Table 2 Best parameter estimates of demographic models analysed with dadi, Akaike information criterion (AIC), and results of the likelihood ratio tests (LRT) for nested models (IM versus IM_2M and IM2 versus IM2_2M). The parameters are as in Fig. 1. Confidence levels for parameters of the best-fitting model for each gene category are shown (± 1.96X, where X = standard deviation in 100 bootstrap estimates).
From: Pericentromeric recombination suppression and the ‘large X effect’ in plants
Gene category | Model | No. of free param | log-like | θ | AIC | ΔAIC | Rel. like | (LRT) 2ΔLL | (LRT) p-value | s | N1 | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Rarely-recombining genes (rare) | split_mig | 4 | − 9717 | 23147 | 19441 | 15841 | 0.00 | 0.69 | |||||
IM | 5 | − 8249 | 18385 | 16507 | 12907 | 0.00 | 0.26 | 1.34 | |||||
IM_2M | 7 | − 2710 | 17227 | 5433 | 1833 | 0.00 | 11,078 | 0.00 | 0.26 | 1.38 | |||
IM2 | 6 | − 8235 | 18259 | 16481 | 12882 | 0.00 | 0.43 | 1.33 | |||||
IM2_2M | 9 | − 1791 | 9461 | 3600 | 0 | 1.00 | 12,888 | 0.00 | 0.62 ± 0.41 | 2.29 ± 1.12 | |||
Frequently-recombining genes (freq) | split_mig | 4 | − 5686 | 37420 | 11380 | 8117 | 0.00 | 1.13 | |||||
IM | 5 | − 4434 | 37078 | 8878 | 5615 | 0.00 | 0.70 | 1.58 | |||||
IM_2M | 7 | − 1789 | 34987 | 3592 | 329 | 0.00 | 5290 | 0.00 | 0.60 | 1.59 | |||
IM2 | 6 | − 4431 | 40,578 | 8875 | 5611 | 0.00 | 0.13 | 1.75 | |||||
IM2_2M | 9 | − 1623 | 20533 | 3263 | 0 | 1.00 | 5617 | 0.00 | 0.28 ± 0.37 | 2.23 ± 0.99 | |||
Rarely-recombining, autosomal genes (rareA) | IM2 | 6 | − 5576 | 13,081 | 11164 | 8116 | 0.00 | 0.43 | 1.22 | ||||
IM2_2M | 9 | − 1515 | 7470 | 3048 | 0 | 1.00 | 8122 | 0.00 | 0.27 ± 0.21 | 1.82 ± 0.80 | |||
Rarely-recombining, X-linked genes in Xpr region (rareX) | IM2 | 6 | − 1649 | 1803 | 3311 | 2129 | 0.00 | 0.72 | 0.77 | ||||
IM2_2M | 9 | − 582 | 1109 | 1182 | 0 | 1.00 | 2135 | 0.00 | 0.29 ± 0.21 | 1.20 ± 0.62 | |||
Frequently-recombining, autosomal genes (freqA) | IM2 | 6 | − 3687 | 29,379 | 7386 | 4723 | 0.00 | 0.35 | 3.78 | ||||
IM2_2M | 9 | − 1323 | 25831 | 2664 | 0 | 1.00 | 4729 | 0.00 | 0.38 ± 0.37 | 1.38 ± 0.92 | |||
Frequently-recombining, X-linked genes in qXdr region (freqX) | IM2 | 6 | − 1306 | 3879 | 2623 | 1445 | 0.00 | 0.82 | 1.20 | ||||
IM2_2M | 9 | − 580 | 2477 | 1179 | 0 | 1.00 | 1451 | 0.00 | 0.65 ± 0.43 | 1.62 ± 1.03 |
Gene category | Model | N2 | T | M | M1 | M2 | MA | MB | MA1 | MA2 | MB1 | MB2 | P |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rare | split_mig | 0.85 | 1.32 | 0.46 | |||||||||
IM | 1.29 | 1.96 | 0.32 | ||||||||||
IM_2M | 1.41 | 2.37 | 0.12 | 1.71 | 0.55 | ||||||||
IM2 | 1.16 | 2.14 | 0.24 | 0.43 | |||||||||
IM2_2M | 2.99 ± 1.03 | 6.17 ± 2.15 | 0.06 ± 0.03 | 0.10 ± 0.06 | 2.12 ± 1.30 | 1.21 ± 0.65 | 0.56 ± 0.22 | ||||||
freq | split_mig | 1.28 | 0.54 | 1.34 | |||||||||
IM | 2.41 | 0.63 | 1.16 | ||||||||||
IM_2M | 2.01 | 0.84 | 0.23 | 2.22 | 0.19 | ||||||||
IM2 | 2.03 | 0.45 | 2.56 | 0.62 | |||||||||
IM2_2M | 2.78 ± 0.75 | 3.43 ± 1.85 | 0.25 ± 0.13 | 0.18 ± 0.08 | 2.03 ± 1.06 | 1.39 ± 0.61 | 0.26 ± 0.07 | ||||||
rareA | IM2 | 1.18 | 1.58 | 0.32 | 0.41 | ||||||||
IM2_2M | 2.48 ± 0.85 | 4.84 ± 1.53 | 0.10 ± 0.04 | 0.11 ± 0.05 | 2.52 ± 1.16 | 0.75 ± 0.70 | 0.55 ± 0.19 | ||||||
rareX | IM2 | 0.59 | 1.31 | 0.15 | 0.74 | ||||||||
IM2_2M | 1.24 ± 0.63 | 3.85 ± 1.92 | 0.04 ± 0.05 | 0.13 ± 0.09 | 3.13 ± 1.65 | 2.88 ± 1.07 | 0.50 ± 0.21 | ||||||
freqA | IM2 | 2.17 | 0.18 | 0.27 | 1.22 | ||||||||
IM2_2M | 2.36 ± 1.01 | 0.55 ± 0.31 | 0.38 ± 0.18 | 0.39 ± 0.34 | 7.90 ± 3.55 | 0.52 ± 0.42 | 0.31 ± 0.26 | ||||||
freqX | IM2 | 1.57 | 0.93 | 0.60 | 0.86 | ||||||||
IM2_2M | 1.95 ± 0.72 | 3.77 ± 1.79 | 0.15 ± 0.08 | 0.18 ± 0.09 | 2.50 ± 1.03 | 1.26 ± 0.67 | 0.28 ± 0.14 |
