Scientists map illegal trade of wild chimpanzees for first time

By Mark Waghorn via SWNS

The illegal trade in endangered wild chimpanzees has been mapped by scientists for the first time.

A catalogue of genomic diversity offers a detailed reconstruction of population structure and fine-scale patterns of isolation, migration and connection.

It is based on 828 poo samples from across their range - accurately linking confiscated animals to their place of origin within about 60 miles.

Chimps are our closest relatives - sharing 98 percent of our DNA. As pets in wealthy homes or as performers in zoos, they can command a price tag of over $12,000.

First author Dr. Claudia Fontsere, of the Pompeu Fabra University in Barcelona, said: "Chimpanzees are an endangered species with massive population declines in recent years.

"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."

Babies are seized from the wild and sold. The usual tactic used by poachers is to shoot as many of the adults in a family as possible.

This prevents them from resisting the capture of the infant. Their bodies can then be sold as bushmeat. To obtain one alive, up to 10 adults are typically slaughtered.

An estimated 3,000 great apes, two-thirds of which are chimpanzees, are lost from the wild every year as a result of the illegal trade, according to the UN Environment Program.

The new chart is based on thousands of feces collected by the Pan African Program (PanAf) at 48 locations combined with DNA analysis.

They contain only small amounts but also have advantages as they are easy to gather with minimal interference to the animals.

The approaches opens the door to studying many endangered primates - and other species.

Co-lead author Professor Tomas Marques-Bonet, also from Pompeu Fabra, said: "We are using sequencing of a whole chromosome with thousands of independent markers, compared to a 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.

"Impressively, we are doing it with non-invasive samples, which, in a sense, are the best of all worlds - a valuable source of genomic DNA but collected in a way that animals never need to be contacted or disturbed beyond researchers existing in their habitat."

The fossil record and ancient DNA for chimps is limited. The only way to reconstruct their past is through studies of living individuals.

Scientists recognize four chimp subspecies, but questions had remained about their relationships.

There have been long-standing questions about how connected those subspecies are and have been to each other.

Dr. Fontsere and colleagues retrieved partial genome information from more than 800 non-invasively-collected wild chimpanzee fecal samples from across their current range.

They focused on a portion of DNA in the genome called chromosome 21. It contains a wealth of information for inferring chimpanzee population structure.

Fontsere said: "Just by our sampling method, we have discovered around 50% more, and new, genetic variants on chromosome 21 than previous studies.

"Our dataset has been key in understanding recent and past gene flow between populations where previous sampling gaps impeded their study.

"Also, it has allowed us to describe if populations have been isolated recently or whether there was a historical event that did so.

"By characterizing the genomic singularities of each community or population, we also created a map that links genomic information to geographic location so we were able to devise a strategy to infer the geographic location of chimpanzee individuals."

Previously, only 59 whole chimpanzee genomes had been sequenced with limited information on their origin.

Large datasets from thousands of geo-referenced fecal samples also exist. But they represent only very small fragments of the entire genome.

With the new samples and genomic data, the researchers have been able to fill the previous gaps in the distribution of Eastern and Central chimpanzees.

Fontsere says they've also provided a more nuanced understanding of the genetic differentiation of the four recognized chimpanzee subspecies.

A link was identified between historical population structure, barriers of genetic continuity between populations and geographical obstacles such as rivers and lakes.

Co-lead author Dr. Mimi Arandjelovic, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, said: "We were able to show, using different analyses that look at very old and more recent variation, that the history of chimpanzees is complex, much like that of our own species.

"Chimpanzee subspecies were indeed separated in the past but have since also experienced genetic exchange between populations.

"This nicely explains why different studies aiming at reconstructing different ancestral periods have come to different conclusions about the evolutionary history of chimpanzees.”

Among many other insights, the evidence also reveals extensive connectivity in Western chimpanzees.

Marques-Bonet said: "This is so critically important to their conservation and really argues connectivity between forests across Western Africa, especially in the northern region, needs to be preserved for the protection of these populations and the subspecies."

The researchers are now using the methods to investigate other great apes and primates.

Their findings confirm fecal samples - although more complex than blood - are a fine source of host DNA for any species.

The PanAf also continues to analyze data collected over eight years from 18 countries across Africa, at over 40 temporary and long-term research and conservation sites.

The goal is to understand the evolutionary and ecological drivers of chimpanzee cultural and behaviural diversity.

Anyone interested can pitch in and help by annotating videos at the citizen science project .

The study is in the journal Cell Genomics.