Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).

  title={Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).},
  author={Tao Sang and D. Crawford and Tod F. Stuessy},
  journal={American journal of botany},
  volume={84 8},
The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information… 

Phylogenetic relationship and evolution analysis of the peony Paeonia species using multi-locus deoxyribonucleic acid (DNA) barcodes

Combined phylogenetic relationship of all four peony species is more clearer than any single-locus one, but the 5S rRNA gene and nrDNA ITS region showed higher variation rate.

Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae).

The fossil data, easily dispersible mucilaginous seeds, widespread autogamous breeding systems, and low levels of sequence divergence between species from different continents or islands suggest a rapid radiation of Lepidium by long-distance dispersal in the Pliocene/Pleistocene.

Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK genes of cpDNA and internal transcribed spacers of 18S–26S nrDNA

Both matK and ITS phylogenies reveal that T. rivale together with clades T. govanianum, Daiswa‐Kinugasa and Paris is basally diverged as a sister group to the remainder of Trillium.

Molecular phylogenetic evidence for the origin of a diploid hybrid of Paeonia (Paeoniaceae).

Paeonia anomala is identified as a diploid hybrid that originated from a cross between P. veitchii and P. lactiflora and Phenotypic evolution resulting from the combination of two diverged genomes might have occurred primarily at the physiological level and allowed P. anomalia to adapt to geographic regions different from those of its parents.

Chloroplast DNA variation and reticulate evolution in sexual and apomictic sections of dandelions

Sequencing of the trnL–trnF intergenic spacer in chloroplast DNA (cpDNA) from 237 sexual and apomictic species of dandelions (genus Taraxacum) from Europe, Asia and arctic North America revealed 46

Plastid DNA sequence data help to clarify phylogenetic relationships and reticulate evolution in Lycoris (Amaryllidaceae)

Comparing the phylogenetic results obtained using nuclear genomic data to those from the plastid genome, a much clearer picture of the role that hybridization and reticulation have played in the evolution of Lycoris is emerging.

Phylogeny and biogeography of Asian Schefflera (Araliaceae) based on nuclear and plastid DNA sequence data

The phylogeny of Asian Schefflera was inferred from sequences of the nuclear ribosomal internal transcribed spacer region, and six plastid regions (the ndhF gene, the trnL‐trnF region, the atpB‐rbcL intergenic spacer, the rpl16 intron, and the psbA‐ TrnH intergenicSpacer region) to support the monophyly of the genus.

Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences.

The results suggested that: the St, H, P, and W genomes in polyploid Elymus were donated by Pseudoroegneria, Hordeum, Agropyron and Australopyrum, respectively; and some Elymus species showed multiple origin and experienced recurrent hybridization.


The joint use of ITS and cpDNA markers facilitates independent assessment of intraspecific phylogenetic hypotheses and can expose cases in which introgression or phylogenetic sorting has caused incongruencies among haplotype trees.

A Molecular Phylogenetic Study of Arnica (Asteraceae): Low Chloroplast DNA Variation and Problematic Subgeneric Classification

The analyses revealed that A. nevadensis is most closely related to A. dealbata and A. mallotopus forms a strongly supported clade with A. unalaschcensis, and earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported.

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.

Reconstruction of reticulate evolution with sequence data provides gene records for distributional histories of some of the parental species and demonstrates that the sequence data could be highly informative and accurate for detecting hybridization.

The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences.

P pairwise comparisons among dicots and monocots for rbcL and two noncoding sequences of cpDNA show that these regions evolve faster (more than three times faster, on average) than rBCL, and that the trnL intron evolves at a rate that is the same as that of the intergenic spacer.


Comparison of relationships based on cpDNA and ITS sequences for the Heuchera group underscores the need for caution in the use of organellar variation for retrieving phylogeny at lower taxonomic levels, particularly in groups noted for hybridization.

Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level.

With primers constructed against highly conserved regions of tRNA genes in chloroplast DNA, two different non-coding spacers and one intron from four species within the genus Echium L. (Boraginaceae) and from two confamilial outgroups are amplified.

Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK

The family as a whole was monophyletic with no support for the segregate family Cobaeaceae, and several well supported groups allowed us to test hypotheses of relationship within Polemoniaceae.

Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of Ribosomal DNA in Winteraceae

The internal transcribed spacers and the 5.8S coding region of nuclear ribosomal DNA were sequenced and analyzed to address questions of generic relationships in Winteraceae. The molecular data

Evidence for replication slippage in the evolution of Oenothera chloroplast DNA.

The length mutations reported here allow a finer resolution of the phylogeny of the closely related Oenothera plastomes than would have been possible if only base substitutions had been considered.

Phylogenetics of the Cotton Genus (Gossypium): Character-State Weighted Parsimony Analysis of Chloroplast-DNA Restriction Site Data and Its Systematic and Biogeographic Implications

The maternal phylogenetic hypothesis and area cladogram suggest that Gossypium originated in either Africa or Australia, and the possibility that New World allopolyploids originated following a trans-Pacific transfer of an ancestral A-genome taxon to the Pacific coast of Mesoamerica or South America.

A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae).

  • R. JansenJ. Palmer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1987
The distribution of a chloroplast DNA inversion among 80 species representing 16 tribes of the Asteraceae and 10 putatively related families demonstrates the potential of such mutations for resolving phylogenetic relationships at higher taxonomic levels and defines an ancient evolutionary split within the family.

Evolution of a noncoding region of the chloroplast genome.

The relative rate of occurrence of nucleotide substitutions versus indel (insertion/deletion) events is investigated by comparing complete DNA sequence data from the noncoding portion of the chloroplast genome that maps between the genes rbcL and atp beta, and the phylogenetic tree based on nucleotide substitution events is consistent with accepted phylogeny.