Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Table 4 Genetic variability determinants and neutrality tests on Tomato leaf curl virus Arusha virus-like populations from Kenya with other worldwide tomato begomoviruses

Population	Gene^a	N^b	h^c	S^d	Hd^e	Eta^f	π^g	k^h	θ-Wⁱ	θ-Eta^j	Tajima's D	Fu and Li's D	Fu and Li's F
Tomato begomoviruses	Genome	2920	46	1666	1.000	2985	0.22424	569.5749	0.14924	0.2674	− 0.5971	− 0.2912	− 0.4859
(n = 46)	V1	372	43	241	0.996	419	0.22538	76.1768	0.16224	0.28206	− 0.7389	− 0.8229	− 0.9463
	V2	1261	46	752	1.000	1334	0.22421	271.971	0.14106	0.25023	− 0.3842	− 0.0052	− 0.1764
	C1	1179	46	692	1.000	1213	0.21165	225.4106	0.14784	0.25915	− 0.6771	− 0.3609	− 0.5737
	C2	431	45	264	0.999	458	0.23777	97.486	0.14651	0.25417	− 0.2374	− 0.0923	− 0.1752
	C3	469	45	303	0.999	550	0.24589	108.1903	0.15669	0.28442	− 0.4989	− 0.3631	− 0.4949
	C4	316	44	210	0.997	360	0.21015	65.1459	0.15414	0.26423	− 0.7516	− 0.4512	− 0.6736
Kenyan ToLCArV-like	Genome	2766	12	211	1.000	224	0.0264	72.955	0.0253	0.0268	− 0.0774	− 0.4189	− 0.3751
isolates (n = 12)	V1	360	9	22	0.939	24	0.02298	8.2727	0.02024	0.02208	0.1819	0.1216	0.1564
	V2	1239	12	71	1.000	72	0.0209	25.8788	0.01899	0.01926	0.3958	− 0.0631	0.0659
	C1	1116	12	94	1.000	102	0.02744	30.6212	0.02789	0.03027	− 0.4355	− 0.7775	− 0.7841
	C2	422	11	39	0.985	40	0.02761	11.6515	0.0306	0.03139	− 0.5481	− 1.072	− 1.065
	C3	450	11	23	0.985	23	0.01872	8.4242	0.01692	0.01692	0.4703	− 0.3193	− 0.1286
	C4	312	10	11	0.955	11	0.00869	2.7121	0.01167	0.01167	− 1.0628	− 1.4718	− 1.552

^aV1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
^bN: Number of nucleotide sites
^ch: Haplotype number
^dS: Total number of variable or segregation sites
^eHd: Haplotype diversity
^fEta: Total number of mutations
^gπ: Nucleotide diversity
^hk: Average number of nucleotide differences between sequences
ⁱθ-W: Waterson’s estimate of population mutation rate based on the total number of segregating sites
^jθ-Eta: Waterson’s estimate of population mutation rate based on the total number of mutations

ISSN: 1743-422X