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Table 1 Genes and sites inferred to be under positive selection using three ML methods

From: Insights into body size variation in cetaceans from the evolution of body-size-related genes

Genes

PAML

Datamonkey

 

-Ln(M8a)

-Ln(M8)

-2â–³Lnl (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)

  1. 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. 
  2. aCodons identified by M8 model in PAML using a Bayes Empirical Bayes (BEB) analysis with posterior probabilities ≥85%
  3. bCodons detected by FEL implemented in Datamonkey web server with significance levels of 0.1
  4. cCodons determined by REL in Datamonkey web server with Bayes factors >50
  5. dNo. of sites indicate positively selected sites identified by both ML method
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BMC Ecology and Evolution

ISSN: 2730-7182

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