|RELATIVE EVOLUTIONARY RATE||_|
The utility of a phylogenetic marker can be described by its relative evolutionary rate (RER):
faster (respectively slower) evolving markers will be more suitable for lower (respectively deeper) taxonomic levels.
In a first approximation, the total branch length (TBL) of the maximum likelihood (ML) tree is a reasonable descriptor of the evolutionary rate of a given exon.
However, the TBL will preclude fair comparisons among different exons when the taxon sampling differs: the higher the species number, the longer the TBL.
To circumvent this problem, we use the Super Distance Matrix (SDM) approach [Criscuolo et al. 2006], with a three-step procedure:
(i) The ML tree inferred from each of the exons / CDS is converted into a matrix of additive distances by computing the path-length between each pair of species.
(ii) Each of the matrices is brought closer to the others by a factor (αp), according to the least-squares criterion.
This operation is equivalent to multiplying by αp every branch length of the initial trees.
(iii) Optimal values of the alpha_p parameters are calculated following Criscuolo et al. (2006).
As αp are inversely proportional to the evolutionary rates, 1/αp values provide a measure of rate heterogeneities among exons / CDS even if the number of taxa differs.
Here, relative evolutionary rate SDM estimates range from 0.01 to 5 (OrthoMaM mean = 1.2 ; standard-error = 0.6).
For example, if exons / CDSs X and Y are respectively characterized by relative rates rX = 0.2 and rY = 2.0, this means that Y is evolving 10 times faster than X.
Request guidelines: In the [0-5] range of values, type RER < 1 to query rather conserved markers, 1 < RER < 2 for more variable markers, and RER > 2 for fast-evolving ones.
Reference: Criscuolo A., Berry V., Douzery E. J. P. & Gascuel O., 2006.
SDM: a fast distance-based approach for (super)tree building in phylogenomics.
Systematic Biology 55 (5) : 740-755.