Appendix 3—table 1. Parameter values used for simulating Demographic Model A1.

A Demes-format YAML file for each demographic model is available from the genomatnn git repository.

Parameter	Description	Value	Units	Source
$N_{Anc}$	ancestral pop. size	18500		Kuhlwilm et al., 2016
$N_{Nea}$	Neanderthal pop. size	3400		Kuhlwilm et al., 2016
$N_{YRI}$	YRI pop. size	27600		Kuhlwilm et al., 2016
$N_{CEU0}$	CEU bottleneck pop. size	1080		Ragsdale and Gravel, 2019
$N_{CEU1}$	CEU growth-start pop. size	1450		Ragsdale and Gravel, 2019
$N_{CEU2}$	CEU current pop. size	13377
$r_{CEU}$	CEU growth rate	0.00202		Ragsdale and Gravel, 2019
$T_{CEU2}$	CEU time at growth start	31.9	kya	Ragsdale and Gravel, 2019
$T_0$	Nea/other split time	550	kya	Prüfer et al., 2017
$T_1$	CEU/YRI split time	65.7	kya	Ragsdale and Gravel, 2019
$T_2$	time of Nea → CEU gene flow	55	kya	Prüfer et al., 2017
$g$	generation time	29	years	Prüfer et al., 2017
$\alpha$	Nea → CEU admixture proportion	2.25		Prüfer et al., 2017
$T_{\text{Altai}}$	sampling time	115	kya	Prüfer et al., 2017
$T_{\text{Vindija}}$	sampling time	55	kya	Prüfer et al., 2017
$n_{\text{Nean}}$	sample size	2	diploid individuals
$n_{\text{Afr}}$	sample size	108	diploid individuals
$n_{\text{Eur}}$	sample size	99	diploid individuals
$s$	selection coefficient	${10}^{\text{Unif(-4,-1)}}$
$T_{\text{sel1}}$	selection onset (sweep)	Unif(1, $T_1$)	kya
$T_{\text{mut1}}$	mutation (sweep)	Unif($T_{\text{sel1}}$, $T_1$)	kya
$T_{\text{sel2}}$	selection onset (AI)	Unif(1, $T_2$)	kya
$T_{\text{mut2}}$	mutation (AI)	Unif($T_2$, $T_0$)	kya