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35 results for “cpDNA”
Data from: Phylogenetic relationships of Iranian Allium sect. Allium (Amaryllidaceae, Allioideae) as inferred from nrDNA ITS, cpDNA rps16 and trnL–F sequences
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Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences
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Simulation of the evolution of codon usage in cpDNA
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Data from: Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences
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Context-dependent substitution matrices for coding regions of angiosperm cpDNA
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SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
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Data from: Next-Gen phylogeography of rainforest trees: measuring landscape-level cpDNA variation from whole-genome sequencing.
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Data from: Analyzing reticulate relationships using CpDNA and pyrosequenced ITS1 as exemplified by Veronica subgen. Pseudolysimachium (Plantaginaceae)
Veronica subgen. Pseudolysimachium constitutes a group of about 28 species across northern Eurasia, many of them with considerable intraspecific morphological variation. This intraspecific variation may be due to large geographical distribution area, wide ecological amplitude, or widespread hybridization and polyploidization. Several recent studies using molecular data have shown that hybridization as an explanation for generating evolutionary novelties and high intraspecific variation may be more common than previously thought. Here we investigate the importance of hybridization in generating morphological variation and blurring species boundaries in V. subgen. Pseudolysimachium using analyses of cpDNA sequences from 139 individuals from 18 species and ten putative hybrids, and pyrosequenced ITS1 nrDNA sequences from 37 individuals from 16 species and four putative hybrids. In addition, we estimated ploidy levels for 42 individuals of ten species and five putative hybrids using flow cytometry. Analyses of cpDNA did not resolve phylogenetic structure (most of the species were polyphyletic). Our second approach, pyrosequencing of ITS1, generated up to nine different unique sequences per individual and phylogenetic analyses of the dataset resolved some basal nodes but, again, species were often non-monophyletic. The results are most compatible with a scenario of an East Asian origin and repeated spread across Pleistocene Eurasian steppes, known as important plant diversification center, with frequent interspecific hybridization. We compare the applicability of these molecular regions for resolving hybridizing species complexes and specifically address hypotheses of hybrid origins for several species within the subgenus. However, any population genetic, phylogeographic or other analysis of evolutionary questions in one species alone would be futile without considering introgression from related species.
FIGURE 3 in Phylogeny of Chinese Chamaesium (Apiaceae: Apioideae) inferred from ITS, cpDNA and morphological characters
FIGURE 3. Geographic distribution of Chamaesium in China.
Figure 2 from: Groppo M, Kallunki J, Pirani J, Antonelli A (2012) Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family. PhytoKeys 19: 9-29. https://doi.org/10.3897/phytokeys.19.3912
Figure 2 - A summary of the phylogenetic relationships of proposed subfamilies in Rutaceae, with some non-molecular characteristics plotted onto a simplified cladogram based on the Bayesian tree. Chloroxylon is doubtfully attached to Aurantieae. Haplophyllum and Cneoridium (both from Englerian Ruteae but closer to Aurantieae that to remaining Ruteae, see Salvo et al. 2010) are missing. Amyris (from Englerian Toddalioideae), also close to Aurantieae (unpublished results) is also missing. The RTF clade corresponds to the bulk of Englerian Rutoideae, plus Toddalioideae and Flindersia. For discussion of characteristics see Waterman and Grundon (1983), Stace et al. (1993), Groppo et al. (2008), and Appelhans et al. (2011, 2012b).
Figure 1 from: Groppo M, Kallunki J, Pirani J, Antonelli A (2012) Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family. PhytoKeys 19: 9-29. https://doi.org/10.3897/phytokeys.19.3912
Figure 1 - Majority-rule consensus tree of Rutaceae estimated using Bayesian inference on a combined rps16 and trnL-trnF dataset. Posterior probabilities (PP ≥50%) are shown above branches. Bootstrap percentages (BP, only for branches in agreement with those obtained in the Bayesian analysis) follow posterior probabilities; when only one number appears supporting a clade it refers to Bayesian posterior probabilities. Taxon names are color-coded to indicate their Englerian assignment to subfamilies. A new proposal that recognizes monophyletic groups (subfamilies Cneoroideae and Rutoideae and tribe Aurantieae) is indicated by the vertical bars. The position of Pitavia punctata, as well as the Rutaceae, the "RTF" (from Rutoideae, Toddalioideae and Flindersia) and "AAMAO" ("African-Asian-Malesian-Astralasian-Oceanic") clades (see text) are indicated by arrows. Note: Zanthoxylum is pantropical.
Data from: Analyzing reticulate relationships using CpDNA and pyrosequenced ITS1 as exemplified by Veronica subgen. Pseudolysimachium (Plantaginaceae)
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FIGURE 2 in Systematic position of Rivina humilis var. humilis, R. humilis var. bracteata and R. bengalensis based on nrDNA ITS and cpDNA rbcL & trnH-psbA sequence data
FIGURE 2. Best ML tree retrieved after analysing 14 taxa of family Phytolaccaceae. (Combined rbcL + trnH-psbA. The best fit model of evolution GTR+G+I. The tree rooted at Phytolacca acinose (Lee et al. 2013).
cpDNA sequecnes of Themeda triandra and Heteropogon contortus
<p>To investigate the historical continuity of grassy biomes in southwest China, we examined the biogeographies and evolutionary histories of two widespread and dominant C<sub>4</sub> grasses, <i>Themeda triandra</i> and <i>Heteropogon contortus</i>, in Yunnan and southern Sichuan provinces, using chloroplast DNA markers in combination with climate data.</p>
cpDNA sequecnes of Themeda triandra and Heteropogon contortus
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