NEWS OF THE WEEK
Briggs and his colleagues sequenced
Neander Valley
Vindija
Cave
El Sidrón
Cave
ANCIENT DNA
Sequencing Neandertal Mitochondrial
Genomes by the Half-Dozen
Fourteen years ago, sequencing just a few
hundred bases of mitochondrial DNA from a
Neandertal drew applause worldwide.
Ancient DNA studies have come a long way
since then. On page 318, a team led by
Svante Pääbo of the Max Planck Institute for
Evolutionary Anthropology in Leipzig, Ger-
many, describes a new technique the team
used to decipher the entire mitochondrial
genomes from five of these extinct humans.
These genomes show relatively little genetic
diversity among Neandertals scattered
across Europe and Russia.
“This is an important step for ancient
DNA,” says Eddy Rubin, whose lab at the
Lawrence Berkeley National Laboratory in
California did some of the f irst work
sequencing Neandertal nuclear DNA. Adds
Eske Willerslev, who studies ancient DNA at
the University of Copenhagen in Denmark,
the new technique “provides a solution to a
technical problem: … how to target specific
regions of interest.”
Ancient DNA is diff icult to sequence
because genetic material degrades over time
into small fragments just tens of bases long
and errors are often introduced into the aging
sequence. Moreover, 99% of fossil DNA tends
to be contaminating sequence from microbes
and fungi that have infiltrated the decaying
bone. Three years ago, researchers began
sequencing all of the DNA in Neandertal sam-
ples, then separating out what looked like
human sequence from the mix. New sequenc-
ing technologies made the project affordable
enough to go after the entire Neandertal
nuclear genome (Science, 17 November 2006,
252 17 JULY 2009
Across the continent. Entire
mitochondrial genomes now
exist for these four Neandertal
bones and two more, suggesting
low genetic diversity in this
extinct human.
Mezmaiskaya
Cave
p. 1068), which was announced in February
(Science, 13 February, p. 866).
Some of that project’s DNA came from
mitochondria, and researchers assembled it
into the first entire Neandertal mitochon-
drial genome in 2008. Sequencing another
mitochondrial genome that way would cost
as much as $400 million, says Pääbo gradu-
ate student Adrian Briggs. That would make
comparing multiple Neandertal genomes—
the only way to understand the population
size and structure of our closest relative—
prohibitively expensive. So Briggs came up
with a better way. His new cost: about $8000
per mitochondrial genome.
The approach uses probes that recognize
and isolate only Neandertal mitochondrial
DNA from all the contaminating DNA in a
sample. Thus, Briggs winds up sequencing
just the material he’s looking for.
To do this, he first attaches short sequence
tags to all the pieces of DNA in his sample,
creating a DNA “library” that can be copied
to ensure there will be enough ancient DNA
for future use. Using the already-sequenced
Neandertal mitochondrial genome as a tem-
plate, Briggs designed 574 probes to cover
the entire mitochondrial genome. When a
probe links up with its target sequence in a
mass of DNA fragments, an enzyme copies
the rest of the DNA in that piece many times
over. Thus, Briggs was able to isolate the
whole mitochondrial genome and sequence it
using the latest high-throughput sequencing
technologies. Others have used similar
approaches, but Briggs tailored his for the
short, degraded fragments found in fossils.
VOL 325 SCIENCE www.sciencemag.org
Published by AAAS
16,565 mitochondrial bases extracted from
bones from Spain, Germany, Croatia, and
Russia (see map) and analyzed those genomes
along with the one sequenced earlier, which
comes from a long bone fragment from Croa-
tia. The bones ranged in age from 38,000 to
70,000 years old. The team also compared the
ancient DNA with mitochondrial genome
data from about 100 modern individuals.
Briggs and postdoc Jeffrey Good found
55 places out of the 16,565 bases where the
mitochondrial genomes varied across the six
ancient samples. On average, they found
20 differences between any two samples. In
modern humans, about 60 differences exist
between any two samples, making Neander-
Downloaded from www.sciencemag.org on March 27, 2010
tals about one-third as diverse. That isn’t
unexpected given that humans come from
across the globe and that the Neandertals were
confined to Europe and Russia, notes John
Relethford, a biological anthropologist at the
State University of New York College at
Oneonta. The results call into question earlier
suggestions that Neandertals were divided
into separate, regional populations, but more
data are needed to be sure, says Briggs.
By the Max Planck group’s calculations,
this diversity translates into the equivalent of
at most 3500 breeding Neandertal females, or
up to 7000 including males, lower than previ-
ous rough estimates of about 10,000. This
so-called effective population size is far less
than the actual population and represents a
theoretical attempt, based on the population’s
genetic diversity, to quantify the number of
individuals who are breeding at any given
time. For example, Anders Götherström of
Uppsala University in Sweden calculates that
although the Swedish population numbers
9 million, the effective population size is
about 100,000; he estimates that the 3500
might translate very roughly into about
70,000 Neandertals.
“Low population size may have been a
general aspect of Neandertal biology,” says
Briggs. With relatively few individuals, the
species may have been more vulnerable to
extinction from climate change or competi-
tion from our ancestors, he adds.
CREDIT: ADRIAN BRIGGS AND JOHANNES KRAUSE
Such a small number “is not too surpris-
ing,” says ancient DNA expert Alan Cooper
of the University of Adelaide in Australia, as
archaeological evidence had been pointing
toward this. Cooper and others caution that
analyzing mitochondrial DNA has limits as it
is “in effect ‘one gene’ because all its genes
are so tightly linked.” Thus, says Cooper,
“this is just one view of Neandertal evolution-
ary history.”
–ELIZABETH PENNISI