"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