Genetics and Archaeology: Helping Us Understand the Past

Recently I came across several examples of how genetic information has greatly helped us understand the past. Quite often this data is gathered in the most unexpected places. Consider these examples.

In an article published in December 2009, an international group of scientists addresses the issue of the extinction of North American megafauna traditionally dated some 11,000 years ago. A skeleton of a woolly mammoth on display in a museum never fails to impress us. At the same time, most of us would agree that it is a good thing we don’t have to worry any more about these lumbering giants messing up our evening commute. However, what most of us stop worrying about is when these animals became extinct and why. Most of us, that is, but not all of us. This is where the story of ancient DNA retrieved from perennially frozen soil comes in.

A traditional approach to estimate when and where a species became extinct has been to map and date the last known survivors. The thinking was that knowing when and where the last specimens lived would automatically clue us in as to why they died out. Is this true, however? Do these last known survivors really represent that last ones left standing? Or did we miss them and make wrong assumptions?

Creative Commons License photo credit: rpongsaj

The party line about woolly mammoths was that they survived on remote islands in the far northern regions of Alaska and Siberia, a region referred to as Beringia. That is now old hat. New genetic data tells us a different story. Mammoths may have survived much longer than originally thought in the Alaskan interior. Scratch 13,000 years ago. Now it looks like woolly mammoths may have survived for an additional 2,600 to 3,700 years in parts of Alaska. Mitochondrial DNA was retrieved from perennially frozen soil near Stevens Village in the Yukon Flat. What we have here then is a suggestion that we can establish the presence of certain animals in a region at a certain time in the past. No bones needed. Just animal DNA left behind in the soil and preserved because of the permanent frozen condition of the dirt.

While the researchers were careful to address any shortcomings of their approach (contamination of the soil, migration of more ancient DNA from lower-lying areas to more recent layers closer to the surface), there will be reactions from other members in the scientific community. This may be frustrating to those among us who like to see “the final answer” to questions like these, this dialogue is part of what science is all about. We will have to see if these new results will stand up to the criticism that will come.

As megafauna slowly disappeared from the North American landscape, human settlers were making their presence felt. I have written about the questions of where these earlier migrants into the Americas may have come from. There is very good evidence that the Paleoindians migrated from parts of Asia.

Research into a disease known as multifocal leukoencephalopathy resulted in the discovery of a virus labeled as the “JC virus.”

It turns out that we all have a copy of this virus residing within us. It is harmless to most of us, unless your immune system is compromised. Geneticists studying this virus found that it was remarkably stable and very rarely mutated into a new variety. Moreover, the strain of the JC virus carried by the Navajo today is nearly identical to that carried by the modern inhabitants of Tokyo. The JC virus bolsters an Asian origin theory for the First Americans.

Beringia – Image courtesy of NASA.

As to how Paleoindians arrived into the Americas, genetics can help us focus that picture as well. If one accepts that the Bering Strait was an ancient migration route – and most people have no problem accepting this – then the issue is: exactly what route did they follow? A coastal route and an interior, overland route, often suggested by archaeologists, now both seem to have been used.

North American mitochondrial DNA, collected from contemporary populations, points to two migration routes. In a paper published Jan. 19, 2009, scientists studied various mitochondrial DNA haplogroups, zooming in on two rare groups. One of these (known as D4h3) is found only along the Pacific coast and is mostly in South America, while the second group (X2a) is restricted to northern North America.

The presence of X2a in North America east of the Rocky Mountains may support the idea of an ice-free corridor between two ice sheets covering Canada and parts of the US. Some of the earliest migrants may have followed that route which would have taken them into the Great Plains, where the glacial corridor would have ended. The presence of D4h3 along the Pacific may represent a coastal migration route.

Woolly mammoths leaving their DNA in the soil, viruses carried by all of us and DNA shared through the mother’s family line all help us refine and refute some of the ideas on how the first immigrants arrived in the Americas. I am sure genetics will continue to add to our understanding of this momentous period in human history. Stay tuned.

Lucy’s Monstrous Misfits II: Upside-Down Mastodon

Dr. Bakker’s series on Lucy continues below. Check out  Part 1: Lucy – Out of Africa. Not! and Part 2: Lucy’s Monstrous Misfits: The Moose-Giraffe.

Why did some of Lucy’s neighbors score big bio-geographical successes, spreading over many continents?

Three More Cases: Hairy Monsters With Tusks & Trunks

Elephant bull 2
Creative Commons License photo credit:
Tambako the Jaguar (on the sea)

The Order Proboscidea includes all elephant and elephant kin – large to giant to super-giant herbivores with long upper lips transformed into trunks, plus long tusks. Tusks can sprout from the upper jaw or the lower jaw or both jaws.

Regular Short-Tusked Mastodons – “The Ohio Incognitum”

Regular Mastodons were the first fossil Proboscidea to be discovered – way back in the early 1700’s.  The legs looked like elephants’. The teeth looked like giant pig teeth.  Explorers in the Ohio Valley called the monster the “Unknown  Creature (Incognitum) from Ohio.” Formal name: Mammut.

By the late 1700’s full skeletons showed the whole beast – it was very like an elephant but shorter with a low forehead and short, stout upper tusks.  Lucy lived with Regular Mastodons who were very close to the Ohio Beast.

Regular Mastodons – The Long-Tuskers (Anancines)

DeinoAnancine copyLiving side by side with the Ohio Regulars in Lucy’s Africa was a close relative: The Long-Tusked Regulars. Technical name: the Anancine mastodons. In the Anancines, the super-long tusks stuck out so far we’d expect the beast to trip itself if it ran fast.

Upside Down Mastodon.

Now for the maximum weirdness among proboscideans: the Deinotheres.  Large to super large, Deinotheres had a long, long history in Africa, beginning way before Lucy or any other australopithecine. Body was elephantine – but the feet were small, with tiny side toes and three big ones in the middle.

The astonishing feature was the curved tusks. They were upside down. Instead of being in the upper jaw and curving up, the way they did in all normal mastodons, Deinothere tusks curved down and were in the lower jaw.

What good were upside-down tusks?

Old-timer scientists speculated:

“Maybe they hauled themselves out onto ice flows, like walruses do.”

Wrong. Deinotheres never lived in cold regions.

“Maybe they killed their prey with a downward jab.”

Wrong.  Deinothere molars were vegetable choppers, designed to munch big leaves and branches. All deinotheres were vegetarian.

“Maybe they used the tusks to cash down onto branches to break them off.”  “Maybe they fought each other in the mating season.”


World MapDeino

As global travelers, Deinotheres are intriguing. They were like hippos. Deinotheres spread over Europe and India and China. But they never conquered Siberia and never entered the New World, via the Bering Land Bridge.

Makes you think……


The Earth’s First Apocalypse: Texas Red Beds, 285 Million Years Ago

At a dig site in North Texas, the Houston Museum of Natural Science is investigating the animals that would have died off when this first mass extinction event occurred. Recently, a production crew from the History Channel came along on-site – and their footage of Dr. Bakker and the Museum’s team airs tonight at 8 p.m. as part of a two hour special called (aptly) First Apocalypse. UPDATE: In case you missed it, the special re-airs locally Saturday, Jan. 10 at 9 p.m. and a few hours later, Sunday morning at 1 a.m. (Check your local listings.)

In this post, Dr. Bakker explores several extinction events, including the first, Permian extinction you’ll see featured on the History Channel tonight.

Big Hairy Elephant
Creative Commons License photo credit: Yogi


In the early 1800’s, paleontology astounded the world when fossils documented the phenomenon of mass extinctions, times when the whole menagerie of big terrestrial critters went extinct.

The first mass die-off that was discovered killed the gigantic mammoths, mastodons, ground sloths, saber-tooth tigers and dozens of other large mammals. This extinction event occurred during the Ice Age. The Ice Age Event didn’t hit small species – if you were a vole, mole, rat, bat or chipmunk, your species had a good chance of surviving.

Today, we know that the extinction took place between 2 million and ten thousand years ago.


By the 1830s, a second giant extinction event was revealed. All the huge Dinosauria disappeared at the end of the Age of Reptiles. Small creatures – birds and salamanders, lizards and frogs, snakes and furry mammals – survived in great numbers.


Mass extinctions weren’t all negative. Dino-die-offs kick-started evolution in the survivors. From the little furry mammals who survived came a wonderful new evolutionary wave of big predators and herbivores – horses, rhinos, hippos, water buffalo, elephants, bears, tigers, cheetahs and wolves. This Darwinian bounce happened every time there was a catastrophic extinction.


Digging in oceanic strata during the mid-1800s showed yet another catastrophe, when the Permian Period ended. Most common species of marine life disappeared, including trilobites, corals, and many species of shellfish.

Die-offs struck the land too – most of the big land reptiles, who filled the role of Top Predator and Top Herbivore, died out. Many small species persisted and from these humble survivors came the next wave of big land animals, including the dinosaurs.


Many theories sprung up to explain the great die-offs: the agent of extinction was identified as:

sudden increases in earth temperatures, or

sudden decreases in temperature, or

changes in atmospheric gases, or

changes in humidity, or

abrupt rise of mountains, or

abrupt disappearance of mountains, or

draining away of shallow seas, or

increase in volcanic eruptions, or

sudden impacts of meteorites, or

invasion of foreign species from one continent to another.


Diadectes, side and top view. (c) Dr. Robert T. Bakker

To sort through all the possible solutions, it would help to find the very first case when large land animals evolved and then died-off. North Central Texas preserves this earliest apocalypse in the red-stained rocks laid down in the Early Permian. This extinction was long before the event that struck at the Late Permian.

Beginning in 1877, Texas excavations showed how the earliest large land herbivores evolved. These plant-eating pioneers were wide-bodied, low-slung reptiles known as “Cross-Biters,” Diadectes. Diadectes and its kin were the first large land animals to acquire the wide molars and big guts needed to digest leaves and branches from terrestrial bushes and trees.

The members of the Diadectes Family were the commonest land herbivore for fifteen million years…..and then, suddenly, they went extinct. The pattern at this first die-off matches what we’ve seen in the other land extinctions – small species were far more successful in living through the event.


This first die-off opened niches for the survivors. New and spectacular large herbivores evolved from small ancestors. In the Texas Red Beds, we find super-wide-bodied caseid reptiles who reached weights of more than a half ton.

The wide-bodied caseid reptile. (c) Dr. Robert T. Bakker


The wide-bodied caseids flourished for millions of years in the Middle Permian – then, the second extinction struck. Caseids disappeared. Evolving into the gap were advanced mammal-like reptiles with thick bone foreheads. There were both giant carnivores (anteosaurs) and giant herbivores (keratocephs).

Keratocephus, having a bit of trouble with anteosaurus. (c) Dr. Robert T. Bakker

The Houston Museum continues digging in north Texas, where the Red Beds record the earliest waves of large land animal evolution and the first extinction events. Many mysteries remain. But one pattern seems confirmed:

Mass die-offs on land are targeted like smart bombs. If you’re a big herbivore or big carnivore, you have the highest probability of going extinct.

Learn more about the First Apocalypse, and see Dr. Bakker and the Museum’s paleontology team in action, tonight at 8 p.m. on The History Channel.