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Summary details of the HA and NA sequences from each subtype are given in Tables 1 and 2. A distance matrix for every dataset was calculated using Kimura's two-parameter model [40].

From the FastUnifrac distance matrix the amount of variance that each clinical variable e.g. sample collection method, age etc. contributed to the dataset was calculated using the adonis function of the vegan package in R [26].

The principal AGB dataset was calculated using the three-parameter moist tropical forest model from Chave et al.

mRNA abundance of the genes in our dataset was calculated using EST data obtained from DFCI Gene Indices.

mRNA abundance of the genes in our dataset was calculated using EST data attained from DFCI Gene Indices (http://compbio.dfci.harvard.edu/tgi/).edu/tgi/

The line of best fit for the complete dataset was calculated using the general linear model (the data files are available as md_arrhenius_crambin.sav, md_arrhenius_crambin.spv).spv

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The accessible surface areas for all residues in our dataset were calculated using the DSSP program [38].

The average pairwise differences among species of the A. gambiae complex for each sequence dataset were calculated using Arlequin v3.11 [ 34].

Differences in age and gender between children with and without a complete dataset were calculated using mixed linear or logistic regression models with child care center (= cluster) as random effect.

Finally, coverage statistics for each sequence in both datasets was calculated using MosaikCoverage.

Subsequently the overlap of the two datasets was calculated using the database mentioned above.

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