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.