Revisiting phylogenetic relationships in Phoradendreae (Viscaceae): utility of the trnL-F region of chloroplast DNA and presence of a homoplasious inversion in the intergenic spacer

Botany ◽  
2017 ◽  
Vol 95 (3) ◽  
pp. 247-258 ◽  
Author(s):  
Vanessa E.T.M. Ashworth
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Relationships ◽  
Nucleotide Substitution ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Maximum Parsimony Analysis ◽  
Tropical Species ◽  
F Region

The utility of the trnL-F region of the chloroplast DNA for inferring relationships in 26 taxa in the mistletoe tribe Phoradendreae (Viscaceae) was compared with that of sequences from three regions of the nuclear ribosomal DNA (nrDNA). Chloroplast- and nuclear-inferred phylogenies generally were congruent based on maximum parsimony analysis of nucleotide substitution data. Results suggested that the intron and intergenic spacer of the chloroplast partition were not sufficiently variable to resolve phylogenetic relationships among either close relatives or more distantly related species. The distribution of insertions and deletions generally supported the phylogeny inferred from nucleotide substitution data. However, presence or absence of a 59-nucleotide inversion in the trnL-F intergenic spacer of eight Phoradendron species showed no agreement with the topology inferred from molecular and morphological data. Combined analyses of the nuclear partitions and the chloroplast region (with the homoplasious inversion inserted in reverse orientation) provided strong support for P. californicum as sister to a clade uniting North American species and not as sister to a clade comprising more tropical species. Consistent with results from previous studies using nrDNA, a lineage in the Phoradendron leucarpum complex (comprising subsp. leucarpum and macrophyllum) was strongly supported, but subspecies tomentosum was not confidently placed.

scholarly journals Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology

2009 ◽  
Vol 22 (3) ◽  
pp. 158 ◽  
Author(s):  
Adele K. Gibbs ◽  
Frank Udovicic ◽  
Andrew N. Drinnan ◽  
Pauline Y. Ladiges
Keyword(s):  
Chloroplast Dna ◽  
Intergenic Spacer ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Taxonomic Rank ◽  
Intergenic Spacer Region ◽  
Main Clade ◽  
Rdna Sequences ◽  
South Wales

Phylogenetic analysis of Eucalyptus subgenus Eudesmia is presented on the basis of the following three datasets: sequences of the internal transcribed spacer (ITS) and the external transcribed spacer (ETS) regions from nuclear rDNA, sequences of the psbA–trnH intergenic spacer region from chloroplast DNA, and morphological characters, including stamen bundling, operculum development, seeds and trichomes. Studies of floral development were essential for understanding the morphology of mature flowers and interpretation of synapomorphy and homoplasy. A summary phylogeny was constructed from a maximum parsimony analysis of those nodes coded as characters that had support in the molecular trees together with morphological characters. A revised infra-subgeneric classification is presented on the basis of the summary phylogeny, and compared with classifications of Hill and Johnson (1998) and Brooker (2000). Differences relate to relationships between clades and taxonomic rank (sections, series and subseries) and valid names of Brooker (2000) are conserved where possible. One main clade of 14 species (section Limbatae), many of mallee growth form, was found in all analyses; this clade is distributed in the South-West of Western Australia and adjacent Interzone and desert areas. A second main clade (section Complanatae) occurs in the northern and eastern tropical and subtropical regions of Australia, including Kimberley, Arnhem, Queensland and New South Wales. This section includes E. tetrodonta, previously treated as an isolated taxon in a monotypic section; however, this species is related to E. baileyana, E. similis, E. lirata and series Miniatae. The hypothesised phylogeny provides a framework for further analyses of biogeography and ecology, including functional traits.

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.

Allium gilanense, a new species of Allium sect. Codonoprasum (Amaryllidaceae) from Iran: evidence from morphological and molecular data

Phytotaxa ◽  
2020 ◽  
Vol 474 (3) ◽  
pp. 283-292
Author(s):  
ALI BAGHERI ◽  
FRANK R. BLATTNER ◽  
REINHARD M. FRITSCH
Keyword(s):  
New Species ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Morphological Data ◽  
Morphological Description ◽  
Allium Species ◽  
The North ◽  
North Of Iran

As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.

The Phylogeny of Rosoideae (Rosaceae) Based on Sequences of the Internal Transcribed Spacers (ITS) of Nuclear Ribosomal DNA and the trnL/F Region of Chloroplast DNA

2003 ◽  
Vol 164 (2) ◽  
pp. 197-211 ◽  
Author(s):  
Torsten Eriksson ◽  
Malin S. Hibbs ◽  
Anne D. Yoder ◽  
Charles F. Delwiche ◽  
Michael J. Donoghue
Keyword(s):  
Chloroplast Dna ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
F Region

Phylogenetic evaluation of systematics and biogeography of the leech family Glossiphoniidae

2005 ◽  
Vol 19 (2) ◽  
pp. 105 ◽  
Author(s):  
Mark E. Siddall ◽  
Rebecca B. Budinoff ◽  
Elizabeth Borda
Keyword(s):  
Parental Care ◽  
North American ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
The North ◽  
Combined Use ◽  
Vertebrate Hosts ◽  
High Degree

The phylogenetic relationships of Glossiphoniidae, a leech family characterised by its high degree of parental care, were investigated with the combined use of morphological data and three molecular datasets. There was strong support for monophyly of most accepted genera in the group, many of which are consistent with eyespot morphology. The genera Desserobdella Barta & Sawyer, 1990 and Oligobdella Moore, 1918 are suppressed as junior synonyms of Placobdella Blanchard, 1893 and thus recognising each of Placobdella picta (Verrill, 1872) Moore, 1906, Placobdella phalera (Graf, 1899) Moore, 1906, and Placobdella biannulata (Moore, 1900), comb. nov. The species Glossiphonia elegans (Verrill, 1872) Castle, 1900 and Helobdella modesta (Verrill, 1872), comb. nov. are resurrected for the North American counterparts to European non-sanguivorous species. Glossphonia baicalensis (Stschegolew, 1922), comb. nov. is removed from the genus Torix Blanchard 1898 and Alboglossiphonia quadrata (Moore, 1949) Sawyer, 1986 is removed from the genus Hemiclepsis Vejdovsky, 1884. The biogeographic implications of the phylogenetic hypothesis are evaluated in the context of what is already known for vertebrate hosts and Tertiary continental arrangements.

scholarly journals Phylogenetic Relationships within the Nematode Subfamily Phascolostrongylinae (Nematoda: Strongyloidea) from Australian Macropodid and Vombatid Marsupials

2020 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Tanapan Sukee ◽  
Ian Beveridge ◽  
Ahmad Jawad Sabir ◽  
Abdul Jabbar
Keyword(s):  
Large Intestine ◽  
Phylogenetic Relationships ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Unexpected Finding ◽  
Generic Level ◽  
Grey Kangaroo ◽  
Generic Composition

The strongyloid nematode subfamily Phascolostrongylinae comprises parasites of the large intestine and stomach of Australian macropods and wombats. In this study, we tested the phylogenetic relationships among the genera of the Phascolostrongylinae using the first and second internal transcribed spacers of the nuclear ribosomal DNA. Monophyly was encountered in the tribe Phascolostrongylinea comprising two genera, Phascolostrongylus and Oesophagostomoides, found exclusively in the large intestine of wombats. The tribe Hypodontinea, represented by the genera Hypodontus and Macropicola from the ileum and large intestine of macropods, was also found to be monophyletic. The tribe Macropostrongyloidinea, comprising the genera Macropostrongyloides and Paramacropostrongylus, was paraphyletic with the species occurring in the stomach grouping separately from those found in the large intestines of their hosts. However, Macropostrongyloidesdissimilis from the stomach of the swamp wallaby and Paramacropostrongylus toraliformis from the large intestine of the eastern grey kangaroo were distinct from their respective congeners. This study provided strong support for the generic composition of the tribe Phascolostrongylinea. The unexpected finding of M. dissimilis and P. toraliformis being distantly related to their respective congeners suggests a requirement for future taxonomic revision that may warrant separation of these species at the generic level.

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