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Table S1 Sampling details and sequence accession numbers.

Table S2 Primers used for the PCR amplification of Cryptosporidium nuclear genes.

Table S3 Nucleotide diversity at gp60 within Cryptosporidium subtypes, expressed as % (GenBank data).

Table S4 Estimates of pairwise nucleotide divergence at synonymous (%; below the diagonal) and nonsynonymous sites (above) between C. hominis, C. parvum and C. meleagridis subtypes.

Table S5 Maximum likelihood Hudson-Kreitman-Aguade test on variation data at gp60 synonymous sites.

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