Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing

  title={Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing},
  author={Gitte Petersen and Ole Seberg and Jerrold I. Davis},
A phylogenetic analysis of the monocot order Liliales was performed using sequence data from three mitochondrial (atp1, cob, nad5) and two plastid genes (rbcL, ndhF). The complete data matrix includes 46 terminals representing all 10 families currently included in Liliales. The two major partitions, mitochondrial and plastid data, were congruent, and parsimony analysis resulted in 50 equally parsimonious trees and a well resolved consensus tree confirming monophyly of all families… 

Phylogeny of the Alismatales (Monocotyledons) and the relationship of Acorus (Acorales?)

An almost completely resolved strict consensus tree is results in, but all data partitions, genomic as well as morphological, are incongruent, and Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons.

Familial relationships of the monocot order Liliales based on a molecular phylogenetic analysis using four plastid loci: matK, rbcL, atpB and atpF‐H

Phylogenetic relationships among families of Liliales were better defined here than in a previous molecular analysis, although the placement of Corsiaceae with plastid data remains problematic.

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

Functional plastid genes found in C. dispar may be applicable to other species in Corsiaceae, which will provide a basis for in-depth molecular analyses of interspecies relationships within the family, once molecular data from other members become available.

Plastid phylogenomics and molecular evolution of Alismatales

Ancestral‐state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae, and investigates the molecular evolution of plastid NADH dehydration, a large enzymatic complex that may play a role in photooxidative stress responses.

Phylogeny and Comparative Analysis for the Plastid Genomes of Five Tulipa (Liliaceae)

Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of Tulipa and the sister relationship between TulipA and Amana, Erythronium.

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau: the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe, contributing to a better understanding of the evolutionary history of lilies.

Phylogenomics of the plant family Araceae.

Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia.

The study shows that biotic interchanges between the QTP region and Irano-Turanian region and the Mediterranean Basin were bi-directional, suggesting the latter was a secondary centre of diversity.



Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.

It seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.

Molecular phylogeny of monocotyledons inferred from combined analysis of plastid matK and rbcL gene sequences

Using matK and rbcL sequences from 113 genera of 45 families, a combined analysis to contribute to the understanding of major evolutionary relationships in the monocotyledons finds that Acorus (Acorales) is a sister group to the rest of themonocots, which receives 100% bootstrap support.

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families, whereas support for many families increases, and the increased support is dominated by plastid data.

Mitochondrial Data in Monocot Phylologenetics

RNA editing of mitochondrial genes is regarded only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly in phylogenetic reconstruction, and edited sites may prove a valuable tool in identifying processed paralogs.

Phylogenetic Analyses of the Diploid Species of Hordeum (Poaceae) and a Revised Classification of the Genus

A new infrageneric classification of Hordeum including only monophyletic groups is presented, and one new taxon, Hordeum L. sect.

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales-Pandanales in the strict consensus; Pandanales are sister to Dioscoreale in the bootstrap majority-rule tree, just above Petrosaviales.

Multigene Analyses of Monocot Relationships

Analysis of supra-familial relationships of monocots based on a combined matrix of nuclear 18S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atpl DNA sequences provides higher bootstrap support for nearly all relationships than in previously published analyses.

Rna editing and phylogenetic reconstruction in two monocot mitochondrial genes

Using mtDNA sequence data encoding for apocytochrome B and the alpha subunit of F1-ATP synthase (atp1) across the monocots, and in two subclades, alismatids and Agavaceae, it is shown that edited sites, despite being more homoplasious than non-edited sites, perform well on the trees.

Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences

Placement of Psilotum in a class of its own receives no support from the mitochondrial sequences, which rather suggest its inclusion among eusporangiate ferns (Ophioglossales).