Table 2. Summary of parameters for experiments involving the generalized mammalian model.

Experiment	Sample sizes	Mutation (μ) [θ] and recombination (r) [ρ] rates	Sequence length; window size	Split time (τ, generations) [coalescent units]	Selection coefficient (s) [σ] and time (t, generations) [coalescent units]	Other parameters	Figures
Generalized mammalian model, including star tree and nonsimultaneous sweeps ($K\in \left\{2,3,4,5\right\}$)	100 per population	$\mu =2.5\times {10}^{-8}$ [${10}^{-3}$], $r={10}^{-8}$ (uniform across replicates) [$\rho =4\times {10}^{-4}$]	100; 40	$\tau \in \{250$,500,750,$1000\}$ [$\tau /(2N_{\text{e}})\in \{0.0125$, 0.025, 0.0375, $0.05\}$]; $\tau =1000$ for $K=2$ and star tree ($K=4$), and sequential starting from $\tau =1000$ otherwise	$s=0.1$ [$\sigma =4000$]; $t\in [200,4000]$ [$t/\left(2N_{\text{e}}\right)\in [0.01,0.2]$]	Population splits separated by 250 generations for $K>2$ scenarios; $K>2$ trees are asymmetric	S1; S4; S9 and Supplemental note SN1–SN3; SN5; SN6, SN7
Admixture, distant donor ($K=2$)	Same as above	Same as above	Same as above	$\tau =1000$ [$\tau /\left(2N_{\text{e}}\right)=0.05$] between sampled sisters	s same as above; $t=1400$ [$t/\left(2N_{\text{e}}\right)=0.07$] for ancestral sweeps, and $t=600$ [$t/\left(2N_{\text{e}}\right)=0.03$] for convergent and divergent sweeps	Distant donor split from sampled populations $\tau =20000$ generations [$t/\left(2N_{\text{e}}\right)=1$] ago; admixture occurred 200 generations [0.01 coalescent units] ago; admixture proportion $\alpha \in \left\{0.05,0.1,\dots ,0.4\right\}$	4; S19
Admixture, intersister ($K=2$)	Same as above	Same as above	Same as above	Same as above	Same as above	Adaptive mutation originates in donor population and may be adaptive or not in its target sister; timing and proportion of admixture same as above	Supplemental note SN4
Uneven sample sizes ($K=2$)	Pooled sample size is 200 diploids; smaller sample size is $n_{\text{small}}\in \left\{20,40,60\right\}$	Same as above	Same as above	Same as above	s and t same as generalized mammalian model	Protocol identical to unmodified generalized mammalian model	S20–S22

We provide diploid sample sizes, per-site per-generation mutation and recombination rates, and sequence length in kilobases. Additionally, we indicate the population-scaled values for mutation and recombination rates in brackets upon their first appearance, scaling by $4N_{\text{e}}$ where $N_{\text{e}}={10}^4$ ($\theta =4N_{\text{e}}\mu$; $\rho =4N_{\text{e}}r$; $\sigma =4N_{\text{e}}s$). The relationship between generations and coalescent units is $2N_{\text{e}}$ generations per coalescent unit.