TABLE 3

Test of selection among lineages using revised branch-site model A and test 2 as implemented in PAML 315 (see materials and methods)

Parameter estimates
Model ASite classpω0 backgroundω1 foregroundLn likelihood, LRT test 2Selected codon, posterior P
Domestic cat lineageκ = 2.084400.423680.278110.27811−1618.646K125R (0.943)
10.5702411−1623.128 (Null)
2a0.002590.2781174.02392
2b0.00349174.02392LRT = 8.965, P < 0.1
Asian leopard cat lineageκ = 2.0413400.117850.126840.12684−1622.952
10.1868011−1622.952 (Null)
2a0.268990.126841
2b0.4263711LRT = 0, NS
Ocelot lineageaκ = 2.0460800.382170.210980.21098−1623.179
10.6178311−1623.179 (Null)
2a0.000000.210981
2b0.0000011LRT = 0, NS
Puma lineageκ = 1.99378000.167750.16775−1618.396S6R**M97R**
1011−1621.544 (Null)V14A**A161D**
2a0.496900.16775999.000Q18P**M187V*
2b0.503101999.000LRT = 6.295, P > 0.01V25A**A213P**
R46G*Y223C*
V75M**
Lynx lineageκ = 2.060900.391580.220670.22067−1621.591
10.5769111−1623.132 (Null)
2a0.012350.2206784.78123
2b0.01816184.78123LRT = 3.082, NS
Caracal lineageκ = 2.0460900.382160.210970.21097−1623.179
10.3178411−1623.179 (Null)
2a00.210971
2b011LRT = 0, NS
Bay cat lineageκ = 2.04401000.224580.22458−1622.007
1011−1623.139 (Null)
2a0.400680.22458277.069
2b0.599321277.069LRT = −2.263, NS
Panthera lineageaκ = 2.0460900.382160.210970.21097−1623.179
10.6178411−1623.179 (Null)
2a00.210971
2b011LRT = 0, NS
  • κ, transition/transversion ratio; NS, not significant results of Ln likelihood-ratio test; ω0, background ratio of dN/dS; ω1, lineage-specific ratio of dN/dS. *Posterior P > 0.95%, **Posterior P > 0.99%.

  • a Neofelis nebulosa and Leopardus pardalis were omitted due to frameshift mutations incompatible with PAML.