The 'Butterfly effect' in Cayley graphs, and its relevance for evolutionary genomics

Suppose a finite set $X$ is repeatedly transformed by a sequence of permutations of a certain type acting on an initial element $x$ to produce a final state $y$. We investigate how 'different' the resulting state $y'$ to $y$ can be if a slight change is made to the sequence, either by deleting one permutation, or replacing it with another. Here the 'difference' between $y$ and $y'$ might be measured by the minimum number of permutations of the permitted type required to transform $y$ to $y'$, or by some other metric. We discuss this first in the general setting of sensitivity to perturbation of walks in Cayley graphs of groups with a specified set of generators. We then investigate some permutation groups and generators arising in computational genomics, and the statistical implications of the findings.

[1]  Raul Rabadan,et al.  Frequency Analysis Techniques for Identification of Viral Genetic Data , 2010, mBio.

[2]  Gene Cooperman,et al.  Harnessing parallel disks to solve Rubik's cube , 2009, J. Symb. Comput..

[3]  Guillaume Fertin,et al.  Combinatorics of Genome Rearrangements , 2009, Computational molecular biology.

[4]  Elena Konstantinova,et al.  Some problems on Cayley graphs , 2008 .

[5]  Sagi Snir,et al.  Fast and reliable reconstruction of phylogenetic trees with very short edges , 2008, SODA '08.

[6]  Amit U. Sinha,et al.  Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements , 2007, Pacific Symposium on Biocomputing.

[7]  Elchanan Mossel,et al.  How much can evolved characters tell us about the tree that generated them? , 2004, Mathematics of Evolution and Phylogeny.

[8]  Anthony Labarre,et al.  New Bounds and Tractable Instances for the Transposition Distance , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[9]  Tandy J. Warnow,et al.  Distance-Based Genome Rearrangement Phylogeny , 2006, Journal of Molecular Evolution.

[10]  Elchanan Mossel,et al.  Evolutionary trees and the Ising model on the Bethe lattice: a proof of Steel’s conjecture , 2005, ArXiv.

[11]  R. Hilborn Sea gulls, butterflies, and grasshoppers: A brief history of the butterfly effect in nonlinear dynamics , 2004 .

[12]  Li-San Wang,et al.  Genome Rearrangement Phylogeny Using Weighbor , 2002, WABI.

[13]  Tandy J. Warnow,et al.  A Few Logs Suffice to Build (almost) All Trees: Part II , 1999, Theor. Comput. Sci..

[14]  P. Erdös,et al.  A few logs suffice to build (almost) all trees (l): part I , 1997 .

[15]  João Meidanis,et al.  Introduction to computational molecular biology , 1997 .

[16]  Steven Skiena,et al.  Sorting with Fixed-length Reversals , 1996, Discret. Appl. Math..

[17]  Terence P. Speed,et al.  Invariants of Some Probability Models Used in Phylogenetic Inference , 1993 .

[18]  David B. A. Epstein,et al.  Word processing in groups , 1992 .

[19]  Noga Alon,et al.  The Probabilistic Method , 2015, Fundamentals of Ramsey Theory.

[20]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[21]  M. Kimura Estimation of evolutionary distances between homologous nucleotide sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[22]  George W. Polites,et al.  An introduction to the theory of groups , 1968 .