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Table S1 List of the isolates with information regarding their species, natural host, geographic origin and GenBank accession numbers.

Table S2 Partitioning schemes for the substitution and clock models of *BEAST. Combined partitions are represented inside ‘()’. For the MAT1-2-1 partition, codon partitioning was also performed for the first (CP1), second (CP2) and third positions (CP3).

Table S3 2ln Bayes Factors results of comparisons of all partition strategies, calculated from the marginal likelihood of each scheme using Tracer v1.4. A positive value indicates evidence against alternative hypotheses.

Table S4 Summary of the neutrality test statistics for the UG1—Colletotrichum kahawae group.

Table S5 Log Likelihood Ratio Test (LLRT) of nested models with different patterns of gene flow compared with the Full model, as estimated from IMa analyses.

Fig. S1 50% majority rule Bayesian tree for each molecular marker used in this study.

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