Table 2. Effects of host, household, village, and time point on the genetic variation of Ascaris.

	Nuclear genome phylogeny*			Mitochondrial genome phylogeny
	R†	p-value	p-adjusted (Bonferroni)	R†	p-value	Samples†
Individual	0.933	0.001	0.004	0.996	0.095	68 worms from 60 people
Household	0.020	0.110	0.440	0.011	0.340	68 worms from 43 houses
Village	0.052	0.001	0.004	0.013	0.335	Five villages with 43, 17, 4, 3, and one individual each
Time point	0.018	0.162	0.648	0.024	0.100	55 at baseline and 13 post-deworming

^* Results based on PERMANOVA using phylogenetic distances among worms. Results were largely similar using a distance matrix generated from the PCA plot (Figure 6) and using the Multi-Response Permutation Procedure (MRPP) method (Supplementary file 9).

^† Since some worms did not have metadata associated with each variable examined, and some variables were over-represented in the sample (for example, 43 of 68 worms came from a single village) the samples are specified in this column.