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.
ABSTRACT
PUBLICATION RECORD
- Publication year
2004
- Venue
IEEE/ACM Transactions on Computational Biology & Bioinformatics
- Publication date
2004-07-01
- Fields of study
Biology, Medicine, Computer Science, Mathematics
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- clock-like tree
A phylogenetic tree whose branch lengths are constrained by a molecular-clock-style time structure.
Aliases: molecular-clock tree
- edge length
The length of a branch in the phylogenetic tree, representing the amount of evolutionary change or time on that edge.
Aliases: branch length
- gamma family
A parametric family of positive-valued distributions commonly used for modeling variation in site-specific evolutionary rates.
Aliases: gamma distribution
- identifiability
A property of a statistical model in which different parameter settings induce different data distributions.
Aliases: identifiable
- rates-across-sites model
A phylogenetic model class in which a character-specific scale factor multiplies an edge-specific rate matrix to describe evolutionary change across sites.
Aliases: rates-across-sites assumption, rates-across-sites assumption in phylogenetic inference
REFERENCES
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CITED BY
Showing 1-17 of 17 citing papers · Page 1 of 1