www.sciencemag.org SCIENCE VOL 334 9 DECEMBER 2011 1335

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For nearly 15,000 years, the indigenous peo-

ples of North and South America had these

vast continents to themselves. But that all

changed when Columbus’s “discovery” of

the New World launched relentless waves of

European colonization that went on for centu-

ries. Many historians say these invasions dec-

imated native populations through warfare,

enslavement, and epidemics of new diseases

such as smallpox, infl uenza, and measles.

Some estimates suggest that up to 90%

of indigenous peoples were wiped out. But

other scholars have argued that the decline

was relatively modest and transient, and that

populations eventually recovered to precon-

tact levels. The latter view is supported by

recent genetic studies of Native Americans,

which have failed to detect signs of popula-

tion crashes.

Now, a study published

this week in the Proceed-

ings of the National Acad-

emy of Sciences pushes

the pendulum back

toward dramatic popula-

tion declines. Using both

modern and ancient mito-

chondrial DNA (mtDNA)

from Native Americans,

an international team

concludes that about 500

years ago, the number

of reproductively active

Native American women

quickly plunged by half,

indicating a “widespread

and severe” contraction in

population size.

“This is a very nice

paper, with results that

seem sound,” says genet-

icist Sandro Bonatto of

the Federal University of Rio Grande do Sul

in Porto Alegre, Brazil. “I have always been

intrigued by the lack of genetic evidence for

such an obvious population reduction.” But

Bonatto and others caution that the study’s

innovation of using both ancient and modern

DNA could also add a dose of uncertainty to

its conclusions.

Anthropologists and historians have

argued about such uncertainties for

decades, in large part because estimating

early Native American population numbers

is very difficult. Most researchers agree

that in North America north of Mexico,

Native Americans numbered only about

500,000 by the year 1900. But estimates

for the year 1500 have varied wildly, from

20 million to just over 1 million, thus gener-

ating dramatically different percentages for

post-European contact population crashes.

(The Native American population has since

rebounded, reaching about 3 million in the

United States today.) “The demographic

history of the Americas before and after

Columbus has been among the most hotly

debated topics in archaeology and history,”

says anthropologist Clark Larsen of Ohio

State University in Columbus.

Brendan O’Fallon, a population geneticist

at the University of Washington, Seattle, and

Lars Fehren-Schmitz, an anthropologist at

the University of Göttingen in Germany, took

a new look at the issue. They analyzed data

from 137 complete mtDNA genomes rep-

resenting indigenous Americans from both

North and South America, as well as smaller

segments of 63 ancient mtDNA sequences

from both continents ranging from about

3000 to 700 years ago.

By combining modern and ancient DNA,

they were able to calibrate a more accu-

rate molecular clock. They then used high-

resolution statistical models to date demo-

graphic changes indicated by changes in

the distribution of DNA variants. With these

methods, they pinpointed a dramatic popu-

lation decrease that other major studies had

missed, O’Fallon says.

Because mtDNA is inherited through the

mother, the pair was able to estimate the so-

called effective population size—in this case

the number of women actually bearing chil-

dren—from the time of the peopling of the

Americas about 15,000 years ago to nearly

the present day. The team found that this num-

ber reached its highest point about 5000 years

ago and precipitously declined, by about 50%,

about 500 years ago. It then began to rise

again. (The team did not try to estimate actual

population numbers, because the relationship

between effective population size and total

population size can vary widely.)

The Native American population eventu-

ally recovered, implying that it was probably

never in danger of extinction, but “from a

cultural or moral perspective, a 50% drop is

severe,” O’Fallon notes.

This sudden plunge in

numbers fits the histori-

cal documentation, Larsen

says: “The historical re cord

of population collapse in

the post-Columbus era is

just too well documented

to doubt the remarkable

and negative impact on

native peoples.” Quentin

Atkinson, a bio logist at

the University of Auckland

in New Zealand and lead

author of one of the earlier

genetic studies that failed

to f ind such an effect,

agrees that “the results

certainly seem to suggest

a dip in population size

about 500 years ago.”

But Atkinson and

geneticist Phillip Endicott

of the Museum of Man in

Paris have concerns about the study’s meth-

odology. Endicott cautions that the research-

ers mixed genetic apples and oranges: They

used whole mtDNA sequences from mod-

ern Native American populations, combined

with only small segments of ancient mtDNA.

“This would be a much stronger fi nding if

they could have obtained it using compat-

ible data sets,” Endicott says, by using only

segments of the modern mtDNA or whole-

genome sequences of the ancient mtDNA.

Bonatto prefers the second option: “To

settle the debate we need a lot more ancient

[DNA] data.”

–MICHAEL BALTER

Genes Confi rm Europeans’ Blow to Native Americans

H U M A N E VO L U T I O N A RY G E N E T I C S

Deadly invasion. European colonizers brought smallpox and other diseases that killed many

Native Americans, as depicted in this 16th century woodcut.

Published by AAAS

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