Baboon Genomes Offer Clues to the Past and Future of Humanity

“Once upon a time, in a cave in the Altai Mountains of southern Siberia, different types of ancient peoples were having sex,” I wrote last year in “The Cave Where It Happened: The Daughter of a Neanderthal Mom and a Denisovan Dad.”

That long-ago admixture, plus other episodes, is why some of us have echoes of Neanderthal and Denisovan genomes in our DNA today. It’s why some people learn from consumer genetic testing that 4% of their ancestors were Neanderthal. (Not the oft-claimed 3 or 4% of a genome, given that we share 98% of our genomes with chimpanzees.)

A new paper in Science Advances from the Baboon Genome Analysis Consortium provides a compelling possible view of our own prehistory, exploring genetic relationships among the six living species of genus Papio, the baboon. The animals maintain the traits that we say make them distinct species, differing in shape, size, and behavior, yet when members of different species meet, in geographical “hybrid zones,” sometimes they indeed swap genes.

Have sex, that is.

These sorts of analyses call into question the very idea of a species. The bestowing of names to designate who can mate with whom, after all, is us deciding what’s sexually attractive and what isn’t for another type of organism, in a more or less binary fashion. For baboons, that means variations on red, yellow, or olive brown fur; short or tall; pinkish face or not; harems or polygamy.

Or, or, or. Might the characteristics that separate species be a continuum in nature? Might such designations be as fluid as skin color and gender for us?

A Dual Humanity

I’ve often lamented the fact that we’re the only species of humans on the planet. Once at least eight species of our genus Homo lived, some overlapping in time. And before them at least 10 species of Australopithecus dwelled in Africa, some contemporaneous, separated by geography and climate over the vast continent. They diverged into what we dub species in eastern Africa before 3 million years ago. (See my “guys banging rocks” post at Scientific American).

Does the new baboon genome study mirror a time when we weren’t alone? The authors think it might.

Human evolution wasn’t the chain of chimp-to-office worker that festoons tee-shirts and bumper stickers – lineages branched. We share an ancestor with chimps, we didn’t descend from them. But the baboons offer a compelling contemporary example of co-existing primate species of the same genus, like what happened to the overlapping australopithecines, and then more recently to genus Homo.

Of Genes and Geography

Fossil evidence indicates that the oldest baboons lived in sub-Saharan Africa about 2 million years ago. That single group began to disperse as the savannah waxed and waned with the cycles of climate. DNA analysis of modern genomes reveals pockets of genetic uniformity echoing from the past, the population bottlenecks that mark long-ago winnowing of genetic diversity.

By 1.4 million years ago, the changing ecology had separated the ancestral group into six species, split between north and south. The Kinda baboon (P. kindae) emerged a mere 100,000 years ago, a yellow-brown animal from western sub-Saharan Africa.

Genetic distance between pairs of modern baboon species for the most part tracks with their past geographic separation. Today the broad habitat ranges in sub-Saharan Africa and southwest Arabia don’t overlap, but along their borders members of different baboon species do meet and mate. These are the hybrid zones.

Like modern human genomes with their scant contributions from Neanderthals or Denisovans, modern baboon genomes harbor a few “ghost” DNA sequences from archaic lineages that didn’t make it. In the Guinea baboon (P. papio), for example, up to a tenth of the modern genome may be a remnant of an extinct ancestor from the north.

The Stories in Genomes

The researchers consulted a smorgasbord of DNA sequence types, from single-base SNPs to protein-encoding genes to full genomes. Y chromosome sequences traced the male lineage and mitochondrial DNA the female.

Alu sequences are short repeats that litter genomes, and their appearance can function as a sort of clock as they originate and expand. Baboon genomes harbor many Alu repeats, which increase in number following action along those hybrid zones. The researchers constructed “gene trees” representing cognitive skills and reproductive behaviors to further flesh out the baboon species.

The genetic evidence coalesced into a few stories, albeit mere glimpses and deductions. Until we have a Time machine, the stories written in fossils and DNA sequences will suffice.

• The olive baboon (P. anubis) in the north and yellow baboon (P. cynocephalus) in the south share chunks of chromosomes (haplotypes), so they’re close relatives. They interbreed in southern Kenya in the wild and do just fine. But when they mate in captivity, offspring have skull and dental anomalies.
• Chacma baboon (P. ursinus) females can produce fertile offspring with Kinda males, but not the other way around. The Y chromosome and mitochondrial DNA studies showed that.
• Chacma baboons are polygamous: males and females have multiple sex partners. Hamadryas baboons (P. hamadryas) have harems in which a single male covets his group of females. What seems like two distinctive lifestyles to human observers isn’t so to the baboons – Chacma and hamadryas sometimes ignore their societal differences and just mate.

The researchers conclude with an obvious extension to human evolution:

“These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.”

But what about the future? Our species seems to be both blending and separating at the same time. When I peruse Ancestry.com daily, I see the admixture of humanity reverberating up from the past few centuries. It’s why I chose a beautiful mixed-race face for the cover of my genetics textbook.

And then I turn to Facebook and see, yet again, we in the U.S. dividing ourselves by ideologies and politics. Continually yelling at each other over words and actions. Hopefully the mixing will prevail and the current divide ultimately become nothing more than a brief behavioral aberration in our supposedly superior species. Perhaps we can take a few cues from the baboons making peace at those hybrid zones.