"Supporting Information Table S5 Parameters estimates (time periods scaled in years) for the best model PAM2Nex, ancient migration model with two periods of contact, heterogeneity of Ne and recent expansion with mean and standard deviation (stdev) derived from 100 bootstrapped datasets"																		
model	k	LogL	AIC	Theta	Nref	Nalba	Ntrem	NalbaE	NtremE	Mtrem--> alba	Malba-->trem	TS	TAM	TE	Ttotal	nr 	bf	O
Best run	12	-2086.311267	4196.622535	229.689	1926	42381	192640	187632	192640	0.000	0.220	924673	338276	309765	2835664	51.40%	0.001	90.20%
mean	-	-	-	231.239	1939	43310	193851	177422	192061	0.000	0.523	907485	341715	309038	2807436	51.01%	0.004	90.19%
stdev	-	-	-	12.420	104	3385	10549	24937	22031	0.000	1.816	128583	120399	12071	128819	5.98%	0.009	0.33%
k the number of free parameters in the model																		
LogL highest likelihood estimate over 30 independent runs																		
AIC Akaike Information Criterion																		
"Theta Theta parameter for the ancestral population before split (? = 4Nref?), with Nref being the effective size of the ancestral population, and ? the per-site mutation rate per generation."																		
Nref The effective size of the ancestral population before the split																		
Nalba The scaled effective size of P. alba population before expansion																		
Ntrem The scaled effective size of P. tremula population before expansion																		
NalbaE The scaled effective size of P. alba population after expansion																		
NtremE The scaled effective size of P. tremula population after expansion																		
Mtrem-->alba The neutral movement of genes from P. tremula to P. alba in units of 2Nrefm2->1 generations																		
Malba-->trem The neutral movement of genes from P. alba to P. tremula in units of 2Nrefm1->2 generations																		
TS The time of divergence in strict isolation in unit of number of years																		
TAM The time of ancient migration in units of number of years																		
TE The time of expansion in units of number of years																		
Ttotal The total time since the split in number of years 																		
"nr Proportion of ""non-recombining"" regions affected by background selection."																		
"bf Background factor, which defines the extent of population size reduction in ""nr"" regions"																		
O The proportion of correctly orientated SNPs when inferring ancestral allelic states using P. trichocarpa as an outgroup species																		
																		
"Supporting Information Table S4 B Parameters estimates (time periods scaled in 2Nref generations) for the best model PAM2Nex, ancient migration model with two periods of contact, heterogeneity of Ne and recent expansion with mean and standard deviation (stdev) derived from 100 bootstrapped datasets"																		
model	k	LogL	AIC	Theta	Nref	nalba	ntrem	nalbaE	ntremE	Mtrem--> alba	Malba-->trem	tS	tAM	tE	ttotal	nr 	bf	O
Best run	12	-2086.311	4196.623	229.689	1926.402	22.000	100.000	97.400	100.000	0.000	0.220	12.000	4.390	4.020	36.800	51.40%	0.001	90.20%
mean	-	-	-	231.239	1939.408	22.398	99.950	91.890	10.060	0.000	0.523	11.765	4.368	3.995	36.261	51.01%	0.004	90.19%
stdev	-	-	-	12.420	104.164	2.180	0.334	13.130	98.918	0.000	1.816	1.637	1.185	0.264	5.907	5.98%	0.009	0.33%
k the number of free parameters in the model																		
LogL highest likelihood estimate over 30 independent runs																		
AIC Akaike Information Criterion																		
"Theta Theta parameter for the ancestral population before split (? = 4Nref?), with Nref being the effective size of the ancestral population, and ? the per-site mutation rate per generation."																		
Nref The effective size of the ancestral population before the split																		
nalba The effective size of P. alba population before expansion																		
ntrem The effective size of P. tremula population before expansion																		
nexalbaE The effective size of P. alba population after expansion																		
nextremE The effective size of P. tremula population after expansion																		
Mtrem-->alba The neutral movement of genes from P. tremula to P. alba in units of 2Nrefm2->1 generations																		
Malba-->trem The neutral movement of genes from P. alba to P. tremula in units of 2Nrefm1->2 generations																		
ts The time of divergence in strict isolation in units of 2Nref generations																		
tAM The time of ancient migration in units of 2Nref generations																		
tE The time of expansion in units of 2Nref generations																		
ttotal The total time since the split in units of 2Nref generations																		
"nr Proportion of ""non-recombining"" regions affected by background selection."																		
"bf Background factor, which defines the extent of population size reduction in ""nr"" regions"																		
O The proportion of correctly orientated SNPs when inferring ancestral allelic states using P. trichocarpa as an outgroup species