Question

Which of the following is incorrect statement about Choosing Substitution Models?

(a) There is one substitution at a particular position, in divergent sequences

(b) The evolutionary divergence is beyond the ability of the statistical models to correct

(c) The statistical models used to correct homoplasy are called substitution models or evolutionary models

(d) For constructing DNA phylogenies, there are nucleotide substitution models available

The question was posed to me in an interview for internship.

I need to ask this question from Gene Phylogeny Versus Species Phylogeny topic in portion Molecular Phylogenetics of Bioinformatics

Answer 1

Right choice is (a) There is one substitution at a particular position, in divergent sequences

To elaborate: The caveat of using these models is that if there are too many multiple substitutions at a particular position, which is often true for very divergent sequences, the position may become saturated. This means that the evolutionary divergence is beyond the ability of the statistical models to correct. In this case, true evolutionary distances cannot be derived. Therefore, only reasonably similar sequences are to be used in phylogenetic comparisons.