Degraded DNA samples
For the degraded DNA samples, we applied the 3-pool approach. The amplification from fecal samples was successful except for four (out of 42) loci (two autosomal and two gonosomal loci; Table S10). The number of loci and alleles amplified per sample was comparable to the results obtained from high-quality DNA samples (Table 2). However, ten of the 42 amplified loci were monomorphic in our P. papio population, i.e., all twelve individuals showed the same allele. The remaining 32 loci showed a level of 46.3% heterozygosity (Table 2).
All autosomal loci were in accordance with Mendelian inheritance besides D7s503 and D13s1291. For D7s503, the two alleles with the highest read counts for male MRX (99/109) did not match one of the two alleles of his offspring THL (111/113; mother MMI: 103/113). A closer look at the data revealed that MRX also had many reads for allele 111 (only 23 reads less than for allele 109), indicating that the allele 109 of MRX was likely an overamplified stutter sequence. For D13s1291, the two alleles of male MLK (130b/132b) did not match with his offspring PTC (130a/132a; mother LCY: 128/130a). MLK was the only individual with these two cryptic alleles (each with a GA point mutation) and further showed reads with 130 and 132 bp length without this mutation. At this point, we can neither exclude the occurrence of a PCR artifact in this particular case, nor that this locus indeed does not follow the rules of Mendelian inheritance.