CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees

Short tandem repeats (STRs), also known as microsatellites, are commonly used tononinvasively genotype wild-living endangered species, including African apes. Untilrecently, capillary electrophoresis has been the method of choice to determine thelength of polymorphic STR loci. However, this technique is labor intensive, difficult tocompare across platforms, and notoriously imprecise. Here we developed a MiSeqbased approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Usingdata from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically callsalleles after filtering stutter sequences and other PCR artifacts. Applying this methodto the entire Gombe population, we confirmed previously reported genotypes, butalso identified 31 new alleles that had been missed due to sequence differences andsize homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one caseof an ambiguous paternity. Using both singleplex and multiplex locus amplification,we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem.