Table 1.
Genes and sites inferred to be under positive selection using three ML methods
| Genes | PAML | Datamonkey | ||||||
|---|---|---|---|---|---|---|---|---|
| -Ln(M8a) | -Ln(M8) | -2△Lnl (p-value) | ω value | Positively selected sites (P ≥ 85%)a | FEL (p < 0.1)b | REL (p > 50)c | % of Sites d | |
| ACAN | (16 sequences) | |||||||
| (2022aa) | 13,517.793 | 13,357.328 | 320.930 (<0.001) | 11.434 | 9, 360, 703, 806, 975, 980, 985, 992, 1002, 1068, 1100, 1185, 1270, 1411, 1532, 1626, 1710, 1734, 1944 | 9, 146, 360, 407, 703, 980, 985 | 9, 146, 219, 360, 396, 407, 686, 703, 975, 980, 985, 1016, 1100, 1567, 1734, 1750, 1944 | 0.544(11) |
| AIP | (14 sequences) | |||||||
| (330aa) | 1859.035 | 1855.058 | 7.953 (<0.005) | 4.488 | 43, 45, 78, 86, 131, 218 | 43, 131 | 43, 45, 56, 78, 131, 301 | 1.212(4) |
| CDKN1B | (16 sequences) | |||||||
| (198aa) | 1015.965 | 1013.544 | 4.841 | 21.427 | 162 | 162 | 0.505(1) | |
| EIF2AK3 | (16 sequences) | |||||||
| (964aa) | 5985.966 | 5976.756 | 18.42 (<0.001) | 3.978 | 154, 358, 558, 628, 677, 897 | 154 | 154, 677, 795, 897 | 0.311(3) |
| FBN1 | (15 sequences) | |||||||
| (2871aa) | 15,888.036 | 15,872.839 | 30.393 (<0.001) | 3.387 | 300, 2443, 2696, 2699, 2701, 2737, 2741 | 1946, 2701, 2741 | 120, 1175, 1946, 2336, 2443, 2696, 2699, 2701, 2737, 2741, 2775 | 0.244(7) |
| MED12 | (16 sequences) | |||||||
| (2050aa) | 9844.493 | 9840.242 | 8.502 (<0.005) | 12.298 | 312, 1621 | 1621 | 1621 | 0.049(1) |
| MEN1 | (16 sequences) | |||||||
| (610aa) | 3657.161 | 3628.394 | 57.534 (<0.001) | 7.403 | 526, 536, 542, 594 | 394, 459, 475, 526, 542 | 0.328(2) | |
| NPR2 | (16 sequences) | |||||||
| (1047aa) | 5716.770 | 5687.387 | 58.825 (<0.001) | 14.294 | 325 | 325 | 0.096(1) | |
| NSD1 | (16 sequences) | |||||||
| (2696aa) | 13,297.254 | 13,276.127 | 42.253 (<0.001) | 4.399 | 111, 652, 964, 978, 1144, 1493, 1518, 1853, 2236, 2264, 2335, 2411 | 111, 652, 964, 978, 1493, 1518, 1853, 2236, 2264, 2335, 2411 | 0.408(11) | |
| OBSL1 | (16 sequences) | |||||||
| (1729aa) | 10,250.581 | 10,242.647 | 15.868 (<0.001) | 4.348 | 638, 1242, 1395, 1423, 1428, 1564, 1617 | 592, 638, 1242, 1395, 1428, 1617 | 0.289(5) | |
Note: The codons identified to be under positive selection by at least two or three ML methods are marked in bold and "bold and Italic", respectively.
aCodons identified by M8 model in PAML using a Bayes Empirical Bayes (BEB) analysis with posterior probabilities ≥85%
bCodons detected by FEL implemented in Datamonkey web server with significance levels of 0.1
cCodons determined by REL in Datamonkey web server with Bayes factors >50
dNo. of sites indicate positively selected sites identified by both ML method