Table 1.

Summary of the genetic metrics used in this study and their expected relationship with transmission intensity. Clones are defined as a parasite whose barcode is observed more than once in the population and is calculated only for monogenomic infections. COI was calculated using THE REAL McCOIL.

Genetic Metric	Definition	Transmisison Reflected	Expectation
Polygenomic Fraction	Proportion of infections that are polygenomic	Superinfection & Cotransmission	Increase with transmission intensity
Complexity of Infection (COI)	Number of strains per infection	Superinfection & Cotransmission	Increase with transmission intensity
Monogenomic clone proportion	Proportion of monogenomic infections carrying a clone that was sampled elsewhere in the population	Clonal Transmission	Decrease with transmission intensity
RH	Estimate of polygenomic inbreeding based on intra-host heterozygosity	Superinfection & Cotransmission	Decrease with transmission intensity
Cotransmission Fraction	Proportion of polygenomics resulting from cotransmission	Cotransmission	Decrease with transmission intensity