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. 2012 Oct 1;12:195. doi: 10.1186/1471-2148-12-195

Table 1.

Branch models: estimated parameters and log-likelihood ratio tests

Paralog pair Model logL np Branchs ω LRT p-value
 
 M0
 −2847.12
 58
 OG
 0.05
  
  
  
 
  
  
  
 Lax
 0.08
  
  
  
 
  
  
  
 OG
 0.05
  
  
  
 
 MP
 −2846.50
 59
 Lax2
 0.07
 vs. M0
 1.24
 0.26
 
  
  
  
 Lax4
 0.10
  
  
  
 
  
  
  
 OG
 0.05
  
  
  
 Lax2/Lax4
 MA
 −2840.62
 59
 Laxearly
 0.14
 vs. M0
 13.0**
 0.00031
 
  
  
  
 Laxlate
 0.05
  
  
  
 
  
  
  
 OG
 0.05
  
  
  
 
  
  
  
 Lax2early
 0.19
 vs. MP
 13.8**
 0.001
 
 MPA
 −2839.60
 61
 Lax4early
 0.11
  
  
  
 
  
  
  
 Lax2late
 0.04
 vs. MA
 2.04
 0.36
 
  
  
  
 Lax4late
 0.06
  
  
  
 
 M0
 −4127.20
 62
 OG
 0.06
  
  
  
 
  
  
  
 Pg
 0.33
  
  
  
 
  
  
  
 OG
 0.06
  
  
  
 
 MP
 −4125.06
 63
 Pg3
 0.25
 vs. M0
 4.28*
 0.04
 
  
  
  
 Pg11
 0.41
  
  
  
 
  
  
  
 OG
 0.06
  
  
  
 Pg3/Pg11
 MA
 −4124.78
 63
 Pgearly
 0.22
 vs. M0
 4.84*
 0.03
 
  
  
  
 Pglate
 0.38
  
  
  
 
  
  
  
 OG
 0.06
  
  
  
 
  
  
  
 Pg3early
 0.24
 vs. MP
 3.68
 0.16
 
 MPA
 −4123.22
 65
 Pg11early
 0.21
  
  
  
 
  
  
  
 Pg3late
 0.29
 vs. MA
 3.12
 0.21
 
  
  
  
 Pg11late
 0.44
  
  
  
 
 M0
 −3604.36
 40
 OG
 0.27
  
  
  
 
  
  
  
 Pg11
 0.44
  
  
  
 
  
  
  
 OG
 0.27
  
  
  
 
 MP
 −3603.75
 41
 Pg11a
 0.38
 vs. M0
 1.22
 0.27
 
  
  
  
 Pg11c
 0.50
  
  
  
 
  
  
  
 OG
 0.27
  
  
  
 Pg11a/Pg11c
 MA
 −3604.19
 41
 Pg11early
 0.50
 vs. M0
 0.34
 0.57
 
  
  
  
 Pg11late
 0.42
  
  
  
 
  
  
  
 OG
 0.27
  
  
  
 
  
  
  
 Pg11aearly
 0.50
 vs. MP
 0.72
 0.70
 
 MPA
 −3603.39
 43
 Pg11cearly
 0.54
  
  
  
 
  
  
  
 Pg11alate
 0.35
 vs. MA
 1.60
 0.45
        Pg11clate 0.49      

*Note. Models: for M0, ω is allowed to take a different value only in the branch of the outgroup (OG); for MP, MA and MPA ω is allowed to take a different values according to the tested effect, i.e. “paralogs”, “age” or combined as explained in Figure 1. np: number of free parameters; logL: log-likelihood; LRT: likelihood ratio test statistic between indicated models; one (respectively two) asterisk indicates that the probability of observing such an LRT or higher under the compared model is <0.05 (respectively <0.01), assuming that the LRT follows a χ2 distribution with the difference of free parameters between the compared models as the number of degrees of freedom.