TABLE 1.
Positive selection analyses of primate, rodent, and bat NTCP/SLC10A1 and GPC5 as well as of the orthohepadnavirus preS1 regiona
| Data set | Gene | M1 vs M2 P valueb | % positively selected sites in M2c | M2 ω (dN/dS ratio)d | M7 vs M8 P valueb | % positively selected sites in M8c | M8 ω (dN/dS ratio)d |
|---|---|---|---|---|---|---|---|
| Primates | |||||||
| All primate species | NTCP | 4E−03 | 2.61 | 3.87 | 2E−04 | 3.38 | 4.02 |
| Simians (hominoids, NWM, OWM) | NTCP | 6E−04 | 5.19 | 3.68 | 8E−05 | 2.91 | 5.74 |
| All primate species excluding hominoids | NTCP | 0.02 | 3.25 | 3.20 | 0.001 | 5.14 | 3.69 |
| Rodents | NTCP | 2E−08 | 2.10 | 4.16 | 8E−10 | 2.67 | 3.32 |
| Bats | NTCP | 2E−04 | 4.1 | 2.77 | 7E−08 | 7.31 | 2.20 |
| Primates | GPC5 | 1 | — | — | 0.20 | — | — |
| Rodents | GPC5 | 1 | 0.38 | ||||
| Bats | GPC5 | 1 | — | — | 1 | — | — |
| Hominoid HBV | HBV preS1 | 1 | — | — | 1 | — | — |
| Bat orthohepadnaviruses | HBV preS1 | 1 | — | — | 1 | — | — |
Results of the positive-selection analyses performed with PAML Codeml and comparing models that disallow positive selection (models M1 and M7; dN/dS ratio of ≤1) to models allowing for positive selection (M2 and M8). Positive selection in the primate NTCP/SLC10A1 gene was assessed for different data sets: the whole primate data set (n = 27), the simian primate data set (excluding the prosimians; n = 24), and the primate data set excluding hominoid species (n = 21). Evolutionary analyses were also carried out on rodents (18 species). For bats, the analyses were performed on 21 species, including the newly obtained sequences in this study. The GPC5 gene was analyzed for 20 primate, 19 rodent, and 7 bat species. The data shown were obtained with codon frequencies F61 and a starting omega dN/dS ratio of 0.4. Similar results were found with a codon frequency of F3*4 and a starting omega value of 1.5. NWM, New World monkeys; OWM, Old World monkeys.
P values generated from maximum likelihood ratio tests indicate whether the model that allows positive selection (models M2 and M8) better fits the data than the nearly neutral one (M1 and M7).
Percentage of codons evolving under positive selection (dN/dS ratio of >1). —, not applicable.
Average dN/dS ratio (ω) associated with the positively selected sites.