Table 2 Summary of EasyCodeML branch model analyses for detecting variable selective pressures among HIFA genes. The two-ratio Model 2 allowed the ratio of non-synonymous to synonymous substitutions (ω) in the indicated HIFA gene to differ from ω for other HIFA genes. Model 0 assumed a constant ω for all HIFA genes. For each HIFA gene, the difference in likelihood of the two models was evaluated with likelihood-ratio tests (LRT).

From: Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection

Foreground branch

Model

− lnL

Parameter estimates

LRT P value

HIF1A

Two ratio Model 2

932.93

ω0 = 0.0406, ω1 = 0.1139

0.463

Model 0

933.20

ω = 0.0415

HIF2A

Two ratio Model 2

933.20

ω0 = 0.0415, ω1 = 2.2060

0.994

Model 0

933.20

ω = 0.0415

HIF3A

Two ratio Model 2

933.30

ω0 = 0.0438, ω1 = 0.0260

0.378

Model 0

932.91

ω = 0.0442

HIF4A

Two ratio Model 2

932.50

ω0 = 0.0452, ω1 = 0.0001

0.121

Model 0

933.71

ω = 0.0408

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