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Table 1 Positively selected sites detected using two maximum likelihood (ML) methods across cetacean phylogeny

From: Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes

Gene

Test of Selection

Sites under Selection Identified by ML Methods

-Ln (M8a)

-Ln (M7)

-Ln (M8)

−2△L (M7 vs.m8)

−2△L (M8a vs.m8)

ω value

PAML M8a

FELb

no. of Sitesc

% of Sites

WDR62

(1298aa)

7703.049

7703.257

7690.821

24.872*

24.456*

10.203

262, 458, 479, 972, 1008, 1133, 1244

207, 262, 458, 479, 648, 705, 763, 972, 1008, 1076, 1092, 1107, 1133, 1158

6

0.46%

CDK5RAP2

(1414aa)

10,316.782

10,317.746

10,285.732

64.082*

62.101*

4.438

23, 108, 182, 201, 283, 382, 394, 426, 445, 518, 523, 531, 558, 615, 678, 686, 700, 717, 720, 724, 726, 727, 740, 760, 763, 786, 787, 832, 849, 913, 982, 1012, 1020, 1030, 1166, 1167, 1284, 1370, 1396

6, 10, 23, 30, 108, 174, 182, 201, 204, 283, 426, 427, 445, 531, 720, 760, 787, 832, 849, 887, 913, 1166, 1280, 1284, 1310, 1313

16

1.13%

CEP152

(1523aa)

9948.922

9949.080

9939.249

19.662*

19.347 *

7.312

79, 305, 477, 510, 543, 613, 1147, 1163, 1360, 1398

73, 79, 239, 305, 328, 401, 510, 717, 941, 966, 1088, 1097, 1147, 1163, 1281, 1398

6

0.39%

ASPM

(3128aa)

20,714.804

20,714.924

20,700.708

28.432*

28.191*

5.236

69, 347, 387, 595, 692, 805, 806, 1311, 1602, 1684, 1787, 1864, 2096, 2098, 2350, 2619, 2693, 2798, 2819, 3111

22, 23, 69, 347, 387, 542, 677, 692, 1178, 1311, 1602, 1657, 1660, 1682, 1737, 1741, 1758, 1864, 2106, 2187, 2205, 2445, 2465, 2507, 2510, 2546, 2619, 2817, 3098

8

0.26%

CENPJ

(998aa)

7086.280

7086.473

7086.040

1.700 (NS)

0.488 (NS)

1.593

__

112, 366, 370, 451, 473, 488, 499, 513, 544, 567, 645

__

__

STIL

(1125aa)

6173.275

6173.287

6172.437

0.866 (NS)

1.677

(NS)

4.921

__

471, 575, 991

__

__

  1. The positively selected sites picked out by two methods are shown in bold
  2. * indicates P < 0.05 whereas NS indicates ‘No significant’
  3. aCodons were detected by M8 model in PAML using a Bayes Empirical Bayes (BEB) analysis with posterior probabilities ≥0.80
  4. bCondons was determined by FEL implemented in HYPHY with significance levels of 0.2
  5. cNo. of sites indicate positively selected sites identified by both ML methods