Estimate of demographic history
In order to better understand the demographic history of the N.
ingens complex, we employed Stairway plot version 2 (Liu and Fu 2015,
Liu 2020) to reconstruct the historical demography of focal populations
using the semi-filtered dataset . Similar to SNAPP, the eight
populations with pure ancestry coefficients were used to minimize any
bias of recent gene flow. The input folded site allele frequency
spectrum was estimated for each population using the custom program
easySFS
(https://github.com/isaacovercast/easySFS).
We used a point mutation rate of 2.8×\(10^{-9}\) per site per
generation, which was estimated based on Drosophila and is close
to the nuclear mutation rate of other non-social insects (Keightley,
Ness, Halligan, & Haddrill, 2014, Keightley et al., 2015, Oppold and
Pfenninger 2017). Other parameters were set to default.