Such an assumption of evolutionary and ecological equivalence is typical of many neutral paleontological and neontological biogeographic models [26], [34] [37].
Different criteria for comparison can be relevant in different contexts: similarity, functional equivalence, evolutionary relationships or the implication in similar phenotypes (Mabee et al., 2007; McGary et al., 2010; Roux and Robinson-Rechavi, 2010).
We took advantage on the ability of the above learning method in generating several optimal BN structures (structures with the same maximum fitness found along the evolutionary process) to get equivalence classes.
Pursuing this end will complement and may provide insight into non-network studies that demonstrate the non-equivalence of evolutionary conservation and functional importance, with many genomic regions showing experimentally demonstrable functional roles without evolutionary constraint.
The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids.
The neutral theory of biodiversity has successfully explained the observed composition of many ecological communities but it relies on strict demographic equivalence among species and provides no room for evolutionary processes such as selection and adaptation.
However, orthology is an evolutionary term defined by the relationships among the sequences under study, and functional equivalences are not always inferable 13.
The fact that Dichaete mutants can be rescued by mouse Sox2 of Sox subgroup B1 [16] is not strong evidence for orthology, because functional equivalence is not a part of the definition of orthology as a strict evolutionary concept [32].
Note that the definition of the unit rate matrix associated with a given homogeneous model is somewhat arbitrary b, but once the unit R is defined, it implies a bijection (or equivalence) between rate matrices in ℳ R and the parameter t, which corresponds to evolutionary time.
This equivalence belies history.
