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Figure S1 Map of the study landscape showing the location of 217 individual leopards.

Figure S2 Selection of K from output of STRUCTURE and TESS.

Figure S3 Output of TESS at K = 4.

Figure S4 Bar plot of STRUCTURE analysis at K = 3 with individuals sampled at Kanha, Pench and Melghat (excluding Satpura).

Table S1 Characteristics of microsatellite amplification, success and error rates of faecal amplification of leopards at 7 microsatellites.

Table S2 Frequency of private alleles in different populations.

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