Chimpanzee fossils are thin on the ground. After their lineage parted ways with ours, our human ancestors spent millennia kicking about in arid regions and caves ideal for preserving our remains. The ancestors of modern chimpanzees and bonobos, meanwhile, were hanging out in the lush jungles of central Africa.

“There’s a reason pretty much every image of a paleontologist in the field is in a desert or badlands,” writes paleontologist Dave Hone. Fossils can be found only when we have access to exposed rocks that were formed in the epoch of interest, and so “the rainforests of the Congo... are useless.” Add to that the quick decomposition of bodies in rich, acidic rainforest soil, and you have a huge gap in understanding where our modern cousins come from.

But “genomic fossils” could fill some of that gap. A paper published in Nature Ecology and Evolution this week reports finding the footprint of an extinct ape species in the genome of modern bonobos. That footprint can tell us roughly when these ancient apes must have lived, and where. It can even—with a lot of speculation—hint at some of the characteristics of the “ghost ape.”

A ghost in the Congo

At some point before six million years ago, the ancestor species we share with chimps and bonobos was living in Africa. The story of what happened in our own lineage after the split has a lot of detail to be worked out, but we have a rough roadmap. But we lack a similar roadmap for chimps and bonobos, which may explain why it’s so easy to think of them as having stayed essentially the same in all that time. It’s a faulty image, though: our cousins will have done a lot of evolving of their own in the millions of years since we split.

The split between chimps and bonobos began around two million years ago, but the boundaries were messy for a long time. The emerging picture is that some group within the ancestral chimp/bonobo species migrated across the Congo River, leading to a division but not total estrangement. Traces of ongoing gene flow from both sides suggest that there was crossing back and forth for a while.

The migration brought a surprise for the adventurous wanderers, suggest geneticist Martin Kuhlwilm and his colleagues. During their expansion, it looks like they “encountered a distinct branch of the [chimpanzee] clade,” the researchers write. This was a third branch on their family tree: the “ghost ape” that left its footprint in the modern bonobo genome. It branched off the tree around three million years ago, before the split between chimps and bonobos, and seems to have interbred with bonobos sometime after they went their own way. Around half a million years ago, traces of this species disappear.

Kuhlwilm had gone looking for “genomic fossils” in the DNA of chimps, he writes in a blog describing the research. Although we have their genomes, genetic data from individual chimps and bonobos is hard to come by. He and his colleagues had managed to get the complete genomes of 59 chimpanzees and 10 wild bonobos. But when he went looking through that data for hints of an ancient lineage, it popped up not in the chimps, but in the bonobos. “This was confusing,” he writes. “It took a long effort, discussions with other experts, and extensive computer simulations to understand that this must indeed come from an unknown lineage.”

The key was longer stretches of DNA that showed up in the bonobos but not the chimps. Different species must, by definition, have differences in their DNA, but these differences emerge gradually as a result of mutation, making them likely to appear in short sequences. Longer sequences that are different are more likely to be the signal of breeding with a different lineage.

Much like our own interbreeding with Neanderthals, this evidence shows that the lines between species are not bright and clean: closely related groups can have fertile offspring, leaving traces of their genome long after one of the groups has vanished.

Digging up “genomic fossils”

These genes may be partly responsible for some of the features that make bonobos unique: the ancient sequences appeared in regions of the genome that have been tentatively linked to behavioral patterns. And, much like the human genetic inheritance from Neanderthals, “it seems that some of this genetic material contributes to the response to pathogens,” writes Kuhlwilm, giving the bonobos possible immune advantages.

Since only ten bonobo genomes were used for this study, there’s the potential to dig up much more evidence on the ghost species with a broader sample. But ape genomes are a scarce resource: ethics dictates that wild animals shouldn’t be disturbed just to provide DNA samples, and political instability in the bonobos’ territory makes fieldwork difficult to do. One option for getting more genetic data is to sample bonobo poop. This would give researchers much more genetic data to work with, possibly allowing them to reconstruct more of the ancient apes’ genome.

And that might be the only evidence of the ghosts we’ll ever get our hands on. “Since it might well be that no ape fossils with preserved ancient DNA are to be found in the Congo Basin,” write the researchers, “excavating parts of extinct ape genomes from present-day variation could be the only strategy with which to explore these long-gone populations.”

Nature Ecology and Evolution, 2018. DOI: 10.1038/s41559-019-0881-7 (About DOIs).