TABLE 3.
Distributional statistics and estimates of α from the LCBN method
| Model/fit | Shape | Location | Species Ne (×103) | Nes (am) | Nes (hm) | Nes (5%) | Nes (95%) | CV | cne% | αmir%, αpse% | α0.2 M%, α1 M% |
|---|---|---|---|---|---|---|---|---|---|---|---|
| X | |||||||||||
| Lognor 67.9% | 49.8 (4.50/734) | 0.00165 (3.83 × 10−5/0.19) | mir: 292 (215/379) | 27,500 (36.7/142,000) | 14.4 (5.08/28.3) | 2.31 (1.12/7.01) | 292,000 (141/346,000) | 2.62 (0.968/7.91) | 4.03 (1.71/5.71) | 33.9 (2.54/66.5) | 19.3 (−13.7/44.6) |
| pse: 1,200 (1,010/1,440) | 111,000 (153/562,000) | 25.3 (14.7/42.8) | 5.46 (3.00/16.2) | 999,000 (1,810/2,190,000) | 2.66 (0.983/8.03) | 1.75 (1.24/2.98) | 71.1 (51.8/96.3) | 67.6 (48.9/94.7) | |||
| Gamma 83.6% | 0.513 (0.153/1.43) | 0.00137 (2.64 × 10−5/4,300) | mir: 292 (210/372) | 213 (12.0/220,000) | 13.6 (4.98/69.6) | 2.48 (1.27/95.5) | 819 (32.6/301,000) | 1.36 (0.525/1.73) | 3.75 (1.47/5.51) | 38.4 (11.0/69.6) | 25.2 (1.04/52.3) |
| pse: 1,200 (1,000/1,440) | 860 (48.4/854,000) | 27.0 (15.8/88.9) | 6.44 (3.83/225) | 3,360 (126/1,190,000) | 1.38 (0.534/1.76) | 1.81 (0.207/3.65) | 70.4 (42.2/95.3) | 67.5 (40.5/93.9) | |||
| A | |||||||||||
| Lognor 57.1% | 4.03 (2.24/49.3) | 2.72 × 10−5 (1.34 × 10−5/0.00157) | mir: 380 (290/462) | 27.7 (7.13/32,200) | 4.92 (3.45/14.6) | 1.20 (1.00/2.55) | 106 (19.4/313,000) | 2.42 (0.955/8.45) | 1.67 (0.386/4.55) | 53.9 (−10.5/79.0) | −15.3 (−81.4/27.7) |
| pse: 1,800 (1,530/2,020) | 129 (34.4/151,000) | 19.1 (14.3/30.5) | 4.81 (3.26/8.53) | 502 (90.4/1,480,000) | 2.44 (0.957/8.56) | 0.061 (0.001/1.59) | 97.6 (64.8/99.9) | 91.6 (50.4/99.2) | |||
| Gamma 65.4% | 1.60 (0.470/2.86) | 1.64 × 10−5 (5.55 × 10−6/0.00255) | mir: 380 (287/470) | 10.1 (5.77/513) | 4.85 (3.50/17.6) | 1.48 (1.15/3.62) | 26.4 (12.3/2,030) | 0.78 (0.587/1.39) | 1.31 (0.318/4.27) | 65.1 (5.08/87.5) | 10.1 (−53.2/51.4) |
| pse: 1,800 (1,540/2,050) | 47.3 (29.1/2,130) | 19.6 (14.7/38.1) | 6.04 (4.08/12.3) | 125 (62.7/8,450) | 0.79 (0.592/1.41) | 1.11 (0.004/1.84) | 96.9 (60.1/99.8) | 92.2 (46.3/98.9) | |||
The computations assume an effective mutation rate of 4 × 10−9/site/generation, a mutational bias of κ = 2, the absence of completely neutral mutations, and Nes = 0.5 as the border with effective neutrality (Loewe et al. 2006). The values are point estimates for genes in the curated data set for D. miranda (mir) and D. pseudoobscura (pse); parentheses give the lower 5th percentiles and the upper 5th percentiles from the bootstraps that could be fitted. The left-hand column indicates the type of distribution fitted, and the percentage of 1000 bootstraps that could be fitted. Ne gives the estimated current Ne in thousands for the corresponding species; Nes (am), (hm), (5%), and (95%) are the arithmetic mean, the harmonic means, and the lower and upper 5th percentiles of distribution of the product of Ne and s for effectively deleterious but nonlethal selection coefficients; CV is the corresponding coefficient of variation (ratio of standard deviation to mean) of the truncated distribution; cne is the fraction of effectively neutral nonsynonymous mutations; and α is the estimated proportion of nonsynonymous substitutions between the two focal species and D. affinis that were fixed by positive selection, where mir and pse indicate estimates using the Ne estimates for the two species, and 0.2 M and 1 M fix Ne at 200,000 and 1,000,000, respectively.