Recombination in discrete and continuous time from the viewpoint of Markov embedding

Abstract

The classic recombination equation, both in discrete and in continuous time, can be solved in a way that derives from the Markov chain of a partitioning process. Here, we revisit this structure from the point of view of the Markov embedding problem. In particular, we analyse when a discrete-time Markov matrix of recombination type can occur in a time-homogeneous Markov semigroup that is generated by a recombination rate matrix. En route, we also show that such rate matrices (or Markov generators) generally do not form a matrix algebra, but span a real Lie algebra.