Fig. 3: Population history and introgression.
a Population tree inferred with TreeMix assuming five migration events. We used a water buffalo as an outgroup. Arrows represent migration edges, with colour indicating the migration weight (proportion of the admixed population estimated to derive from the source population). b D-statistics calculated by ADMIXTOOLS2 when using water buffalo as outgroup H4, various cattle populations as H1/H2. Left panel: South Asian zebu and captive banteng as H2 and H3; right panel: captive banteng and South Asian zebu as H1 and H3. A significant non-zero value, as depicted by the red arrow in the graphic for each panel, provides evidence for gene flow between H3 and H1 (Left panel), and between H3 and H2 (Right panel). Data are presented as the estimated D-statistic ± 3 standard errors. Star represents significant allele sharing for each combination. Sample sizes for each population are as follows: Aceh (n = 24), Pesisir (n = 17), Pasundan (n = 21), Jabres (n = 3), Madura (n = 17), Sumba Ongole (n = 14), Bali (n = 19), Kupang (n = 14), Australia (n = 12), Captive banteng (n = 5), Unknown-Indonesia (n = 8), South Asian zebu (n = 11), East Asian zebu (n = 8), African zebu (n = 10), Asian admixed (n = 15), East Asian taurine (n = 3), European taurine (n = 10), and African taurine (n = 5). c Individual admixture proportion from LOTER and F4. We used unadmixed zebu and banteng as the two ancestry source references for LOTER. We used water buffalo and taurine as outgroups for the F4 ratio admixture inference.
