Spectral analysis of phylogenetic data

  title={Spectral analysis of phylogenetic data},
  author={Michael D. Hendy and David Penny},
  journal={Journal of Classification},
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… 

Phylogenetic analysis based on spectral methods.

Through simulations, it is shown that the covariance-based methods effectively capture phylogenetic signal even when structural information is not fully retained, and Comparisons of simulation results with the bootstrap permutation results indicate that the covariances are fairly robust under perturbation in sequence similarity but more sensitive to perturbations in structural similarity.

The sampling distributions and covariance matrix of phylogenetic spectra

Recent advances in computing variance-covariance matrices from genetic distances to a sequence method of phylogenetic analysis are extended and the bias induced by the delta method, a convenient approximation in deriving V[y], is evaluated and found to be acceptable in the first case and very good in the second.

Generalizing Phylogenetic Parsimony from the Tree to the Forest

This multitree approach is a simple generalization of cladistic parsimony to reticulate systems of common ancestry, which can be attributed to the algorithmic and conceptual simplicity of trees and the expecta- tion that certain evolutionary processes gener- ate treelike descent patterns.

Distinguishing Convergence on Phylogenetic Networks

It is shown how methods from algebraic geometry, such as Grobner bases, can be used to solve the polynomial equations in phylogenetics and some four-taxon trees and networks can be distinguished from each other.

Phylogenetic tree-building.

  • D. Morrison
  • Biology
    International journal for parasitology
  • 1996

Application of Phylogenetic Network

The phylogenetic network revealed the following pattern: a recombinant allele had a short external branch and was located on a diagonal with the outgroup allele and the two parental alleles were located on another diagonal with long external branches.

Phylogenetic analyses of parasites in the new millennium.

Building trees, hunting for trees, and comparing trees : theory and methods in phylogenetic analysis

It is proved that there exist rules of every order that cannot be reduced to lower order rules, and several new NPcompleteness results and a list of standard NP-complete phylogenetic problems are discussed.

Measuring the fit of sequence data to phylogenetic model: allowing for missing data.

  • P. Waddell
  • Biology
    Molecular biology and evolution
  • 2005
It is fundamentally important to assess the fit of data to model in phylogenetic and evolutionary studies. Phylogenetic methods using molecular sequences typically start with a multiple alignment. It

d Plots: A Tool for Analyzing Phylogenetic Distance Data

The method is shown to be capable of identifying single recombinant taxa on the basis of distance information alone, provided the parents of the recombinant sequence are sufficiently divergent and the mixture of tree histories is not strongly skewed toward a single tree.



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

  • J. Lake
  • Biology
    Molecular biology and evolution
  • 1987
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

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

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

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
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.

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.