RT Journal Article
SR Electronic
T1 Exact calculation of the expected SFS in structured populations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.05.10.540112
DO 10.1101/2023.05.10.540112
A1 Armando Arredondo
A1 Josué Corujo
A1 Camille Noûs
A1 Simon Boitard
A1 Lounès Chikhi
A1 Olivier Mazet
YR 2023
UL http://biorxiv.org/content/early/2023/05/12/2023.05.10.540112.abstract
AB The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in panmictic population has been derived in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We propose here a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system by an iterative method. The simplest case of the symmetrical n-island is then processed to arrive at a ready-to-use demographic parameters inference framework.Competing Interest StatementThe authors have declared no competing interest.