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Table 2 Evolutionary profiles of H5N1 HPAI viruses: comparisons between strict and relaxed (uncorrelated lognormal) molecular clocks using the constant, exponential growth, Bayesian skyride and Bayesian skyline coalescent prior

From: Spatial, temporal and genetic dynamics of highly pathogenic avian influenza A (H5N1) virus in China

   Evolutionary rates (sub/site/year) × 10−3(95% HPD*)
Best fit clock model Strict clock Uncorrelated lognormal molecular clock (ULCN)
Constant size Exponential growth Bayesian skyride Bayesian skyline Constant size Exponential growth Bayesian skyride Bayesian skyline
2000-2001 Strict-Skyride 4.15 (2.97-5.44) 3.49 (2.34-4.76) 3.85 (2.98-4.80) 4.12 (3.07-5.39) 4.36 (2.96-5.98) 4.36 (2.93-5.82) 4.61 (3.25-6.08) 4.65 (2.93-6.37)
2001-2002 Strict-Constant 4.06 (3.03-5.17) 3.24 (2.11-4.48) 3.83 (2.92-4.78) 3.72 (2.73-4.72) 5.17 (3.63-6.74) 4.86 (3.21-6.59) 5.16 (3.58-6.63) 5.48 (3.80-7.18)
2002-2003 Strict-Exponential 2.51 (1.87-3.26) 2.34 (1.68-3.09) 2.29 (1.68-2.93) 2.47 (1.81-3.13) 2.52 (1.78-3.29) 2.97 (2.01-3.94) 2.79 (1.85-3.87) 2.61 (1.77-3.49)
2003-2004 Strict-Constant 4.31 (3.38-5.23) 4.15 (3.31-5.00) 4.19 (3.28-5.12) 4.21 (3.24-5.13) 4.83 (3.76-5.93) 4.84 (3.7-6.22) 1.04 (0.01-5.02) 4.86 (3.38-6.60)
2004-2005 Strict-Skyride 6.81 (5.69-7.95) 6.88 (5.66-8.03) 6.63 (5.73-7.56) 6.70 (5.69-7.67) 8.99 (6.69-11.08) 7.83 (6.31-10) 7.15 (5.55-8.46) 7.37 (4.20-9.98)
2005-2006 Strict-Exponential 3.55 (2.94-4.17) 3.62 (3.09-4.19) 3.85 (2.5-5.14) 3.14 (2.03-3.92) 3.52 (2.73-4.44) 4.31 (3.27-5.38) 4.03 (1.25-5.69) 3.44 (1.29-4.53)
2006-2007 UCLN-Exponential 4.18 (3.28-5.17) 3.76 (2.59-4.68) 4.07 (2.8-5.45) 3.41 (2.28-4.47) 5.72 (3.78-7.44) 5.48 (3.99-6.92) 4.83 (1.25-5.69) 5.61 (2.20-8.40)
2007-2008 Strict-Skyline 4.37 (3.29-5.56) 4.19 (3.06-5.37) 4.52 (3.4-5.62) 4.66 (3.63-5.81) 4.08 (2.76-5.55) 4.58 (3.04-6.27) 4.96 (3.63-6.44) 5.01 (3.22-7.13)
2008-2009 Strict-Exponential 4.91 (3.64-6.12) 4.84 (3.58-6.07) 5.03 (3.85-6.26) 4.74 (3.57-6.02) 5.98 (4.04-8.06) 6.33 (3.94-8.79) 7.31 (4.72-10.08) 6.44 (4.12-8.96)
1996-2004 UCLN-Exponential 3.24 (2.92-3.60) 3.19 (2.86-3.51) 4.03 (3.58-4.52) 3.63 (3.13-4.10) 3.54 (3.08-3.97) 3.77 (3.33-4.22) 4.03 (3.57-4.51) 3.63 (3.13-4.10)
2005-2011 Strict-Constant 4.39 (4.03-4.76) 4.44 (4.06-4.80) 4.35 (3.88-4.81) 4.45 (4.05-4.87) 4.28 (3.67-4.84) 4.26 (3.15-5.11) 4.30 (3.82-4.78) 3.95 (3.58-4.28)
  1. *HPD, highest posterior density.