Distance-Based
Genome Rearrangement Phylogeny

Genomes As Signed Permutations

Genomes Evolve by Rearrangements

Phylogeny Reconstruction

Results

Outline

Our Model: the Generalized
Nadeau-Taylor Model [STOC’01]

Additive Distance Matrix and
True Evolutionary Distance (T.E.D.)

Error Tolerance of Neighbor Joining

Edit Distances Between Genomes

NJ(BP) and NJ(INV)

BP and INV

Objectives

New Estimators

Distance-Based Methods

Estimate True Evolutionary Distances
Using BP

Using Breakpoints to Estimate
True Evolutionary Distances

True Evolutionary Distance (t.e.d.) Estimators for Gene Order Data

Approx-IEBP
[Wang & Warnow, STOC’01]

True Evolutionary Distance Estimators

True Evolutionary Distance Estimators

Regression Formula for E(INV)

Absolute Difference Plot

Error Tolerance of Neighbor Joining

Absolute Difference Plot

120 Genes, Inversion-only Model

120 Genes, Inv:Transp=1:1

120 Genes, Transp Only

Using True Evolutionary Distance Helps

Variance of True Evolutionary Distance Estimators

Using True Evolutionary Distance Helps

Robustness

IEBP is Robust to Model Violations

Beta Splitting Model [Aldous 1995]

Effect of Beta on Accuracy
(120 Genes, 160 Taxa)
(Beta= -1.5: Uniform, -1: Aldous, 0: Yule)

Number of Genes

Number of Taxa

Observations

Summary

Acknowledgements