Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes

Background Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). Here we assess in African great ape DNAs the human-based ForenSeq DNA Sequencing Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results The Forenseq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges, but variation in repeat array structures and little relationship with the known phylogeny, suggesting stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity, indicating a possible mutational difference to humans. Conclusions Despite some variability in amplification success, orthologs of most human aSTRs in the ForenSeq DNA Sequencing Prep Kit can be analysed in African great apes. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.