scholarly journals Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

2017 ◽  
Vol 8 ◽  
Author(s):  
Wenpan Dong ◽  
Chao Xu ◽  
Wenqing Li ◽  
Xiaoman Xie ◽  
Yizeng Lu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Chloroplast Genomes ◽  
Phylogenetic Resolution

scholarly journals Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 830
Author(s):  
Delil A. Chincoya ◽  
Alejandro Sanchez-Flores ◽  
Karel Estrada ◽  
Clara E. Díaz-Velásquez ◽  
Antonio González-Rodríguez ◽  
...  
Keyword(s):  
Population Genetics ◽  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Molecular Variation ◽  
Short Sequence ◽  
Dna Variation ◽  
Chloroplast Genomes ◽  
Evolutionary Studies ◽  
Phylogenetic Resolution

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

Phylogeny and proposed circumscription of Breynia, Sauropus and Synostemon (Phyllanthaceae), based on chloroplast and nuclear DNA sequences

2012 ◽  
Vol 25 (5) ◽  
pp. 313 ◽  
Author(s):  
Kanchana Pruesapan ◽  
Ian R. H. Telford ◽  
Jeremy J. Bruhl ◽  
Peter C. van Welzen
Keyword(s):  
Bayesian Inference ◽  
Dna Sequences ◽  
Dna Markers ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Morphological Features ◽  
Monophyletic Group ◽  
Infrageneric Classification ◽  
Generic Rank ◽  
Phylogenetic Resolution

Previous estimates of phylogeny in the Phyllanthaceae, Phyllantheae, have been hampered by undersampling of species from morphologically distinctive groups and using too few gene regions. To increase the phylogenetic resolution, sequences of two nuclear (ITS1–5.8S–ITS2) and Phytochrome C (PHYC)) and two non-coding chloroplast (accD–psaI, trnS–trnG) DNA markers were analysed using maximum parsimony and Bayesian inference with expanded sampling in Breynia, Glochidion, Sauropus and Synostemon. Our results supported reinstatement of Synostemon, previously included in Sauropus s.str., to generic rank, and provided evidence towards its future infrageneric classification. The results also indicated expansion of Breynia to include Sauropus s.str.; this combined monophyletic group consists of two strongly supported clades. Finally, we showed monophyly for Glochidion, which is sister to Phyllanthus subg. Phyllanthodendron, both still remaining undersampled. Morphological features characteristic of Breynia, Sauropus and Synostemon are discussed, as well as the desirability of dividing Phyllanthus into smaller genera.

scholarly journals Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences

2009 ◽  
Vol 104 (3) ◽  
pp. 403-416 ◽  
Author(s):  
Gerardo A. Salazar ◽  
Lidia I. Cabrera ◽  
Santiago Madriñán ◽  
Mark W. Chase
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Dna

Phylogenetics and evolution of the aphid genus Uroleucon based on mitochondrial and nuclear DNA sequences

1999 ◽  
Vol 24 (1) ◽  
pp. 85-93 ◽  
Author(s):  
Nancy A. Moran ◽  
Matthew E. Kaplan ◽  
Michael J. Gelsey ◽  
Troy G. Murphy ◽  
Edwin A. Scholes
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna

scholarly journals Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Masahiko Muraji ◽  
Norio Arakaki ◽  
Shigeo Tanizaki
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Evolutionary Relationship ◽  
Early Pleistocene ◽  
Ryukyu Islands ◽  
Mtdna Sequences ◽  
Northern Half ◽  
The Ryukyu Islands ◽  
History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

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