eme size
was fixed to N=5000 with m varying accordingly to obtain a
long-term Nm of 1, 5, 10, and 15 in order to encompass the range
of the estimated values (see results). Tcol was fixed to 5,000,
15,000 and 50,000 generations B.P. or to ∞ (i.e., equilibrium model).
Change of connectivity occurred at Tch =10 or 50 generations B.P.,
to mimic human induced effects due to overfishing and/or habitat
modifications (i.e., climate changes). Looking forward in time, we
modelled the change in connectivity by instantaneously decreasingm or N by a factor 10 or 100 with respect to the long-termNm (Tables S4, S7, S8, S9 and S10). For each combination of
parameters, we performed 100 coalescent simulations of 50,000 Rad-like
loci of 115 bp. Mutation rate per site per generations was set to
1.93×10-8 and the generation time to 10 years. We
computed for each scenario (averaged over the 100 replicates): a)
summary statistics (Ɵπ ,Ɵw , and TD ); b) the normalised SFS as in
(Lapierre, Lambert, & Achaz, 2017); c) the stairwayplot , to
reconstruct the apparent variation of Ne through time.