Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

De Bruyn, Alexandre; Harimalala, Mireille; Zinga, Innocent; Mabvakure, Batsirai M.; Hoareau, Murielle; Ravigné, Virginie; Walters, Matthew; Reynaud, Bernard; Varsani, Arvind; Harkins, Gordon W.; Martin, Darren P.; Lett, Jean-Michel; Lefeuvre, Pierre

doi:10.1186/s12862-016-0749-2

BMC Ecology and Evolution

Table 2 List of recombination events detected in CMG DNA-A and DNA-B sequences

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

	Event number	Recombinant	Region		Minor parent	Major parent	Methods	P-value
	Event number	Recombinant	Begin	End
DNA-A	1	EACMMV/SACMV	1685	1974	EACMKV	Unknown	RGBMCST	5.5 × 10⁻¹⁶
	2	SACMV	131	448	ACMV	SACMV	RGBMCST	4.1 × 10⁻⁷⁰
	3	SACMV	502	907	EACMV-like	SACMV	RGBMCST	6.1 × 10⁻⁶⁰
	4	SACMV	177	388	ACMV	SACMV	RGBMCST	3.4 × 10⁻³⁹
	5	SACMV	2093	32	EACMKV	SACMV	RGBMCST	1.2 × 10⁻³⁰
	6	SACMV	340	449	ACMV	SACMV	RGBMCST	4.5 × 10⁻¹⁶
	7	SACMV	163	195	Unknown	SACMV	RGB	4.5 × 10⁻⁰⁶
	8	SACMV	440	479	ACMV	SACMV	RGBS	3.6 × 10⁻¹³
	9	SACMV	580	615	ACMV	SACMV	RGB	4.8 × 10⁻¹⁰
	10	EACMMV	1996	2804	EACMV	SACMV	RGBMCST	2.2 × 10⁻²⁹
	11	EACMMV	54	1052	Unknown	EACMV	RGBMCS	5.0 × 10⁻³⁰
	12	EACMZV	93	1924	EACMV-like	Unknown	RGBMCSt	2.5 × 10⁻⁶⁷
	13	EACMZV	^a1928	2077	Unknown	EACMZV	RGBcST	3.6 × 10⁻¹⁰
	14	EACMCV	1131	1790	Unknown	EACMV-like	RGBMCST	7.8 × 10⁻¹⁴
	15	EACMCV	1836	2800	EACMV	Unknown	RGBMcSt	1.4 × 10⁻³⁹
	16	EACMCV	543	1103	EACMV-like	EACMCV	RGBMCST	2.4 × 10⁻⁴²
	17	EACMCV	623	669	ACMV	EACMCV	RGBS	3.8 × 10⁻¹²
	18	EACMCV	1847	^a1968	EACMV	EACMCV	RGBST	5.7 × 10⁻⁰⁶
	19	EACMCV	1468	1505	ACMV	EACMCV	RGs	3.4 × 10⁻⁰³
	20	EACMCV	1910	2061	EACMV	EACMCV	RGBS	2.0 × 10⁻⁰⁵
	21	EACMCV	185	1079	EACMKV	EACMCV	RGBMCST	1.7 × 10⁻²⁵
	22	EACMCV	33	^a171	Unknown	EACMCV	RGBMCST	1.3 × 10⁻²⁴
	23	EACMCV	10	1054	EACMV-like	EACMCV	RGBMCST	3.6 × 10⁻²¹
	24	EACMCV	509	1089	EACMKV	EACMCV	RGBMCST	4.0 × 10⁻²⁶
	25	EACMCV	1835	42	EACMV	EACMCV	RGBMCST	1.3 × 10⁻¹¹
	26	EACMCV	654	698	ACMV	EACMCV	RGBsT	1.9 × 10⁻⁰⁵
	27	EACMV-UG	549	1007	ACMV	EACMV	RGBMCST	1.2 × 10⁻⁶²
	28	EACMV	^a1710	2084	EACMZV	EACMV	RGBMCST	1.3 × 10⁻²²
	29	EACMV	1680	1902	SACMV	EACMV	rgbMCST	8.9 × 10⁻⁰⁴
	30	EACMV	1309	1988	EACMKV	EACMV	RGBMCST	3.0 × 10⁻¹²
	31	EACMV	1956	2798	EACMV	EACMKV	RGBMCST	1.2 × 10⁻³¹
	32	EACMKV	1	815	EACMV-like	SACMV	RGBMCST	4.0 × 10⁻⁴⁵
	33	EACMKV	1	759	EACMV-like	SACMV	RGBMCST	2.9 × 10⁻⁵⁶
	34	EACMKV	141	570	EACMV-like	SACMV	RGBMCST	6.3 × 10⁻⁵⁹
	35	EACMKV	32	^a128	EACMV	SACMV	RGBST	2.4 × 10⁻¹⁰
	36	EACMKV	1739	2006	Unknown	Unknown	RBM	8.2 × 10⁻⁰⁴
	37	EACMKV	1884	2014	EACMCV	EACMKV	RGBMCST	9.1 × 10⁻¹⁹
	38	EACMKV	1090	1788	EACMCV	EACMKV	RGBMCST	9.9 × 10⁻⁷⁸
	39	EACMKV	1865	2798	SACMV	EACMKV	RGBMCST	4.6 × 10⁻⁷²
	40	EACMKV	549	1160	SACMV	EACMKV	RGBMCST	7.9 × 10⁻⁴⁶
	41	EACMKV	570	1154	Unknown	EACMKV	rGBMC	1.7 × 10⁻¹⁵
	42	EACMKV	1804	2796	SACMV	EACMKV	RGBMCST	1.0 × 10⁻⁴³
	43	EACMKV	759	^a1182	SACMV	EACMKV	RGBMCST	1.9 × 10⁻²¹
	44	EACMKV	35	1056	EACMKV	SACMV	RGBMCST	4.6 × 10⁻³⁵
	45	EACMKV	1510	^a1872	SACMV	EACMKV	RGBMCST	4.4 × 10⁻¹⁴
DNA-B	1	EACMCV	2541	53	EACMV-like	EACMCV	RGBMCST	7.6 × 10⁻³⁵
	2	EACMV-like	1124	1461	EACMCV	EACMV-like	RGBMCST	1.2 × 10⁻⁴⁹
	3	CMMGV	1569	2697	Unknown	EACMV-like	RGBMCST	5.0 × 10⁻⁶⁶
	4	EACMV-like	2227	2287	Unknown	EACMV-like	RGBMCS	9.7 × 10⁻²³
	5	SLCMV	2595	2712	Unknown	SLCMV	RGBMCST	6.7 × 10⁻¹⁷
	6	EACMV-like	2668	2780	EACMCV	EACMV-like	RGBMCST	4.3 × 10⁻¹⁶
	7	EACMCV	1495	2585	EACMV-like	Unkown	RGBmC	1.4 × 10⁻⁰⁷
	8	EACMV-like	854	1120	Unknown	EACMV-like	RGBMCST	3.1 × 10⁻⁰⁹
	9	EACMV-like	2345	2756	Unknown	EACMV-like	RGBMCST	1.9 × 10⁻¹⁵
	10	EACMV-like	2119	2752	EACMV-like	EACMV-like	RBGMCS	2.9 × 10⁻¹⁶
	11	EACMV-like	2638	2699	Unknown	EACMV-like	RGBS	3.0 × 10⁻⁰⁵
	12	EACMV-like	869	1597	EACMV-like	EACMV-like	rMCsT	8.1 × 10⁻⁰⁴

For each event, the species of the recombinants and inferred parents, the recombinant region breakpoints and the list of methods which detected the event are indicated (R: RDP; G: GENECONV; B: BOOTSCAN; M: MAXCHI; C: CHIMAERA; S: SISCAN; T: 3SEQ). The reported p-values are for the methods in bold type and are the smallest p-values calculated for the region in question. Whereas upper-case letters imply that a method detected recombination with a multiple comparison corrected p-value <0.05, lower-case letters imply that the method detected recombination with a multiple comparison corrected p-value >0.05
^aBreakpoints not inferred by RDP

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