The first catalogue of genomic diversity for endangered chimpanzees (Pan troglodytes) in the wild has been produced by international researchers, according to a new study in the journal Cell Genomics.
The DNA information was collected from 828 samples of wild chimpanzee poo from across their current geographic range and offers new insights into how chimp populations are structured, isolated, connected, and to where they are migrating.
The researchers say the genetic data could also be used to combat the illegal trade of chimps by linking animals that have been confiscated from the wild to their place of origin through their genetics.
“Chimpanzees are an endangered species with massive population declines in recent years,” says first author Claudia Fontsere from the Institute of Evolutionary Biology (IBE), a joint research centre of the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF) in Spain.
“Our efforts to describe the current genomic diversity of this species are an attempt to provide a fine-scale map of connectivity between populations that can be of service to conservationists as a baseline and guide to build upon their conservation efforts.”
Using DNA in faeces to uncover chimp history
Thousands of chimpanzee faecal samples were collected at 48 locations as part of the PanAfrican Program: The Cultured Chimpanzee (PanAf).
Analysing faecal samples can be challenging because they only contain small amounts of degraded chimp DNA, but this method also allows DNA collection with minimal interference to the animals, which is important for the study of endangered species.
So, instead of undertaking whole-genome sequencing, the researchers focused specifically on chromosome 21 – the smallest chimpanzee chromosome – and identified 828 unique individuals from the samples.
Since the fossil record and ancient DNA for chimpanzees are limited, the study of living individuals’ DNA is the only way to reconstruct their past.
“Since we are using sequencing of a whole chromosome with thousands of independent markers, compared to few microsatellite markers, we have a much broader view of the genome that is needed to refine and describe the very complex evolutionary history of chimpanzees,” says co-lead author Tomas Marques-Bonet, principal investigator from IBE.
Using this method, the researchers were able to discover around 50% more, and new, genetic variants (mutations) on chromosome 21 than had been found in previous studies. This allowed them to better understand if different populations have isolated recently or whether there was a historical event that caused it to occur.
A way to return confiscated chimpanzees back home
“By characterising the genomic singularities of each community or population, we also created a map that links genomic information to geographic location so that we were able to devise a strategy to infer the geographic location of chimpanzee individuals,” says Fontsere.
The strategy involves finding genetic mutations called single nucleotide polymorphisms (SNPs) – a variation at a single position in a DNA sequence – on chromosome 21 that are present at high frequencies at one sampling location but not the others.
By comparing chimpanzee DNA samples (from known locations) to the populations at each sampling location to see how closely they match, they found that the geographical origin of that chimp could be inferred to within about 100 kilometres.
The team also used this method to estimate the most probable places of origin for 20 chimpanzees from two Spanish rescue centres using hair and blood samples.
The researchers say they are now using these methods to study faecal samples from other great apes and primates.
The PanAf continues to analyse data collected over eight years from 18 countries across Africa to understand the evolutionary and ecological drivers of chimpanzee cultural and behavioural diversity. You can contribute to its citizen science project, Chimp and See, by annotating videos of chimpanzees online.