Evolutionary study of duplications of the miRNA machinery in aphids associated with striking rate acceleration and changes in expression profiles

Table 3 Summary of the analyses of selective pressures on ago-1 and dcr-1 with PAML

	Branch models		Site models		Branch-site models
*ago-1* Region 1 (726 nt)	one-ratio:two-ratio	P<0.0001
	one-ratio:free-ratio	P<0.0001
	two-ratio:free-ratio	P=0.6706	M7:M8	P<0.0001	MAof:MAoe	P=0.0285
	ω _ago1a =0.0001	ω _ago1b =0.8621	4 sites with P>0.95		52 sites with P>0.95
*ago-1* Region 2 (909 nt)	one-ratio:two-ratio	P<0.0001
	one-ratio:free-ratio	P<0.0001
	two-ratio:free-ratio	P=0.0506	M7:M8	P<0.0001	MAof:MAoe	P=0.0218
	ω _ago1a =0.0001	ω _ago1b =0.6236	5 sites with P>0.95		74 sites with P>0.95
*ago-1* Region 3 (276 nt)	one-ratio:two-ratio	P<0.0001
	one-ratio:free-ratio	P<0.0001
	two-ratio:free-ratio	P=0.4675	M7:M8	P=0.9802	MAof:MAoe	P=1
	ω _ago1a =0.0039	ω _ago1b =0.2476	No positively selected sites		No positively selected sites
*dcr-1* (957 nt)	one-ratio:two-ratio	P=0.0002
	one-ratio:free-ratio	P=0.0515
	two-ratio:free-ratio	P=0.6424	M7:M8	P=0.4677	MAof:MAoe	P=1
	ω _dcr-1/1a =0.1247	ω _dcr-1b =0.3577	No positively selected sites		No positively selected sites

For branch models, the best overall model is highlighted (two-ratio model for all the alignments) with its corresponding ω values. For site and branch-site models, the best model is highlighted as well as the number of positively selected sites when relevant. MAof: model MA with omega fixed to 1; MAoe: model MA with omega estimated. See text for further explanations about the models.

ISSN: 2730-7182