2.7 Demographic history reconstruction
Demographic history was reconstructed, both to assess ancient population
history and detect possible recent population declines associated with
founder events in invasive populations. As triploids exhibit unisexual
gynogenesis, the demographic history was only constructed for diploid
populations. The fluctuation of effective population size was estimated
using SMC++ (version 1.15.4) which combines the computational efficiency
of site frequency spectra (SFS) and the advantage of using LD
information in coalescent HMMs and provides a high resolution of recent
demography (Terhorst et al., 2017). The VCF file for each population was
converted to the SMC input format using the vcf2smc module. The
population size was estimated using the estimate module with the option
–knots 20 and a per-generation mutation rate of 1e-8. The plot module
was used for plotting fitted size histories using a generation length of
one year.