A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

A common goal of population genomics and molecular ecology is to
reconstruct the demographic history of a species of interest. A pair of
powerful tools based on the sequentially Markovian coalescent have been
developed to infer past population sizes using genome sequences. These
methods are most useful when sequences are available for only a limited
number of genomes and when the aim is to study ancient demographic events.
The results of these analyses can be difficult to interpret accurately,
because doing so requires some understanding of their theoretical basis
and of their sensitivity to confounding factors. In this practical review,
we explain some of the key concepts underpinning the pairwise and multiple
sequentially Markovian coalescent methods (PSMC and MSMC, respectively).
We relate these concepts to the use and interpretation of these methods,
and we explain how the choice of different parameter values by the user
can affect the accuracy and precision of the inferences. Based on our
survey of 100 PSMC studies and 30 MSMC studies, we describe how the two
methods are used in practice. Readers of this article will become familiar
with the principles, practice, and interpretation of the sequentially
Markovian coalescent for inferring demographic history.