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Unidentifiable Divergence Times in Rates-across-Sites Models
July-September 2004 (vol. 1 no. 3)
pp. 130-134
ASCII Text
x 
 
Steven N. Evans, Tandy Warnow, "Unidentifiable Divergence Times in Rates-across-Sites Models," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 3, pp. 130-134, July-September, 2004.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2004.34,
author = {Steven N. Evans and Tandy Warnow},
title = {Unidentifiable Divergence Times in Rates-across-Sites Models},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {1},
number = {3},
issn = {1545-5963},
year = {2004},
pages = {130-134},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.34},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Unidentifiable Divergence Times in Rates-across-Sites Models
IS - 3
SN - 1545-5963
SP130
EP134
EPD - 130-134
A1 - Steven N. Evans,
A1 - Tandy Warnow,
PY - 2004
KW - Phylogenetic inference
KW - random effects
KW - gamma distribution
KW - identifiability.
VL - 1
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a rate matrix that is particular to that edge. Thus, evolution follows basically the same process for all characters, except that it occurs faster for some characters than others. To allow estimation of tree topologies and edge lengths for such models, it is commonly assumed that the scale factors are not arbitrary unknown constants, but rather unobserved, independent, identically distributed draws from a member of some parametric family of distributions. A popular choice is the gamma family. We consider an example of a clock-like tree with three taxa, one unknown edge length, a known root state, and a parametric family of scale factor distributions that contains the gamma family. This model has the property that, for a generic choice of unknown edge length and scale factor distribution, there is another edge length and scale factor distribution which generates data with exactly the same distribution, so that even with infinitely many data it will be typically impossible to make correct inferences about the unknown edge length.

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Index Terms:
Phylogenetic inference, random effects, gamma distribution, identifiability.
Citation:
Steven N. Evans, Tandy Warnow, "Unidentifiable Divergence Times in Rates-across-Sites Models," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 3, pp. 130-134, July-Sept. 2004, doi:10.1109/TCBB.2004.34
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