M. MÖLLER
Keyword(s):  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Shetland Islands ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Recent Origin ◽  
Higher Rank ◽  
Sample Set ◽  
Larger Sample

The evolutionary relationships of several, mainly Iberian, Jasione taxa (Campanulaceae) were investigated using molecular data. A parsimony analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA was partially successful in elucidating some interspecific alliances. One of the main clades included three morphologically rather disparate species from S Spain and Morocco which might indicate that these areas were refugia during the last glaciations. The fact that most of the other taxa fell in a large polytomy suggests a recent origin of these species. Amplified fragment length polymorphisms (AFLPs) were analysed for a larger sample set of two taxa from within the ITS polytomy to assess the partition of genetic variation between and within populations. All the British accessions named J. montana var. montana were found to be close to those so-named from Spain. However, individual accessions of J. montana var. montana from Argyll (Scotland), Devon (SW England) and the Shetland Islands proved to be genetically different from each other. This might suggest a low level of genetic diversification from a common progenitor due to a rapid northward migration. It is proposed that J. montana var. bracteosa and J. maritima var. sabularia merit recognition at higher rank. The possibility that J. montana vars gracilis and latifolia are mere repetitive segregants of J. montana var. montana is considered.

The phylogenetic relationships of the anaerobic chytridiomycetous gut fungi (Neocallimasticaceae) and the Chytridiomycota. I. Cladistic analysis of rRNA sequences

1992 ◽  
Vol 70 (9) ◽  
pp. 1738-1746 ◽  
Author(s):  
Jinliang Li ◽  
I. Brent Heath
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
18S Rrna ◽  
Cladistic Analysis ◽  
Anaerobic Fungi ◽  
Confidence Limits ◽  
Maximum Likelihood Algorithm ◽  
Rrna Sequences ◽  
Partial 18S

To clarify the phylogenetic relationships of the Chytridiomycota and the anaerobic fungi from the rumen and caecum of herbivorous animals, we analyzed the partial 18S rRNA sequences from 28 species ranging from protists to mammals and internal transcribed spacer 1 (ITS1) and its adjacent sequences from four gut fungi and one chytrid by using three algorithms from the Phylogeny Inference Package (PHYLIP). To get the confidence limits for each branch, we applied bootstrapping for each algorithm. Our analysis on partial 18S rRNA sequences shows that the Chytridiomycota are clustered with other fungi with 98, 76, and 30% confidences in the Fitch–Margoliash, neighbour-joining, and maximum parsimony algorithms. None of these three algorithms place any of 17 protists from 12 phyla with the fungi, including the chytrids. The same analysis also shows that the Spizellomycetales and Chytridiales cluster with the gut fungi but does not identify which order is closest to them. These results suggest that the Chytridiomycota, including the gut fungi, are indeed fungi but the gut fungi might not belong to the Spizellomycetales. The phylogenetic trees generated by the above three algorithms, plus the maximum likelihood algorithm, based on ITS1 and its adjacent regions show that Anaeromyces is more distant from Orpinomyces, Neocallimastix, and Piromyces. However, they failed to determine the relationships among the last three genera. Key words: Chytridiomycota, gut fungi, rumen fungi, phylogeny, rRNA sequences.

Peucedanum huangshanense (Apiaceae), a new species from Anhui, China

Phytotaxa ◽  
2020 ◽  
Vol 430 (1) ◽  
pp. 17-24
Author(s):  
SHAN-SHAN CHU ◽  
DE-QUN WANG ◽  
HUA-SHENG PENG ◽  
LU-QI HUANG
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
A New Species

Peucedanum huangshanense, a new species discovered in Anhui, China, is illustrated and described. Detailed morphological comparisons have showed that it is similar to P. praeruptorum but differs from the latter by having larger compound umbels (5–14 cm across), rays up to 25, and long-ovoid mericarps with lateral ribs narrowly winged. To explore the phylogenetic position of this species, nuclear ribosomal DNA internal transcribed spacer (ITS) region was sequenced for P. huangshanense and P. praeruptorum collected in different places. The morphological and molecular evidences support the hypothesis that P. huangshanense is a new distinct species.

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