A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes

@article{Qiu2007ANL,
  title={A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes},
  author={Yin Long Qiu and Libo Li and Bin Wang and Zhiduan Chen and Olena Dombrovska and Jungho Lee and Livija Kent and Rui-Qi Li and Richard W. Jobson and Tory A. Hendry and David Winship Taylor and Christopher M. Testa and Mathew Ambros},
  journal={International Journal of Plant Sciences},
  year={2007},
  volume={168},
  pages={691 - 708}
}
Nucleotide sequences of seven chloroplast (atpB and rbcL, SSU and LSU rDNAs), mitochondrial (atp1, LSU rDNA), and nuclear (18S rDNA) genes from 192 land plants and their algal relatives were analyzed using maximum likelihood and maximum parsimony methods. Liverworts, mosses, hornworts, lycophytes, monilophytes (ferns), seed plants, and angiosperms all represent strongly supported monophyletic groups. Three bryophyte lineages form a paraphyletic group to vascular plants, with liverworts… 
Angiosperm phylogeny inferred from sequences of four mitochondrial genes
TLDR
A mitochondrial gene‐based angiosperm phylogeny is reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3 from 380 species that represent 376 genera and 296 families of seed plants to reconstruct the underlying organismal phylogeny.
Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages
TLDR
Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; and posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
TLDR
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.
Tree of life for the genera of Chinese vascular plants
TLDR
A phylogenetic tree of Chinese vascular plants (Tracheophyta) is reconstructed using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR and the results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma.
Chloroplast phylogenomics resolves key relationships in ferns
TLDR
Chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns, and has recent parallel advances in the phylogenetics using nuclear data.
Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships
TLDR
The first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data is provided, identifying that extant gymnosperms are monophyletic and cycads plus Ginkgo form a clade that is sister to all remaining extant gymnOSperms.
Phylogeny and evolution of charophytic algae and land plants
  • Y. Qiu
  • Biology, Environmental Science
  • 2008
TLDR
P phylogenetic results will facilitate evolutionary developmental studies of these key traits of the plant life cycle, multicellularity, and gravitropism, which will help to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.
Phylogeny and evolution of charophytic algae and land plants
  • Y. Qiu
  • Biology, Environmental Science
  • 2008
TLDR
P phylogenetic results will facilitate evolutionary developmental studies of these key traits of the plant life cycle, multicellularity, and gravitropism, which will help to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.
Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies
TLDR
The molecular phylogenetic evidence for relationships is reviewed and evaluated and it is concluded that the two better-supported hypotheses are, firstly, that the bryophytes are a monophyletic group, and secondly, and less likely, that a lineage consisting of liverworts and mosses branched first among land plants with the hornworts the most-closely related lineage to tracheophytes.
Major transitions in the evolution of early land plants: a bryological perspective.
TLDR
This paper reviews phylogenetic, developmental, anatomical, genetic and paleontological data with the aim of reconstructing the succession of events that shaped major land plant lineages and concludes that bryophytes are the key to a better understanding of the early evolution of land plants.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 138 REFERENCES
Phylogeny of seed plants based on evidence from eight genes.
TLDR
A data set of four plastid genes, three mitochondrial genes, and one nuclear gene for 19 exemplars representing the five groups of living seed plants revealed a gymnosperm clade that is sister to angiosperms and the preferred topology based on the LR test is that Gnetales are sister to Pseudotsuga.
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.
To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and
Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants.
A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate
Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes
TLDR
This study indicates caution in total evidence approaches in that some of the genes employed added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree.
The phylogeny of land plants: A cladistic analysis based on male gametogenesis
TLDR
Longer treelengths are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors, and provides new insight into land plant evolution.
Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
TLDR
The Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and G netales arose independently.
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
TLDR
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.
Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes1
TLDR
The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms.
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants
TLDR
It is shown that there are three monophyletic groups of extant vascular plants: (1) lycophytes, (2) seed plants and (3) a clade including equisetophytes (horsetails, psilotophytes) and all eusporangiate and leptosporangiates ferns.
Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.
TLDR
Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.
...
1
2
3
4
5
...