2.10 Demographic history reconstruction
To reconstruct the demographic history for 20 scabies mite populations,
we applied the pairwise sequentially Markovian coalescence (PSMC) model
to evaluate the long-term changes in effective population size
(H. Li & Durbin, 2011). To ensure the
consensus sequence quality, all 20 samples with high sequencing depth
were used for each geographic region. Bases of low sequencing depth (a
third of the lowest depth) or high depth (three times of the highest
depth) were masked. The required input format files were converted from
consensus sequence by the utility fq2psmcfa provided by the PSMC
software. The parameters were set as follows: -N30 -t15 -r5 -p
4+25*2+4+6. The generation time (g) was 0.0575 year per generation (21
days) and the mutation rate (u) is 8.4 x 10-9 per site
per generation.