Table 1.

Rate matrix for Markov chain describing transitions between states in multispecies coalescent with migration model with two populations ( and ) and three sequences (, , and )

Note: and are mutation-scaled migration rates, and and are the coalescent rates. The state of the chain is given by the population IDs ( or ) and sequence IDs (such as , , ). For example the initial state means that the three sequences , and are from populations , , and , respectively. States with three sequences are abbreviated, with the three sequences assumed to be in the order so that the sequence IDs are suppressed. Thus is ‘’. State means that two sequences remain in the sample, with the ancestor of sequences and is in population while sequence is in population . This is abbreviated ‘’, with the sequence ID ‘’ suppressed. ‘’ is an absorbing state in which only one sequence remains in the sample, in either or , after two coalescent events have occurred.