Table 1.
Likelihood ratio test (LRT) statistics for F3x4 and F61 models in primate phylogenies.
| Gene (Protein) |
Human Disordera | N° species | Model | M1a vs M2ab | M7 vs M8b | % negatively selected sitesd | Positively selected sitese | ||
|---|---|---|---|---|---|---|---|---|---|
| −2ΔlnLc | p value | −2ΔlnLc | p value | ||||||
|
ACTB
(Actin beta) |
23 | ||||||||
| F3x4 | 0.004 | 0.998 | 0.004 | 0.998 | 35.47 | na | |||
| F61 | 0.004 | 0.998 | 0.0003 | 0.999 | |||||
|
ADD1
(Adducin 1) |
23 | ||||||||
| F3x4 | 0 | 1 | 0.22 | 0.898 | 34.19 | na | |||
| F61 | 0 | 1 | 0.02 | 0.989 | |||||
|
ADD2
(Adducin 2) |
23 | ||||||||
| F3x4 | 0.08 | 0.959 | 1.68 | 0.433 | 33.20 | na | |||
| F61 | 0 | 1 | 0.003 | 0.999 | |||||
|
ANK1
(Ankyrin-1) |
HS | 22 | |||||||
| F3x4 | 0 | 1 | 19.03 | 7.39 × 10−5 | 40.67 | na | |||
| F61 | 5.47 | 0.07 | 23.33 | 8.57 × 10−6 | |||||
|
DMTN
(Dematin) | |||||||||
| F3x4 | 0 | 1 | 2.59 | 0.27 | 26,67 | na | |||
| F61 | 0 | 1 | 2.97 | 0.23 | |||||
|
EPB41
(Protein 4.1) |
HE | 23 | |||||||
| Reg1 (241 aa) | F3x4 | 0.009 | 0.99 | 0.83 | 0.660 | 8.68 | na | ||
| F61 | 0.006 | 0.99 | 0 | 1 | |||||
| Reg2 (55 aa) | F3x4 | 3.57 | 0.17 | 5.14 | 0.077 | 9.09 | na | ||
| F61 | 3.17 | 0.21 | 4.17 | 0.124 | |||||
| Reg3 (568 aa) | F3x4 | 0.001 | 0.99 | 0 | 1 | 17.96 | na | ||
| F61 | 0 | 1 | 0 | 1 | |||||
|
EPB42
(Protein 4.2) |
HS | 23 | |||||||
| F3x4 | 40.25 | 1.82 × 10−9 | 53.78 | 2.10 × 10−12 | 12.62 | R9, P24, I102, R117, L159, Q163, R224, R243, F251, R289, L390, E487, R495, T501, H562, I572, N581, E675 | |||
| F61 | 31.63 | 1.35 × 10−7 | 37.80 | 6.19 × 10−9 | |||||
|
MPP1
(p55) |
24 | ||||||||
| F3x4 | 0.003 | 0.999 | 0.009 | 0.995 | 32.83 | na | |||
| F61 | 0 | 1 | 0.011 | 0.994 | |||||
|
RHAG
(Ammonium transporter Rh type A) |
OHS | 24 | |||||||
| F3x4 | 4.12 | 0.127 | 9.37 | 0.009 | 13.17 | na | |||
| F61 | 2.52 | 0.283 | 6.08 | 0.048 | |||||
|
SLC4A1
(Band 3) |
HS, SAO | 31 | |||||||
| F3x4 | 6.43 | 0.04 | 29.02 | 5.01 × 10−7 | 32.69 | E28, R112, E152, D235, H309, E658 | |||
| F61 | 15.76 | 3.79 × 10−4 | 32.44 | 9.02 × 10−8 | |||||
|
SPTA1
(α spectrin) |
HE, HS | 22 | |||||||
| F3x4 | 30.43 | 2.47 × 10−7 | 55.68 | 8.12 × 10−13 | 26.50 | E117, L148, V164, D430, Q434, T459, D466, I745, V1233, Q1332, Q1584 | |||
| F61 | 18.80 | 8.27 × 10−5 | 38.73 | 3.90 × 10−9 | |||||
|
SPTB
(β spectrin) |
HE, HS | 24 | |||||||
| F3x4 | 0 | 1 | 17.94 | 1.27 × 10−4 | 42.69 | na | |||
| F61 | 0 | 1 | 2.90 | 0.234 | |||||
|
TMOD1
(Tropomodulin-1) |
24 | ||||||||
| F3x4 | 0 | 1 | 0.02 | 0.991 | 20.89 | na | |||
| F61 | 0 | 1 | 0 | 1 | |||||
|
TPM1
(Tropomyosin alpha-1 chain) |
23 | ||||||||
| F3x4 | 0 | 1 | 0.05 | 0.974 | 10.92 | na | |||
| F61 | 0 | 1 | 0.16 | 0.922 | |||||
|
TPM3
(Tropomyosin alpha-1 chain) |
24 | ||||||||
| Reg1 (80 aa) | F3x4 | 0 | 1 | 0 | 1 | 15.00 | na | ||
| F61 | 0 | 1 | 0 | 1 | |||||
| Reg2 (205 aa) | F3x4 | 4.22 | 0.121 | 4.26 | 0.119 | 10.24 | na | ||
| F61 | 0.68 | 0.711 | 0.80 | 0.671 | |||||
Notes: aHuman red cell membrane disorders associated with ECP (https://www.ncbi.nlm.nih.gov/medgen/): HS, Hereditary spherocytosis; HE, hereditary elliptocytosis; OHS, overhydratate hereditary stomatocytosis; SAO, Southeast Asian ovalocytosis; bM1a is a nearly neutral model that assumes one ω class between 0 and 1 and one class with ω = 1; M2a (positive selection model) is the same as M1a plus an extra class of ω > 1; M7 is a null model that assumes that 0 < ω < 1 is beta distributed among sites; M8 (positive selection model) is the same as M7 but also includes an extra category of sites with ω > 1; c2ΔlnL: twice the difference of the natural logs of the maximum likelihood of the models being compared; dPercentage of sites evolving under negative selection by FUBAR; ePositions refer to the human sequence.