. 2018 Jun 21;4(1):vey018. doi: 10.1093/ve/vey018

Table 2.

Recovery of expected evolutionary trends under various RNA-structure informed partitioned site models.

Model	Evolutionary rate	Ts/Tv ratio	G + C content
SHAPE reactivity	SIV^w, SIV^b, HIV^b	SIV^w, HIV^b, HIV^w	HIV^w, HIV^b, SIV^w, SIV^b
Final structure pairing status		HIV^b,	HIV^w, HIV^b, SIV^w. SIV^b
Final structure helical position	SIV^w, HIV^w SIV^b, HIV^b	SIV^w, HIV^b	HIV^w, HIV^b, SIV^w. SIV^b
Codon position within predicted structure	SIV^w, SIV^b	SIV^w, SIV^b, HIV^b	HIV^w, HIV^b, SIV^w. SIV^b
Pairing probability	HIV^w, HIV^b, SIV^w, SIV^b	SIV^b, HIV^b	HIV^wa, HIV^b, SIV^wa. SIV^b
Combined model	HIV^w, HIV^b, SIV^w, SIV^b	HIV^w, HIV^b, SIV^w	HIV^w, HIV^b, SIV^w. SIV^b

SIV^w, within-host SIV data; HIV^w, within-host HIV data; SIV^b, between-host SIV data; HIV^b, between-host HIV data.

Entries in plain text indicate that evolutionary measures were influenced by partitioning (significant statistical test, P < 0.05, see text for the description of tests). For entries in bold, the expected trend (Supplementary Fig. S1) was also recovered.

Inverse trend compared with expectation.