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52 results for “chloroplast DNA”
Fig. 3 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 3. — Strict consensus of 10,000 most parsimonious trees resulting from the analysis of 58 ITS sequences; tree length = 725 steps; consistency index = 0.518; retention index = 0.734. Clades denoted by brackets are those referred to in text. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
Fig. 2 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 2. — The single most parsimonious tree resulting from the combined analysis of ITS + trnL-trnF + 5S spacer sequences, based on the identical 24-taxon sampling as used in Fig. 1; tree length = 349 steps; consistency index = 0.663; retention index = 0.770. Values along nodes are bootstrap percentages; nodes with dashed branches have bootstraps below 70%. Identical or near identical clades (labeled A-E) from Fig. 1 are also labeled, as is the placement of Polyscias sambucifolia and P. microbotrys (asterisks), as discussed in text. Outgroups indicated by "OG."
Fig. 4 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 4. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 40 trnL-trnF sequences; tree length = 122 steps; consistency index = 0.938; retention index = 0.972. Values along branches are bootstrap percentages. Placement of Polyscias elegans (discussed in text) is denoted by an asterisk. Labels for the Tieghemopanax group and other clades in "Polyscias sensu lato" follow PLUNKETT et al. (2001).
Fig. 5 in Evolution of Polyscias sect. Tieghemopanax (Araliaceae) based on nuclear and chloroplast DNA sequence data
Fig. 5. — Strict consensus of 156 most parsimonious trees resulting from the analysis of 26 5S spacer sequences; tree length = 147 steps; consistency index = 0.744; retention index = 0.849. Values along branches are bootstrap percentages.
The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China
<p>Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.</p>
Data for: Alignments of chloroplast DNA and ITS of tribe Adonideae
<p><span>The Euro-Siberian steppe flora consists of warm- and cold-adapted species, which may have responded differently to Pleistocene glacials and interglacials. Genotyping-by-sequencing individuals from across the distribution range of the pheasant's eye (<em>Adonis vernalis</em>), we aimed to gain insight into steppe florogenesis based on the species' evolutionary history. Although the primary area of origin of the species group comprising <em>A. vernalis</em>, <em>A. villosa</em> and <em>A. volgensis</em> is in Asia, our results indicate that <em>A. vernalis</em> itself is not of Asian origin but evolved in southern (incl. Southeastern) Europe during the Pleistocene, with Spanish populations being clearly genetically distinct<a> </a></span><span>from the Southeastern European populations. We inferred<a> </a></span><span>that <em>A. vernalis</em> migrated eastwards from the sub-Mediterranean forest-steppes of Southeastern Europe into the continental forest-steppe zone. Eastern European populations</span><span> had the highest private allelic richness, indicating long-term large population sizes in this region. As a thermophilic species, <em>A. vernalis</em> seems unlikely to have survived in the cold deserts of the Last Glacial Maximum in Western Siberia, so this region was likely</span><span> (re)colonized postglacially. Overall, our results reinforce the importance of identifying the area of origin and the corresponding ecological requirements of steppe plants in order to understand the composition of today's steppe flora.</span></p>
Data for: Alignments of chloroplast DNA and ITS of tribe Adonideae
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Concatenated data matrix of DNA sequences from two nuclear and four chloroplast gene regions
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Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae
<p><span>As an ancient clonal root and leaf crop, taro (<i>Colocasia esculenta</i>) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other <i>Colocasia</i> species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea. </span></p>
Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
Data from: Chloroplast DNA-based phylogeography of Tilia americana (Malvaceae)
A comprehensive picture of how plant species and communities move and evolve over time will require that a variety of species be studied, including plants with different life histories, rarity, and distributions. Relatively few phylogeographic studies have focused on trees. In the present study, the phylogeographic history of Tilia americana, American basswood, was investigated. Samples were collected from throughout the United States and Mexican ranges of basswood, and a phylogenetic analysis was conducted based on sequence data from two non-coding chloroplast DNA regions. The results showed no evidence for the various hypotheses of multiple basswood species within the U. S. A., but there is evidence for a divergence between a Mexican and U. S. A. clade within basswood. Population genetics and spatial statistical analyses were also performed, and supported the conclusion that the only significant geographic barrier within the North American basswoods is found between U. S. A. and Mexico. An attempt was also made to interpret the anomalous geographic distribution of certain chloroplast haplotypes, raising further questions about past migration routes of North American temperate forest trees.
Supplementary material 1 from: Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT (2022) Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PhytoKeys 188: 1-18. https://doi.org/10.3897/phytokeys.188.75937
NCBI accession numbers of DNA barcoding sequences, and complete chloroplast genomes used in this study.
Fig. 3 in A phylogeny of Cephaloziaceae (Jungermanniopsida) based on nuclear and chloroplast DNA markers
Fig. 3 Majority-rule consensus tree of trees recovered in stationary phase of Bayesian search; includes Nowellia and Cephalozia. Bayesian posterior probabilities (bold), MP- (italics), and ML-bootstrap percentage values are given at branches
Fig. 4 in A phylogeny of Cephaloziaceae (Jungermanniopsida) based on nuclear and chloroplast DNA markers
Fig. 4 Majority-rule consensus tree of trees recovered in stationary phase of Bayesian search; includes Fuscocephaloziopsis. Bayesian posterior probabilities (bold), MP- (italics), and ML-bootstrap percentage values are given at branches
Fig. 2 in A phylogeny of Cephaloziaceae (Jungermanniopsida) based on nuclear and chloroplast DNA markers
Fig. 2 Majority-rule consensus tree of trees recovered in stationary phase of Bayesian search; includes Alobielloideae and Odontoschismatoideae. Bayesian posterior probabilities (bold), MP- (italics), and ML-bootstrap percentage values are given at branches
FIGURE 2 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 2. Majority rule consensus tree from the BI analysis of the "total evidence" dataset from morphological and molecular data. Black lines represent the branches that remained identical in the strict consensus tree of the MP analysis. Grey lines represent branches obtained only in the BI analysis. Numbers in the nodes correspond to posterior probabilities and bootstrap values (PP/BT); dashes (-) represent low (<50%) or no BT support.
FIGURE 1 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 1. Comparison of the phylogenetic hypothesis provided by the independent morphological and molecular datasets. Species of Ronnbergia are highlighted in red. A. Strict consensus of the four most parsimonious trees from the MP analysis of morphological data. Numbers in the nodes correspond to bootstrap values. B. Majority rule consensus tree from the BI analysis of the molecular dataset. Numbers in the nodes correspond to posterior probabilities and bootstrap values (PP/BT); dashes (-) represent low (<50%) or no BT support.
FIGURE 3 in Is Ronnbergia (Bromeliaceae, Bromelioideae) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data
FIGURE 3. Geographic distribution of the three clades containing species of Ronnbergia. Data points were obtained from the Global Biodiversity Information Facility—GBIF (www.gbif.org).
FIGURE 2 in Phylogenetic position and independent generic status of Indocypraea (Asteraceae-Heliantheae-Ecliptinae): evidence from chloroplast DNA sequences
FIGURE 2. Phylogeny of the subtribe Ecliptinae (Asteraceae: Heliantheae) based on chloroplast DNA sequences by using maximum likelihood analysis. Bootstrap values (≥ 70%; maximum likelihood/maximum parsimony) are indicated above branches, and posterior probabilities (≥ 0.95) below branches.
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