Volume 20, Number 12—December 2014
Research
Molecular Evolution of Peste des Petits Ruminants Virus
Murali Muniraju, Muhammad Munir, AravindhBabu R. Parthiban, Ashley Banyard, Jingyue Bao, Zhiliang Wang, Chrisostom Ayebazibwe, Gelagay Ayelet, Mehdi El Harrak, Mana Mahapatra, Geneviève Libeau, Carrie Batten, and Satya Parida
Table 4
Bayesian Markov chain Monte Carlo analysis for genomes of peste des petits ruminants virus*
| Sequence dataset (no.)† | Models, substitution/ clock/demographic | Mean nucleotide substitution rate, substitutions/site/y (95% HPD) | TMRCA, y (95% HPD) | Bayes factor, –log likelihood |
|---|---|---|---|---|
| PPRV complete genome (12) | GTR + G/strict/BSP | 3.2 x 10–4 (2.02 x 10–4–4.31 x 10–4) | 1763 (1653–1832) | –46,972.98 |
| GTR + G/strict/CS | 3.21 x 10–4 (2.12 x 10–4–4.38 x 10–4) | 1763 (1659–1834) | –46,973.06 | |
| GTR + G/strict/EG | 3.24 x 10–4 (2.12 x 10–4–4.33 x 10–4) | 1765 (1668–1836) | –46,973.06 | |
| GTR + G/UCLD/BSP | 2.89 x 10-3 (3.21 x 10–8–6.92 x 10–4) | 1691 (123 |
–46,935.66 | |
| GTR + G/UCLD/CS | 3.03 x 10–4 (8.99 x 10–9–7.07 x 10–4) | 1705 (123–1961) | –46,935.86 | |
| GTR + G/UCLD/EG | 3.72 x 10–4 (3.01 x 10–5–7.93 x 10–4) | 1767 (1222–1948) | –46,935.89 | |
| GTR + G/UCED/BSP | 7.91 x 10–4 (7.46 x 10–5–1.53 x 10–3) | 1889 (1586–1968) | –46,933.82 | |
| GTR + G/UCED/CS | 7.98 x 10–4 (8.03 x 10–5–1.54 x 10–3) | 1887 (1569–1968) | –46,933.98 | |
| GTR + G/UCED/EG | 9.09 x 10–4 (2.13 x 10–4–1.64 x 10–3) | 1904 (1730–1966) | –46,933.96 | |
| GTR + G/random/BSP | 7.01 x 10–4 (5.55 x 10–4–8.50 x 10–4) | 1888 (1862–1908) | –46,934.75 | |
| GTR + G/random/CS | 6.97 x 10–4 (5.38 x 10–4–8.41 x 10–4) | 1887 (1860–1908) | –46,934.64 | |
| GTR + G/random/EG | 7.04 x 10–4 (5.57 x 10–4–8.57 x 10–4) | 1888 (1861–1908) | –46,934.89 | |
| N partial (159) | GTR + G/strict/BSP | 1.22 x 10–3 (9.39 x 10–4–1.51 x 10–3) | 1890 (1857–1917) | –2,884.524 |
| GTR + G/strict/CS | 1.23 x 10–3 (9.49 x 10–4–1.52 x 10–3) | 1886 (1853–1913) | –2,887.723 | |
| GTR + G/strict/EG | 1.24 x 10–3 (9.71 x 10–4–1.56 x 10–3) | 1893 (1863–1919) | –2,885.44 | |
| GTR + G/UCLD/BSP | 1.45 x 10–3 (1.06 x 10–3–1.87 x 10–3) | 1896 (1815–1943) | –2,806.535 | |
| GTR + G/UCLD/CS | 1.41 x 10–3 (1.05 x 10–3–1.80 x 10–3) | 1882 (1793–1935) | –2,805.535 | |
| GTR + G/UCLD/EG | 1.49 x 10–3 (1.10 x 10–3–1.89 x 10–3) | 1904 (1838–1943) | –2,805.921 | |
| GTR + G/UCED/BSP | 1.52 x 10–3 (1.11 x 10–3–1.98 x 10–3) | 1904 (1817–1949) | –2,799.572 | |
| GTR + G/UCED/CS | 1.46 x 10–3 (1.05 x 10–3–1.88 x 10–3) | 1886 (1785–1940) | –2,799.512 | |
| GTR + G/UCED/EG | 1.56 x 10-3 (1.16 x 10–3–1.99 x 10–3) | 1910 (1846–1947) | –2,799.444 | |
| GTR + G/random/BSP | 1.26 x 10–3 (9.44 x 10–4–1.58 x 10–3) | 1881 (1837–1915) | –2,865.846 | |
| GTR + G/random/CS | 1.24 x 10–3 (9.38 x 10–4–1.57 x 10–3) | 1875 (1831–1910) | –2,866.111 | |
| GTR + G/random/EG | 1.27 x 10–3 (9.62 x 10–4–1.60 x 10–3) | 1880 (1841–1914) | –2,866.929 | |
| N CDS (12) | GTR + G/UCED/EG | 1.01 x 10–3 (2.79 x 10–4–1.83 x 10–3) | 1924 (1799–1970) | NA |
| N complete gene (12) | GTR + G/UCED/EG | 1.08 x 10–3 (3.19 x 10–4–1.93 x 10–3) | 1923 (1804–1970) | NA |
| P CDS (12) | GTR + I/UCED/EG | 1.11 x 10–3 (3.46 x 10–4–1.29 x 10–3) | 1931 (1833–1972) | NA |
| P complete gene (12) | GTR + I/UCED/EG | 1.19 x 10–3 (3.46 x 10–4–2.03 x 10–3) | 1930 (1828–1971) | NA |
| M CDS (12) | GTR + G/UCED/EG | 6.52 x 10–4 (1.20 x 10–4–1.20 x 10–3) | 1897 (1695–1964) | NA |
| M complete gene (12) | GTR + I/UCED/EG | 2.49 x 10–3 (9.96 x 10–4–4.14 x 10–3) | 1944 (1879–1973) | NA |
| FCDS (12) | GTR + I/CED/EG | 8.95 x 10–4 (2.43 x 10–4–1.58 x 10–3) | 1914 (1766–1968) | NA |
| F complete gene (12) | GTR + G/UCED/EG | 1.33 x 10–3 (3.26 x 10–4–2.36 x 10–3) | 1912 (1754–1967) | NA |
| H CDS (12) | GTR + G/UCED/EG | 1.21 x 10–3 (3.96 x 10–4–2.04 x 10–3) | 1926 (1826–1969) | NA |
| H complete gene (12) | GTR + G/UCED/EG | 1.25 x 10–3 (4.34 x 10–4–2.14 x 10–3) | 1925 (1821–1968) | NA |
| L CDS (12) | GTR + I/UCED/EG | 9.82 x 10–4 (3.76 x 10–4–1.67 x 10–3) | 1929 (1834–1969) | NA |
| L complete gene (12) | GTR + I/UCED/EG | 9.69 x 10–4 (3.36 x 10–4–1.64 x 10–3) | 1927 (1820–1969) | NA |
| PPRV/RPV/MV (16) | GTR+ G + I/UCED/EG | 1.89 x 10–3 (5.55 x 10–4–3.31 x 10–3) | 1616 (1072–1859) | NA |
*Bold indicates best-fit models. HPD, highest posterior density; TMRCA, time to most recent common ancestor; GTR + G, general time-reversible with gamma distribution rates; BSP, Bayesian skyline plot; CS, constant size; EG, exponential growth; UCLD, uncorrelated lognormal distribution; UCED, uncorrelated exponential distribution; NA, not applicable; GTR + I, general time-reversible with invariant sites; GTR+ G + I, general time-reversible with gamma distribution rates and invariant sites.
†PPRV, peste des petits ruminants virus; N, nucleoprotein; CDS, coding sequence; P, phosphoprotein; M, matrix; F, fusion; H, hemagglutinin; L, large polymerase; RPV, rinderpest virus; MV, measles virus.
1Preliminary results were presented at the 15th International Negative Strand Virus Meeting, June 16–21, 2013, Granada, Spain.
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