Table 3.
Best model runs from the ∂a∂i analyses. The SC2M scenario had the highest likelihood among all models tested. Model parameters are given as scaled units based on N ref, the size of the ancestral population
| Model | Ln | AIC | AICw | Theta | N Ag | N Ps | M Ag‐Ps | M Ps‐Ag | MeAg‐Ps | MePs‐Ag | T am/sc | T s | P |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SI | –3586.08 | 7,178.16 | 0.00 | 8,621.58 | 0.28 | 0.14 | – | – | – | – | – | 0.19 | – |
| IM | –2896.32 | 5,802.64 | 0.00 | 61,678.91 | 0.09 | 0.01 | 0.08 | 14.56 | – | – | – | 0.52 | – |
| AM | –2497.97 | 5,007.94 | 0.00 | 58,824.98 | 0.08 | 0.01 | 1.65E−09 | 19.90 | – | – | 0.33 | 3.62E−03 | – |
| SC | –2848.03 | 5,708.06 | 0.00 | 1826.07 | 3.23 | 0.23 | 0.01 | 0.68 | – | – | 1.10 | 5.84 | – |
| IM2M | –1494.24 | 3,004.48 | 3.29E−58 | 13,645.78 | 0.27 | 0.16 | 12.53 | 1.42E−04 | 0.02 | 0.11 | – | 0.43 | 0.62 |
| AM2M | –1457.91 | 2,933.82 | 7.28E−43 | 5,320.46 | 1.07 | 0.28 | 18.63 | 17.02 | 0.01 | 0.20 | 2.00 | 0.08 | 0.47 |
| SC2M | –1360.88 | 2,739.77 | 1.00 | 12,092.45 | 0.18 | 0.15 | 29.91 | 1.43E−03 | 0.14 | 0.10 | 0.06 | 0.25 | 0.55 |
Theta: mutation parameter for the ancestral population defined as θ = 4N ref µL, where µ is the mutation rate per nucleotide site per generation and L is the total length of the analysed polymorphic sequences; N Ag: effective population size for A. gigas; N Ps: effective population size for P. soyoae; M Ag‐Ps: migration from P. soyoae into A. gigas in units of 2N ref·m Ag‐Ps generations, where m Ag‐Ps is the fraction of migrants from P. soyoae to A. gigas each generation; M Ps‐Ag: migration from A. gigas into P. soyoae in units of 2N ref·m Ps‐Ag generations, where m Ps‐Ag is the fraction of migrants from A. gigas to P. soyoae each generation; MeAg‐Ps: effective migration rate of genes under selection from P. soyoae to A. gigas; MePs‐Ag: effective migration rate of genes under selection from A. gigas to P. soyoae; T am: scaled time between species split and end of ancient migration in units of 2N ref generations; T sc: scaled time between secondary contact and present in units of 2N ref generations; T s: scaled time between species split and present (IM), species split and secondary contact (SC) or end of ancient migration and present (AM) in units of 2N ref generations; P: proportion of the genome evolving neutrally.
Abbreviations: AIC, Akaike information criterion; AICw, AIC weights; Ln, model likelihood.