Ancient DNA Tells a New Human Story
Armed with old bones and new DNA
sequencing technology, scientists are getting a much better understanding of
the prehistory of the human species, writes Matt Ridley
By Matt Ridley in the Wall Street Journal
Imagine what it must have been like
to look through the first telescopes or the first microscopes, or to see the
bottom of the sea as clearly as if the water were gin. This is how students of
human prehistory are starting to feel, thanks to a new ability to study ancient
DNA extracted from bodies and bones in archaeological sites.
Low-cost, high-throughput DNA
sequencing—a technique in which millions of DNA base-pairs are automatically
read in parallel—appeared on the scene less than a decade ago. It has already
transformed our ability to see just how the genes of human beings, their
domestic animals and their diseases have changed over thousands or tens of
thousands of years.
The result is a crop of new insights
into precisely what happened to our ancestors: when and where they migrated,
how much they intermarried with those they met along the way and how their
natures changed as a result of evolutionary pressures. DNA from living people
has already shed some light on these questions. Ancient DNA has now dramatically
deepened—and sometimes contradicted—those answers, providing a much more
dynamic view of the past.
It turns out that, in the prehistory
of our species, almost all of us were invaders and usurpers and miscegenators.
This scientific revelation is interesting in its own right, but it may have the
added benefit of encouraging people today to worry a bit less about cultural
change, racial mixing and immigration.
Consider two startling examples of
how ancient DNA has solved long-standing scientific enigmas. Tuberculosis in
the Americas today is derived from a genetic strain of the disease brought by
European settlers. That is no great surprise. But there’s a twist:
1,000-year-old mummies found in Peru show symptoms of TB as well. How can this
be—500 years before any Europeans set foot in the Americas?
In a study published late
last year in the journal Nature, Johannes
Krause of the Max Planck Institute for the Science of Human History in Jena,
Germany, and his colleagues found that all human strains of tuberculosis share
a common ancestor in Africa about 6,000 years ago. The implication is that this
is when and where human beings first picked up TB. It is much later than other
scientists had thought, but Dr. Krause’s finding only deepened the mystery of
the Peruvian mummies, since by then, their ancestors had long since left
Africa.
Modern DNA cannot help with this
problem, but reading the DNA of the tuberculosis bacteria in the mummies
allowed Dr. Krause to suggest an extraordinary explanation. The TB DNA in the
mummies most resembles the DNA of TB in seals, which resembles that of TB in
goats in Africa, which resembles that of the earliest strains in African people.
So perhaps Africans gave tuberculosis to their goats, which gave it to seals,
which crossed the Atlantic and gave it to native Americans.
Another genetic puzzle has been the
fact that most modern Europeans have certain DNA sequences that are similar to
those of some American Indians but different from those of most Asians,
including natives of Siberia. How can this be, since American Indians are
supposedly descended from Asians who migrated across the Bering land bridge
from Siberia to Alaska about 14,000 years ago? Were there ancient seafarers in
the Atlantic? Or is it simply from mating between European settlers and
American Indians after Columbus? Neither, as it happens.
Modern DNA could not resolve these
issues, but ancient DNA provides answers. Eske Willerslev’s research group at
the University of Copenhagen, working with Russian scientists, read the genomes
of two bits of human remains found near Lake Baikal in Siberia; one of these
individuals lived 24,000 years ago, the other 17,000.
Both had genes similar to modern
Europeans and modern American Indians but distinct from modern Siberians or
other East Asians. As the researchers say in a paper published early last year in Nature, this implies that a population of hunter-gatherers lived
in northern Eurasia in the last ice age and partly gave rise to the first
Americans in the East and to Europeans in the West, before they themselves died
out in Siberia and were replaced by immigrants from elsewhere in Asia.
This may help to explain the enigma
known as Kennewick Man, a 9,000-year-old skeleton from Washington state, which
seems to have features more like those of a modern European than of a modern
American Indian. The earliest inhabitants of the Americas seem to have been
distant cousins of Europeans, connected through Siberia, with their genes later
diluted by other Asians migrating through Alaska.
As this example shows, one of the
common themes of research on ancient DNA is that the mixing of native and
immigrant populations happened much more often than previously suspected. The
new research allows us to identify the many different elements of that complex
history. It is like watching a cake being reverse-engineered into flour, sugar,
eggs, milk and its other ingredients. The familiar textbook notion that, for
most of human existence, people native to one region developed in isolation
from those native to a different region no longer makes sense.
A long-running debate in archaeology
revolves around how to explain such key events as the advent of agriculture or
the replacement of a certain type of tool by another. The key divide is over
what caused the change: Did hunter-gatherers take up farming, or did farmers
move in and replace hunter-gatherers? This is sometimes called the “pots versus
people” debate.
Geneticists studying the genes of
people alive today have leaned toward theories based on “serial founder
effects” rather than on mass migrations. The idea is that while most people
stayed put, small groups of farmers would have moved short distances and
started new colonies, which would then have expanded. This would account for
the fact that the further from Africa a population lies, the lower is its
genetic diversity: The populations had been through a series of genetic
bottlenecks caused by small numbers of founders.
The study of ancient DNA has
challenged this view. We now know that mass migrations occurred repeatedly,
overwhelming natives while absorbing some of their genes. In a study published
in 2009 in the journal Science, analysis of ancient DNA by Joachim Burger and
Barbara Bramanti of Johannes Gutenberg University in Mainz, Germany, and Mark
Thomas at University College London, showed that the first farmers of central Europe
could not have been descended solely from their hunter-gatherer forerunners.
In response to such research and to
their own findings, Joseph Pickrell of Columbia University and David Reich of
Harvard University argue that “major upheavals” of human population have been
“overwriting” the genetic history of the past 50,000 years. The result, they
say, is that “present-day inhabitants of many places in the world are rarely
related in a simple manner to the more ancient peoples of the same region.” In
short, we are none of us natives or purebred.
Perhaps the most striking example of
this is a discovery announced by Dr. Reich’s team in a paper recently
published in Nature: Just 4,500 years ago, long after
the arrival of farming in Europe from the near East—a transition that had
largely displaced the genes of the indigenous hunter-gatherers—another “massive
migration into the heartland of Europe from its eastern periphery” occurred.
People from the steppes northeast of the Black Sea swamped the European genome
with their DNA, and that relatively new pool of DNA is still ubiquitous among
Europeans today.
This tips the balance in another
long-running argument among anthropologists about the origin of the
“Indo-European” languages. From Irish to Sanskrit, there are close similarities
of vocabulary among most of the languages of Europe and those spoken in parts
of Central Asia, Iran and India—connections not shared by languages like
Basque, Turkish, Arabic, Hungarian and Finnish.
Two main rival theories have been
offered to explain this pattern. The first holds that proto-Indo-European was
spoken by the first farmers who left the fertile crescent of Syria, Turkey and
Iraq for adjacent regions. The second view is that the foundational language
was spoken not by these early farmers but, as certain shared words seem to
suggest, by horse-riding sheep and cattle herders who spilled out of the
Ukrainian steppe a few thousand years later.
The recent research of Dr. Reich and
his colleagues supports this latter hypothesis: Indo-European languages
probably originated in the steppes just two millennia before the Christian era.
The discovery of the massive
migration from the steppes 4,500 years ago was made possible by the analysis of
DNA from 69 different individual bodies from between 8,000 and 3,000 years ago
and the comparison of nearly 400,000 different sections on their genomes. This
sort of massive analysis would have been impossible just a decade ago, but
since the advent of low-cost, high-throughput DNA sequencing, as well as
advances in statistical analysis, it is now almost routine.
Before these technical innovations, reading
DNA required the laborious amplification of short segments, one at a time. By
2008, companies such as 454 Life Sciences in Branford, Conn., and the San
Diego-based Illumina began marketing machines that could read millions of DNA
samples in parallel. In the past, researchers wanting to study ancient or
modern DNA had to sip from raindrops; now they can drink from fire hoses.
For now, such work can only be done
in a few laboratories—not just because the sequencing requires big machines but
also because the procedures needed to avoid contamination of ancient samples by
modern DNA are elaborate and expensive, to say nothing of the skills required
to analyze the massive amounts of data produced. As a result, says Greger
Larson, head of a new ancient-DNA research group at Oxford University,
scientists are conducting this work not at many different laboratories but in
huge teams gathered around the leading experts in the field, such as David
Reich at Harvard Medical School, Eske Willerslev of the University of
Copenhagen or Svante Pääbo of the Max
Planck Institute for Evolutionary Anthropology in Leipzig.
Dr. Pääbo is best known for his
achievement in sequencing the Neanderthal genome in 2009 and for his discovery
that a small amount (up to 4%) of Neanderthal DNA is found in modern Europeans
and other non-Africans. This suggests that when African emigrants overwhelmed
the Neanderthal populations of Europe and western Asia some 40,000 to 30,000
years ago, they interbred with them to some small extent—thus anticipating the
scenarios of admixture described by studies of later waves of migration.
In 2010, Dr. Pääbo and his
colleagues startled the world again by discovering (from the DNA in a
50,000-year-old finger bone found in a cave at Denisova in the mountains of
western Siberia) that a hitherto unsuspected third type of early human lived in
Asia at this time. These “Denisovans” are as distantly related to the Neanderthals
as they are to us “Africans.” A small amount (up to 6%) of their DNA survives
in the genomes of Melanesians and Australian aborigines, which suggests that
somewhere on their way east from Africa, probably in southeast Asia, modern
humans mated occasionally with Denisovans.
Now comes evidence that Tibetans
also have a Denisovan connection. In the thin air of the Tibetan plateau, the
local people can survive only because of specially evolved versions of a gene
called EPAS1. In a study published last
summer in Nature, Emilia Huerta-Sánchez and Rasmus
Nielsen of the University of California, Berkeley, and their colleagues found
this version of the DNA sequence around EPAS1 in the ancient genetic material
of the Denisovans. Mating with Denisovans seems to have enabled people to
survive at high elevations in Tibet.
Ancient DNA is telling us, in short,
not only who mated with whom and when but which genes were then promoted by
natural selection in the resulting offspring to improve their chances of
survival. As Dr. Thomas of University College London points out, changes in the
frequency of particular DNA sequences are the stuff of evolution itself.
Directly measuring how DNA changed over time, by comparing samples from
different periods of human history, allows us to see evolution not in the
survival rates of organisms (that is, through a middleman of sorts) but in
genetic material itself.
Consider, for example, the invention
of farming in Europe about 8,500 years ago, a shift that caused rapid
evolutionary change in the genes of Europeans as they adapted to new diets, new
pathogens and new social structures. Some of this can be inferred from the
study of modern DNA, but ancient DNA can catch it in the act.
A forthcoming paper by Dr. Reich’s group looks at 83 individuals from the period
before, during and after the arrival of agriculture. The study analyzes 300,000
different sections of their genomes and pinpoints just five genes that changed
rapidly.
The strongest signal came from the
mutation for lactase persistence—that is, the ability to continue digesting the
milk sugar lactose after infancy. Normally, mammals don’t need to digest
lactose as adults, and the necessary lactase gene switches off when a baby is
weaned from its mother.
This changed for human beings,
however, when dairy farming introduced milk into the adult diet. A mutation
that prevented the weaning switch-off spread in Europeans fairly late, around
4,300 years ago, probably long after dairy farming was invented, but it gave
its possessors a significant advantage: They derived more nutrition from
drinking milk (and suffered less indigestion) than their rivals.
Two genes that affect skin color
were also subject to rapid evolutionary selection as early farmers tried to
subsist on grain-rich, vitamin-D-poor diets in northern areas with low levels
of sunlight. (Sunlight helps the body to convert a form of cholesterol into a
form of vitamin D.) The shift to pale skin—which produces vitamin D more
efficiently than darker skin—among northern Europeans after the advent of
farming appears to have proceeded
rapidly, pointing to some of the strongest
selection pressures ever recorded in human genetics.
Since the discovery of DNA’s
structure more than a half-century ago, genetic science has promised—and begun
to deliver—a medical revolution, but it keeps producing other kinds of
revolutions too. In the 1990s, it transformed the field of forensics, for
example, and now it is having a similar effect on history and archaeology.
Today, the prehistory of humanity is an open book as never before.
The lessons of this DNA revolution
are not just scientific, however; they are social and political as well. The
discoveries made possible by our new access to ancient DNA show that very few
people today live anywhere near where their distant ancestors lived. Virtually
no one on the planet is a true native—an instructive fact to consider at a time
when ethnic and national differences still abound and the world continues to
throw human beings together in new and unexpected ways.
Mr. Ridley is the author of “The
Rational Optimist: How Prosperity Evolves” and “The Evolution of Everything:
How Ideas Emerge,” to be published in November.
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