Evolution of Three Parent Genes and Their Retrogene Copies in Drosophila Species
Table 1
Sequence evolution analyses on three gene pairs.
Gene pair
Branch-site test (PAML)
Datamonkey
Total no. of sites in codon alignment
Parent as foreground
Retrogene as foreground
Negatively selected sites (FEL)
Sites under episodic diversifying selection (MEME)
Visually identified sites
No. of sitesa
No. of sitesa
No. of sitesb
Proportion of total sites
No. of sitesc
Proportion of total sites
No. of sitesd
Proportion of total sites
CG8331 and CG4960
155
N/A
N/A
95
0.613
4
0.026
2
0.013
CG17734 and CG11825
94
N/A
N/A
67
0.713
0
0
5
0.053
Sep2 and Sep5
398
2
N/A
356
0.894
3
0.0075
58
0.146
Number of positively selected sites identified by Bayes Empirical Bayes when the null model was rejected; number of negatively selected sites with ; number of sites under episodic diversifying selection with P value ≤ 0.05; number of sites with ≥80% amino acid conservation in the parent, ≥80% amino acid conservation in the retrogene, but which were different between parent and retrogene.
