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Table 1 Comparison of diversity, evolution rates and introduction history in Madagascar of the different CMG species

From: Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

  ACMV DNA-A ACMV DNA-B SACMV DNA-A EACMV DNA-A EACMKV DNA-A EACMCV DNA-A EACMV-like DNA-B EACMCV DNA-B
[FS] Total sequences 212 95 132 201 114 29 215 10
[FS] Total diversity (mean Id%) 96.6 % [85.9 %–100 %] 93.2 % [90.0 %–100 %] 98.6 % [90.1 %–100 %] 94.3 % [83.5 %–100 %] 95.7 % [84.3 %–100 %] 94.7 % [89.7 %–99.9 %] 92.2 % [87.3 %–100 %] 90.3 % [84.8 %–97.3 %]
[FS] MG sequences 93 15 130 1 43 13 98 4
[FS] MG diversity (mean Id%) 98.5 % [97.1 %–100 %] 97.1 % [95.5 %–99.9 %] 98.7 % [93.3 %–100 %] / 94.4 % [84.3 %–100 %] 96.3 % [93.1 %–99.9 %] 97.6 % [90.3 %–100 %] 91.1 % [84.8 %–94.8 %]
[FS] MG detected recombinants (%) 0 (0 %) 0 (0 %) 8 (6 %) 1 (100 %) 17 (40 %) 10 (77 %) 2 (2 %) 1 (25 %)
[core CP] Total sequences 218 / 132 244 / /
[core CP] Total diversity (mean Id%) 97.0 % [91.5 %–100 %] / 98.5 % [80.3 %–100 %] 95.6 % [89.8 %–100 %] / /
[core CP] MG sequences 93 / 130 51 / /
[core CP] MG diversity (mean Id%) 98.7 % [95.6 %–100 %] / 98.8 % [82.1 %–100 %] 94.9 % [90.0 %–100 %] / /
Introduction events 1 1 / 3–4 1 /
Introduction dates (95 % HPD) 1996–2004 [1995–2005] 1940–1974 [1924–1986] / 1988–1990 [1982–1997] 1961–1978 [1921–1989] /
1988–1996 [1983–2003]
1984–2003 [1971–2006]
1997–1999 [1994–2003]
Substitution rates (subs/site/year) 3.83 × 10−3 [2.82 × 10−3; 4.89 × 10−3] 5.64 × 10−4 [4.13 × 10−4; 7.14 × 10−4] / 1.69 × 10−3 [1.31 × 10−3 to 2.12 × 10−3] 1.10 × 10−3 [9.57 × 10−4; 1.28 × 10−3] /
  1. For each dataset, the total and Madagascan (MG) number of sequences, mean and range of identity percentages are indicated ([FS] = Full Sequence, [core CP] = core of the capsid protein encoding ORF), as well as the number of recombinant Madagascan sequences isolated in this study. The number and dates of inferred introduction events as well as the inferred substitution rates are based on analyses of the core CP datasets for DNA-A and on full component sequences for DNA-B. Correlation coefficients related to the temporal signal of each dataset are listed