Table 1.
Parameters for evolutionary rates and Bayesian skyline plot analyses in HuNoV GII.4 and the variants.
| Datasets | Number of strains | Substitutionmodels | Clock models | Demographic models | Chain length of MCMC | Log parameter |
|---|---|---|---|---|---|---|
| GII.4 all variants (Complete VP1 gene) | 466 | GTR+Γ+I | Relaxed clock log normal | Coalescent exponential population | 300,000,000 | 2,000 |
| Strict clock | Coalescent Bayesian skyline | 220,000,000 | 8,000 | |||
| GII.4 all variants (Shell domain) | 466 | HKY+Γ+I | Strict clock | Coalescent exponential population | 200,000,000 | 5,000 |
| GII.4 all variants (P1 domain) | 466 | SYM+Γ | Relaxed clock log normal | Coalescent exponential population | 210,000,000 | 2,000 |
| GII.4 all variants (P2 domain) | 466 | GTR+Γ+I | Relaxed clock exponential | Coalescent constant population | 150,000,000 | 5,000 |
| US95_96 | 33 | SYM+Γ+I | Relaxed clock exponential | Coalescent exponential population | 250,000,000 | 2,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 2,000 | |||
| Farmington Hills 2002 | 18 | K80+Γ | Relaxed clock exponential | Coalescent exponential population | 1,400,000,000 | 10,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 5,000 | |||
| Asia 2003 | 17 | K80+Γ | Relaxed clock log normal | Coalescent exponential population | 550,000,000 | 4,000 |
| Strict clock | Coalescent Bayesian skyline | 100,000,000 | 2,000 | |||
| Hunter 2004 | 22 | K80+Γ | Relaxed clock exponential | Coalescent exponential population | 550,000,000 | 4,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 2,000 | |||
| Yerseke 2006a | 13 | TrNef+Γ | Relaxed clock exponential | Coalescent exponential population | 1,160,000,000 | 10,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 2,000 | |||
| Den Haag 2006b | 145 | HKY+Γ+I | Relaxed clock exponential | Coalescent exponential population | 300,000,000 | 10,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 300,000,000 | 10,000 | |||
| Osaka 2007 | 11 | TrNef+Γ | Relaxed clock exponential | Coalescent exponential population | 100,000,000 | 2,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 2,000 | |||
| Apeldoorn 2007 | 25 | TrNef+Γ | Relaxed clock exponential | Coalescent exponential population | 300,000,000 | 10,000 |
| Relaxed clock exponential | Coalescent Bayesian skyline | 100,000,000 | 5,000 | |||
| New Orleans 2009 | 86 | HKY+Γ+I | Random local clock | Coalescent exponential population | 200,000,000 | 2,000 |
| Random local clock | Coalescent Bayesian skyline | 300,000,000 | 6,000 | |||
| Sydney 2012 | 68 | TPM2+Γ+I | Relaxed clock log normal | Coalescent exponential population | 100,000,000 | 5,000 |
| Random local clock | Coalescent Bayesian skyline | 100,000,000 | 5,000 |
Parameters for evolutionary rates and BSP are shown in upper and lower lines, respectively.