Spectral analysis of phylogenetic data

@article{Hendy1993SpectralAO,
  title={Spectral analysis of phylogenetic data},
  author={Michael D. Hendy and David Penny},
  journal={Journal of Classification},
  year={1993},
  volume={10},
  pages={5-24}
}
The spectral analysis of sequence and distance data is a new approach to phylogenetic analysis. For two-state character sequences, the character values at a given site split the set of taxa into two subsets, a bipartition of the taxa set. The vector which counts the relative numbers of each of these bipartitions over all sites is called a sequence spectrum. Applying a transformation called a Hadamard conjugation, the sequence spectrum is transformed to the conjugate spectrum. This conjugation… 

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    International journal for parasitology
  • 1996

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References

SHOWING 1-10 OF 25 REFERENCES

A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.

  • J. Lake
  • Biology
    Molecular biology and evolution
  • 1987
TLDR
The method of evolutionary parsimony accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail), as the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge.

Distributions on bicoloured evolutionary trees

  • M. Steel
  • Mathematics
    Bulletin of the Australian Mathematical Society
  • 1990
A central and challenging problem in contemporary biology is how to reconstruct evolutionary trees from DNA sequence data accurately. This thesis addresses three themes from this endeavour —

Inferring Phylogenetic Trees from Chromosome Inversion Data

TLDR
A model is proposed under which the most likely phylogenetic hypothesis given a set of chromosome inversion data can be identified as the most parsimonious tree for those data, a unique origin of each inversion type being assumed.

A Framework for the Quantitative Study of Evolutionary Trees

TLDR
A direct method for calculating expected data from an evolutionary model for two state characters is described, and it is shown that for n = 4 taxa, parsimony will always converge to the correct tree, but there are examples with n = 5 where Parsimony will converge on an incorrect tree, even for equal rates of evolution.

Estimating Phylogenetic Trees from Distance Matrices

TLDR
The distance Wagner procedure is applicable to data matrices of immunological distance, such as that of Sarich (1969a), in which between-OTU comparisons are evaluated but for which no attributes of the OTUs themselves are directly observable.

The Relationship Between Simple Evolutionary Tree Models and Observable Sequence Data

-Cavender (1978) introduced a model of an evolutionary branching process on a sequence of characters, where the characters take either of two states with symmetric probabilities of change between

Trees from sequences: panacea or Pandora's box.

Advantages of sequence data for reconstructing evolutionary trees include their wide scope, the large number of characters, the easier use of objective methods for building and testing trees, the use

Designer invariants for large phylogenies.

  • D. Sankoff
  • Computer Science
    Molecular biology and evolution
  • 1990
TLDR
This work explores use of events such as "only transitions occur for character i (i.e., position i in a nucleic acid sequence) in subtree a" in analyzing a set of data on ribosomal RNA in the context of the controversy over the origins of archaebacteria, eubacteria, and eukaryotes.

Pinniped origins and the rate of evolution of carnivore albumins.

TLDR
Data resulting from an immunological study of relationships among fissiped and pinniped albumins show that albumin evolution has occurred in a regular fashion in these taxa, which allows the conclusion that the pinnipeds share much more recent common ancestry with the canoids than either group does with the feloids.