Table 1. P-values for non-parametric multivariate regression analyses of pairwise blood and flea sample distances based on ecological similarity (similarity in relative abundances of the different OTUs), phylogenetic similarities (similarity in phylogenetic distance of the different OTUs, calculated by unweighted UniFrac) and a combination of the two (calculated by weighted UniFrac).

Method	Samples included	P-values (cumulative %)
		Type of sample	Period	Flea sex	Flea numbers in the host	Age of host
Ecological similarity	All samples	0.03 (2)	0.24	NA	0.65	0.94
	Only flea samples	NA	0.22	0.0003a (4.8)	0.88	0.90
	Four host (fleas+blood)	0.29	0.01a (8.5)	NA	0.57	0.36
Phylogenetic distance	All samples	0.008a (4.5)	0.02a (4.0)	NA	0.55	0.10
	Only flea samples	NA	0.02a (4.2)	0.02a (4.3)	0.89	0.86
	Four host (fleas+blood)	0.35	0.003a (21)	NA	0.06	0.47
Phylogenetic+ecological similarity	All samples	0.005a (6)	0.11	NA	0.80	0.38
	Only flea samples	NA	0.14	0.14	0.37	0.89
	Four host (fleas+blood)	0.49	0.0002a (20)	NA	0.17	0.06

Abbreviations: NA, not applicable; OTU, operational taxonomic unit.

Analyses were performed on the whole set of samples, only flea samples (to test the effect of flea sex) or on samples collected from the four host individuals who had a complete set of positive samples. Numbers in parentheses indicate the proportion of explained variance in sample similarity by the variable.

^aSignificant values after adjustment for sequential Bonferroni's correction.