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Table 3 SAMD9 and SAMD9L parameter estimates and likelihood ratio test (LRT) for branch-site model A (PAML)

From: Evolution and divergence of the mammalian SAMD9/SAMD9L gene family

Branch-site Model A

LRT

  

Foreground branches a

Parameter estimates

−2ΔlnLb

df c

p-Value

Positively selected sites d

SAMD9

     

Gogo

p 0  = 0.693 p 1  = 0.291 p 2a  = 0.011 p 2b  = 0.005 ω 0  = 0.096 ω 1  = 1.000 ω 2  = 6.192

0.20

1

n.s.

none

Poab

p 0  = 0.701 p 1  = 0.293 p 2a  = 0.004 p 2b  = 0.002 ω 0  = 0.096 ω 1  = 1.000 ω 2  = 21.339

3.65

1

n.s.

none

Nole

p 0  = 0.692 p 1  = 0.291 p 2a  = 0.012 p 2b  = 0.005 ω 0  = 0.095 ω 1  = 1.000 ω 2  = 2.555

0.12

1

n.s.

none

Orcu

p 0  = 0.696 p 1  = 0.290 p 2a  = 0.010 p 2b  = 0.004 ω 0  = 0.094 ω 1  = 1.000 ω 2  = 4.818

3.30

1

n.s.

none

Capo

p 0  = 0.702 p 1  = 0.292 p 2a  = 0.005 p 2b  = 0.002 ω 0  = 0.096 ω 1  = 1.000 ω 2  = 5.728

1.25

1

n.s.

none

Soar

p 0  = 0.696 p 1  = 0.286 p 2a  = 0.013 p 2b  = 0.005 ω 0  = 0.094 ω 1  = 1.000 ω 2  = 8.165

9.56

1

< 0.01

288, 572

SAMD9L

     

Poab

p 0  = 0.729 p 1  = 0.270 p 2a  = 0.001 p 2b  = 0.000 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 409.279

6.59

1

< 0.05

888

Caja

p 0  = 0.714 p 1  = 0.263 p 2a  = 0.016 p 2b  = 0.006 ω 0  = 0.138 ω 1  = 1.000 ω 2  = 3.169

1.12

1

n.s.

none

Mamu

p 0  = 0.727 p 1  = 0.268 p 2a  = 0.004 p 2b  = 0.001 ω 0  = 0.140 ω 1  = 1.000 ω 2  = 11.372

1.22

1

n.s.

none

Loaf

p 0  = 0.717 p 1  = 0.262 p 2a  = 0.015 p 2b  = 0.006 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 2.244

0.80

1

n.s.

none

Calu

p 0  = 0.730 p 1  = 0.269 p 2a  = 0.013 p 2b  = 0.000 ω 0  = 0.140 ω 1  = 1.000 ω 2  = 20.273

0.52

1

n.s.

none

Aime

p 0  = 0.728 p 1  = 0.269 p 2a  = 0.003 p 2b  = 0.001 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 16.318

2.51

1

n.s.

none

Ereu

p 0  = 0.725 p 1  = 0.266 p 2a  = 0.006 p 2b  = 0.002 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 998.998

7.45

1

< 0.01

none

Mumu

p 0  = 0.716 p 1  = 0.264 p 2a  = 0.015 p 2b  = 0.005 ω 0  = 0.138 ω 1  = 1.000 ω 2  = 3.755

0.34

1

n.s.

none

Crgr

p 0  = 0.728 p 1  = 0.268 p 2a  = 0.003 p 2b  = 0.001 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 38.672

2.62

1

n.s.

none

Rano

p 0  = 0.727 p 1  = 0.268 p 2a  = 0.004 p 2b  = 0.001 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 11.843

2.14

1

n.s.

none

Capo

p 0  = 0.722 p 1  = 0.261 p 2a  = 0.012 p 2b  = 0.004 ω 0  = 0.139 ω 1  = 1.000 ω 2  = 6.984

6.36

1

< 0.05

861

Soar

p 0  = 0.717 p 1  = 0.264 p 2a  = 0.014 p 2b  = 0.005 ω 0  = 0.137 ω 1  = 1.000 ω 2  = 7.759

10.49

1

< 0.01

84, 1338,

1346

  1. a Species names on the foreground branches by order of appearance: Gogo - Western gorilla; Poab - Sumatran orangutan; Nole - Northern white-cheeked gibbon; Orcu - European rabbit; Capo - Domestic Guinea pig; Soar - Common shrew; Caja - Common marmoset; Mamu - Rhesus monkey; Loaf - African bush elephant; Calu - Domestic dog; Aime - Giant panda; Ereu - West European hedgehog; Mumu - House mouse; Crgr - Chinese hamster; Rano - Brown rat.
  2. b -2ΔlnL: likelihood ratio test (LRT) to detect positive selection.
  3. c df: degrees of freedom.
  4. d Positively selected sites: posterior probabilities > 90% in the BEB (Bayes Empirical Bayes) analyses.