We implemented both the expectation–maximization algorithm and Monte Carlo Markov chain (MCMC) sampling to estimate θ for adjacent marker pairs and ε for each marker. θ is the template switching rate, which reflects a combination of population recombination rates and relatedness between the samples. ε is the error parameter, which reflects a combination of genotyping error, gene conversion events, and recurrent mutation (for details, see refs. 9,29).
