Top four panels: the metrics characterizing population structure for three host population sizes as a function of transmission intensity (see ‘Materials and methods’). Green, blue and purple represent H = 5,000, H = 10,000, and H = 25,000, respectively. (A) A measure of diversity capturing the number of dominating genomes (R*, in the y-axis) as a function of b, (B), a measure of average antigenic similarity between genomes (F*, in the y-axis) as a function of b, (C) the average number of novel repertoires generated and successfully transmitted each year, and (D) the total number of successful transmission events each year. As transmission intensity increases, the number of dominating genomes increases, and in accordance, the degree of antigenic similarity increases as well—however the number of distinct repertoires that are maintained in the system at epidemiologically relevant frequencies remains extremely low relative to the total number of distinct repertoires that can be crated through recombination. Note the differences in magnitude; while the number of de novo repertoires entering the system is 10-fold higher then the observed diversity, the number of successful transmission events that these dominating repertoires are involved in is on the order of 106. For extremely low biting rates, in a narrow window of parameter values, diversity decreases abruptly (A). This reflects a different dynamic regime in which dominant strains replace each other in a fluctuating manner and population structure does not apply. Parameters: G = 50, g = 6, α = 15, ω = 0.0005, ρ=0.05, τ = 1, κ = 1 year. Bottom four panels: characteristic time series demonstrating structured parasite populations for larger gene pools (G) and longer sequence lengths (g): (A) b = 18, G = 100, g = 6, α = 15, N = 20,000, ω = 0.0005, ρ=0.001, τ = 1. (B) b = 18, G = 200, g = 6, α = 15, H = 20,000, ω = 0.0005, ρ=0.001, τ = 1. (C) b = 18, G = 300, g = 20, α = 15, H = 20,000, ω = 0.0005, ρ=0.001, τ = 1. (D) b = 12, G = 120, g = 6, α = 15, H = 10,000, ω = 0.0005, ρ=0.005, τ = 1, κ = 1 year.