Genes, Hybrids, and Giant Tortoises

Charles Darwin visited the Galápagos Islands in 1835. As he moved from island to island, he saw the subtle differences between finches, tortoises, and other animals. These observations led to the discovery of the theory of evolution as an expanding “tree of life,” first sketched by Darwin in his notebook entry dated just two years later in 1837.

The great tortoises of the Galápagos could not fail to impress. The greatest of all, the tortoise Chelonoidis elephantopus, can live to be a hundred years old and grow to six feet and almost 900 pounds.

Until now, it was believed that whalers hunted the great C. elephantopus to extinction shortly after Darwin’s visit. Now, however, new research suggests that a few of the great tortoises may still be alive.

Caption: G. Becky tortoises are native to Isabela Island in the Galapagos chain and have more domed shape shell. Credit: Courtesy Yale University.

Researchers have found what they believe are direct offspring of purebred C. elephantopus tortoises. By testing the genes of living tortoises, researchers concluded that they were studying hybrids. One parent was from a related species, C. becki. But the other parent was clearly C. elephantopus. And since the living tortoises were still quite young, researchers were drawn to the obvious conclusion that the C. elephantopus parent lived until a few decades ago and may still be roaming the slopes of Isabela Island.

So now it’s a race against time to find surviving purebred C. elephantopus tortoises in hopes that enough of them still exist so the species—truly one of the great animal species—can be brought back from what seemed like extinction. According to the report, “purebred tortoises of the recently ‘extinct’ C. elephantopus from Floreana Island are very likely still alive today.”

Caption: This tortoise is a hybrid of G. Becky and C. elephantopus, a species native to Floreana Island some 200 miles away and thought to be extinct. Genetic analysis of tortoise population on Isabela Island suggests purebred individuals of C. elephantopus must still be alive on Isabela. Credit: Courtesy of Yale University

One interesting parallel. Using a similar approach, researchers have recently concluded that human beings are also hybrids. For example, many of us contain genes from our Neandertal ancestors. The big difference, of course, is that our interbreeding occurred tens of thousands of years ago. In either case, hybridization or interbreeding occurs when the twigs at the end of Darwin's tree of life come together. As evolutionary biologists are discovering, speciation (or branching) is critical to evolution, but so is interbreeding or hybridization.

According to the report, “To our knowledge, this is the first rediscovery of a species by way of tracking the genetic footprints left in the genomes of its hybrid offspring.” The report, "Genetic rediscovery of an ‘extinct’ Galápagos giant tortoise species," appears in the January 9, 2012 issue of Current Biology.

Complicating the Family Tree

Our view of our past keeps getting more complicated. Our family tree, it turns out, is more of a twisted vine than a neatly linear branch.

Evidence keeps building by the day that our anatomically modern human (AMH) ancestors interbred with earlier forms of “archaic” humans. In the 31 Oct 2011 early online issue of PNAS, Pontus Skoglund and Mattias Jakobsson present evidence for the view that the genetic legacy of the Denisovans is wider than ever thought before.

First is was the Neandertals. This branch of the human family diverged from our own somewhere around 500,000 years ago. Somewhere between 100,000 and just 50,000 years ago, however, AMHs and Neandertals interbred successfully. The result lives on today in our genes. For many of us, our DNA is 2-3% from our Neanderthal ancestors. The Neandertals may be extinct, but their DNA lives on in every cell in the human body.

Then it was the Denisovans, a recently discovered branch of the human family more closely related to Neandertals than to us. What about AMH-Denisovan iInterbreeding? An international team of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was able to extract Denisovan DNA from tiny fragments of remains. From the extracts, they reconstructed the Denisovan genome and compared it with the human genome. What they found was clear evidence of interbreeding. Some living human beings—those identified as Melanesians—carry Denisovan genes. That was reported in December 2010.

In September, however, Pääbo was joined by David Reich and Mark Stoneking and other colleagues in reporting that the legacy of Denisovan DNA extends beyond the Melanesians. It’s all over the islands that extend below Southeast Asia, including Australia. Not just Aboriginal Australians but Near Oceanians, Polynesians, Fijians, east Indonesians, and other groups as far as the Philippines are carriers of the Denisovan legacy.

According to this study, the genetic legacy of AMH-Denisovan admixture does not include East Asians. This led the authors to conjecture that there are at least two main waves of AMH migration into southeast Asia. The first wave interbred with Denisovans while the second, apparently, did not.

Their work appeared in the 7 Oct 2011 issue of the American Journal of Human Genetics. Reich discusses these findings in a video. Hint: start at minute 22:30.

But now a study published in the online early edition of the Proceedings of the National Academy of Sciences for the week of 31 Oct 2011 presents evidence that East Asians are also descended in part from the Denisovans. In the paper, the authors (Pontus Skoglund and Mattias Jakobsson) write that “we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome.”

Experts in the field will no doubt debate these findings. Just how widespread is the effect of AMH-Denisovan interbreeding? How widely did AMHs and archaic humans interbreed? To what extent does admixture provide any benefit? Does it shed any light on observable differences between different groups within the human family today?

According to Skoglund and Jakobsson, the “history of anatomically modern and archaic humans might be more complex than previously proposed.”

If our past is more complex than we thought, so is our present. What does it mean to be human? It no longer seems to mean that we are all part of a biological species. Whether we like to call ourselves "anatomically modern humans" (AMHs) or Homo sapiens, we are learning that the very concept of species is becoming unfocused by research. Should we speak of AMH-Denisovan "interbreeding" or "hybridization"? Does it matter? Are we separate species or one slightly-tangled humanity?