Table 2 Demographic simulation in fastsimcoal2 and model selection by Approximate Bayesian Computation via Random Forests (ABCRF).

	Model	Pop. 1/Pop. 2	CV	N_draws
Models of divergence between MT and MS L. infantum groups	AM	MT/MS	0.035	474,177
	IMbot	MT/MS	0.086	452,533
	IM_change	MT/MS	0.243	476,483
	IM	MT/MS	0.085	474,263
	SC	MT/MS	0.350	473,082	*Selected model
	SCbot_nomig	MT/MS	0.109	427,249
	SC_nomig	MT/MS	0.078	474,782
	SI	MT/MS	0.014	466,136
	PP = 0.504
	MIG_MT>>>MS = 0.254
	MIG_MS>>>MT = 0.300
Models of divergence between MT and OW L. infantum groups	AMbot	MT/OW	0.304	432,323	*Selected model
	AM	MT/OW	0.186	458,125
	IM_change	MT/OW	0.106	470,330
	IM	MT/OW	0.215	459,566
	SC	MT/OW	0.161	421,405
	SC_nomig	MT/OW	0.013	464,907
	SIbot	MT/OW	0.003	385,170
	SI	MT/OW	0.012	409,244
	PP = 0.485
	FOU = 0.204
Models of divergence between MS and OW L. infantum groups	AMbot	MS/OW	0.385	413,704	*Selected model
	AM	MS/OW	0.161	472,457
	IM_change	MS/OW	0.145	473,388
	IM	MS/OW	0.170	471,073
	SC	MS/OW	0.025	471,677
	SC_nomig	MS/OW	0.031	472,251
	SIbot	MS/OW	0.035	463,789
	SI	MS/OW	0.048	457,084
	PP = 0.521
	FOU = 0.292

CV classification vote, i.e., the number of times a model is selected in a forest of 1000 trees (the model with the most votes corresponds to the model best suited to the dataset), FOU bottleneck size, i.e., the fraction of prior population size at the end of the bottleneck, MIG_x»>y migration rate from x to y, MS Mato Grosso do Sul, MT Mato Grosso, N_draws number of parameter draws simulated by fastsimcoal2 as input for ABCRF, OW Old World, Pop. population, PP ABCRF approximation of the posterior probability of the selected model.
In fastsimcoal2 simulation, values for past and present population sizes were drawn randomly from a uniform distribution between 100 and 106 individuals. Values for time of secondary contact were drawn randomly from a uniform distribution between 0 and 2 × 10⁴ generations before present. Values for relative migration rates between populations were drawn randomly from a log-uniform distribution between 10⁻¹⁰ and 0.1. Values for bottleneck size were drawn randomly from a uniform distribution between 0.05 and 0.5. The mutation rate was fixed at 1.99 × 10⁻⁹ mutations per bp on all chromosomes. The ten different demographic models are illustrated in Supplementary Fig. 8 and template file content is provided is provided in Supplementary Data 7 at Zenodo³⁶.

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