Genomic tools for great ape population dynamics and conservation

Gorillas were once abundant in the forests of Central Africa, playing a fundamental role in the maintenance of ecosystems. Habitat loss, poaching and illegal wildlife trade have led populations to the brink of extinction. Genetic analysis of forensic DNA markers can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. This study aimed to assess whether cross-species genotyping of forensic DNA markers could provide both individual and sub-species identification. Firstly, massively parallel sequencing (MPS, via Illumina technology) analysis of 27 human orthologous aSTRs (autosomal short tandem repeats, via the Verogen ForenSeq™ DNA Signature Prep Kit) was applied to 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland; 6 eastern lowland, and 12 mountain gorillas). Thirteen loci could be genotyped across all individuals, and were individually and sub-species identifying. This showed that allelic diversity and the power to discriminate sub-species were greater when considering STR and flanking sequences rather than allele lengths alone, which are conventionally typed by capillary electrophoresis (CE). When comparing with humans, interruptions within long repeat arrays in African great apes did not appear to reduce allelic diversity, indicating a possible mutational difference to humans. Secondly, portable sequencing technology (via Oxford Nanopore Technologies Ltd sequencing) was exploited to investigate a panel of about 90 single nucleotide polymorphisms (SNPs) designed ad hoc for individual and sub-species identification in gorilla from non-invasive (i.e. poor quality) DNA samples (e.g. hair and faeces). A core set of 42 loci amplified across all individuals (34 western lowland; 6 eastern lowland, and 6 mountain gorillas) and provided both individual and sub-species identification. This approach helps overcome the current lack of well-established research facilities in habitat countries while facilitating genetic research and thus aid gorilla conservation.