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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.