Molecular evolution of mammalian genes with epistatic interactions in fertilization

Table 1 Summary of codon model results using the aBSREL and MEME methods

gene	taxon	aBSREL				MEME
gene	taxon	number of selected branches (P < 0.01)	total branches	ω^a	proportion of codons under selection	number of selected codons (P < 0.01)	total codons	β^b	proportion of gene tree under selection
Zp3r	Glires	3	37	37	0.08	5	527	63	0.20
C4bpa	Glires	4	39	293	0.05	6	457	34	0.15
	Primates	4	45	431	0.08	9	597	149	0.11
C4bpb	Glires	0	35	n/a	n/a	0	247	n/a	n/a
	Primates	0	47	n/a	n/a	0	256	n/a	n/a
Zp1	Glires	3	31	2232	0.04	3	615	181	0.12
	Primates	2	39	10000	0.02	3	634	1436	0.04
Zp2	Glires	3	35	3561	0.03	4	589	27	0.22
	Primates	1	47	10	0.08	0	745	n/a	n/a
Zp3	Glires	1	37	169	0.04	1	421	7	0.36
	Primates	0	47	n/a	n/a	0	424	n/a	n/a
Zp4	Glires	1	37	10000	0.02	2	532	114	0.11
	Primates	2	47	6010	0.02	3	541	188	0.04
Izumo1	Glires	2	41	51	0.15	1	262	111	0.10
	Primates	1	45	10000	0.05	0	350	n/a	n/a
Juno	Glires	0	41	n/a	n/a	1	243	20	0.13
	Primates	0	41	n/a	n/a	0	250	n/a	n/a

For each analysis (one model fitted to one gene from one taxon) the primary response variable is shown on the left (the number of episodes of positive selection), followed by the size of the sample (the total number of branches in the gene tree or codons in the alignment) and the two secondary response variables (the mean value of the model parameter for episodes of positive selection, and the mean proportion of codons or branch lengths with that model parameter value)
^a Mean estimated value of dN/dS at some codons along positively selected branches; values of 10,000 are high but imprecisely estimated (at the boundary condition for the parameter value)
^b Mean estimated value of dN along some positively selected branches at positively selected codons

ISSN: 2730-7182