Table 1.
Analysis of the impact of rice harvested areas on RYMV dispersal frequency (based on discrete diffusion inference) and velocity (based on continuous diffusion inference).
| Discrete phylogeographic reconstruction + GLM analyses | Data set of Trovão et al. (180 + 117 sequences) |
Extended data set (210 + 240 sequences) |
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|---|---|---|---|---|---|---|---|---|
| West Africa |
East Africa |
West Africa |
East Africa |
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| GLM coefficient | BF | GLM coefficient | BF | GLM coefficient | BF | GLM coefficient | BF | |
| 1° GLM analysis: | ||||||||
| Geographic distance | −0.76 [−1.78, 1.61] | 16 | 0.05 [−3.66, 4.01] | 0.3 | −0.85 [−1.53, 0.66] | 32 | −0.15 [−3.82, 3.76] | 0.8 |
| Rice harvested area 2000 (C) | −0.47 [−1.62, 1.55] | 16.5 | −0.18 [−3.56, 3.54] | 0.9 | −0.39 [−2.55, 2.35] | 7.2 | −0.49 [−2.74, 2.88] | 5.6 |
| 2° GLM analysis: | ||||||||
| Null raster (R) | −1.09 [−1.4, −0.75] | >99 | −0.33 [−3.66, 3.66] | 1.2 | −1.15 [−1.5, −0.82] | >99 | −0.83 [−1.98, 2.34] | 13.7 |
| Rice harvested area 2000 (C) | −0.01 [−3.61, 3.84] | 0.3 | −0.16 [−3.66, 3.52] | 0.9 | 0.03 [−3.59, 3.85] | 0.3 | −0.07 [−3.66, 3.59] | 0.9 |
| 3° GLM analysis: | ||||||||
| Geographic distance | −0.02 [−3.58, 3.96] | 0.6 | −0.06 [−3.98, 3.96] | 0.3 | 0.01 [−3.61, 3.90] | 0.5 | −0.19 [−3.78, 3.77] | 0.9 |
| Null raster (R) | −1.06 [−1.4, −0.68] | >99 | −0.17 [−3.62, 3.84] | 0.9 | −1.12 [−1.5, −0.75] | >99 | −0.82 [−2.11, 2.01] | 16.7 |
| Rice harvested area 2000 (C) | 0.01 [−3.89, 3.78] | 0.2 | 0.00 [−3.62, 3.94] | 0.6 | 0.01 [−3.87, 3.75] | 0.2 | −0.04 [−3.63, 3.75] | 0.8 |
| 4° GLM analysis: | ||||||||
| Geographic distance | −0.09 [−3.91, 3.92] | 0.6 | −0.02 [−3.85, 3.9] | 0.3 | −0.03 [−3.67, 3.71] | 0.5 | −0.10 [−3.64, 3.75] | 0.9 |
| Null raster (R) | −0.97 [−2.02, 1.18] | 34.8 | −0.21 [−3.87, 3.73] | 0.8 | −1.08 [−1.95, 0.75] | 62 | −0.77 [−3.26, 2.47] | 7.8 |
| Rice harvested area 2000 (log, C) | −0.22 [−3.68, 3.35] | 0.9 | −0.11 [−3.88, 3.91] | 0.6 | −0.04 [−3.68, 3.77] | 0.7 | −0.35 [−3.73, 3.37] | 2.1 |
| 5° GLM analysis: | ||||||||
| Geographic distance | 0.00 [−3.62, 3.87] | 0.6 | −0.04 [−3.74, 3.77] | 0.3 | −0.02 [−3.8, 3.73] | 0.5 | −0.13 [−3.85, 3.77] | 0.9 |
| Null raster (R) | −1.04 [−1.4, −0.59] | >99 | −0.17 [−3.80, 3.78] | 0.9 | −1.11 [−1.5, −0.74] | >99 | −0.73 [−2.67, 2.74] | 10.4 |
| Rice harvested area 2005 (C) | 0.09 [−3.71, 3.91] | 0.3 | −0.22 [−3.68, 3.76] | 1.1 | 0.02 [−3.72, 3.76] | 0.2 | −0.18 [−3.63, 3.63] | 1.3 |
| Continuous phylogeographic reconstruction + post hoc analyses |
Data set of Trovão et al. (180 + 117 sequences) |
Updated data set (210 + 240 sequences) |
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|
West Africa |
East Africa |
West Africa |
East Africa |
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| Q statistic | Q > 0 (per cent) | Q statistic | Q > 0 (per cent) | Q statistic | Q > 0 (per cent) | Q statistic | Q > 0 (per cent) | |
| Rice harvested area 2000 (C) | −0.07 [−0.15, 0.05] | 11 | −0.03 [−0.07, 0.00] | 3 | −0.11 [−0.2, −0.03] | 0 | −0.07 [−0.11, 0.02] | 6 |
| Rice harvested area 2000 (log, C) | 0.02 [−0.04, 0.10] | 7 | −0.02 [−0.04, 0.01] | 17 | −0.02 [−0.1, 0.03] | 27 | −0.01 [−0.06, 0.04] | 33 |
| Rice harvested area 2005 (C) | −0.09 [−0.15, 0.00] | 3 | −0.01 [−0.06, 0.05] | 36 | −0.13 [−0.2, −0.05] | 1 | −0.01 [−0.08, 0.05] | 45 |
For GLM coefficients and Q statistics, we report both the median value and 95 per cent HPD interval. ‘BF’ refers to ‘Bayes factor’ and, according to the scale of interpretation defined by Kass and Raftery (1995), BF >3 and >20 can, respectively, be considered as ‘positive’ and ‘strong’ (in bold) evidences of the GLM coefficient or Q statistic significance. ‘C’ and ‘R’ indicate if the considered environmental raster was, respectively, treated as a conductance or resistance factor (see the text for further details).