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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 ParidaComments to Author 
Author affiliations: The Pirbright Institute, Pirbright, UK (M. Muniraju, M. Munir, M. Mahapatra, C. Batten, S. Parida); National Institute for Animal Biotechnology, Hyderabad, India (A.R. Parthiban, S Parida); Animal Health and Veterinary Laboratories Agency, Weybridge, UK (A.C. Banyard); China Animal Health and Epidemiology Centre, Qingdao, China (J. Bao, Z. Wang); National Animal Disease Diagnostics and Epidemiology Centre, Entebbe, Uganda (C. Ayebazibwe); National Veterinary Institute, Debre Zeit, Ethiopia (G. Ayelet); Société de Productions Pharmaceutiques et Vétérinaires, Rabat, Morocco (M. El Harrak); Le Centre de Cooperation Internationale en Recherche Agronomique pour le Développement, Montpellier (G. Libeau)

Main Article

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 bce–1944 ce) –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.

Main Article

1Preliminary results were presented at the 15th International Negative Strand Virus Meeting, June 16–21, 2013, Granada, Spain.

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