Using modern sequencing techniques to study ancient modern humans

Subject:	Using modern sequencing techniques to study ancient modern humans
Date:	Sat, 2 Jan 2010 03:27:09 -0800 (PST)

Not precisely archaeology, but not what address did Joseph and Mary
use when they checked into that inn in Bethlehem, which by the way
didn't exist then.

A team from the Max Planck Institute has created a means of separating
the contamination from modern DNA on ancient DNA in order to study the
ancient DNA. The method allows "reading" ancient DNA, even from very
short samples.

Using modern sequencing techniques to study ancient modern humans

DNA that is left in the remains of long-dead plants, animals, or
humans allows a direct look into the history of evolution. So far,
studies of this kind on ancestral members of our own species have been
hampered by scientists' inability to distinguish the ancient DNA from
modern-day human DNA contamination. Now, research by Svante P=C3=A4=C3=A4bo=
from
The Max-Planck Institute for Evolutionary Anthropology in Leipzig,
published online on December 31st in Current Biology =E2=80=94 a Cell Press
publication =E2=80=94 overcomes this hurdle and shows how it is possible to
directly analyze DNA from a member of our own species who lived around
30,000 years ago.

DNA =E2=80=94 the hereditary material contained in the nuclei and mitochond=
ria
of all body cells =E2=80=94 is a hardy molecule and can persist, conditions
permitting, for several tens of thousands of years. Such ancient DNA
provides scientists with unique possibilities to directly glimpse into
the genetic make-up of organisms that have long since vanished from
the Earth. Using ancient DNA extracted from bones, the biology of
extinct animals, such as mammoths, as well as of ancient humans, such
as the Neanderthals, has been successfully studied in recent years.

The ancient DNA approach could not be easily applied to ancient
members of our own species. This is because the ancient DNA fragments
are multiplied with special molecular probes that target certain DNA
sequences. These probes, however, cannot distinguish whether the DNA
they recognize comes from the ancient human sample or was introduced
much later, for instance by the archaeologists who handled the bones.
Thus, conclusions about the genetic make-up of ancient humans of our
own species were fraught with uncertainty.

Using the remains of humans that lived in Russia about 30,000 years
ago, P=C3=A4=C3=A4bo and his colleagues now make use of the latest DNA
sequencing (i.e., reading the sequence of bases that make up the DNA
strands) techniques to overcome this problem. These techniques, known
as "second-generation sequencing," enable the researchers to "read"
directly from ancient DNA molecules, without having to use probes to
multiply the DNA. Moreover, they can read from very short sequence
fragments that are typical of DNA ancient remains because over time
the DNA strands tend to break up. By contrast, DNA that is younger and
only recently came in contact with the sample would consist of much
longer fragments. This and other features, such as the chemical damage
incurred by ancient as opposed to modern DNA, effectively enabled the
researchers to distinguish between genuine ancient DNA molecules and
modern contamination. "We can now do what I thought was impossible
just a year ago =E2=80=93 determine reliable DNA sequences from modern huma=
ns
- but this is still possible only from very well-preserved specimens,"
says P=C3=A4=C3=A4bo.

The application of this technology to the remains of members of our
own species that lived tens of thousands of years ago now opens a
possibility to address questions about the evolution and prehistory of
our own species that were not possible with previous methods, for
instance whether the humans living in Europe 30,000 years ago are the
direct ancestors of present-day Europeans or whether they were later
replaced by immigrants that brought new technology such as farming
with them.

http://www.eurekalert.org/pub_releases/2009-12/cp-ums122309.php

Current Biology, 31 December 2009

doi:10.1016/j.cub.2009.11.068

Report

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

Johannes Krause1, Go To Corresponding Author, , Adrian W. Briggs1,
Martin Kircher1, Tomislav Maricic1, Nicolas Zwyns1, Anatoli
Derevianko2 and Svante P=C3=A4=C3=A4bo1

1 Max Planck Institute for Evolutionary Anthropology, Deutscher Platz
6, D-04103 Leipzig, Germany
2 Paleolithic Department, Institute of Archaeology & Ethnography,
Russian Academy of Sciences, Siberian Branch, Lavrentieva Prospekt, 17
Novosibirsk, 630090 Russia
Corresponding author

Summary

The recovery of DNA sequences from early modern humans (EMHs) could
shed light on their interactions with archaic groups such as
Neandertals and their relationships to current human populations.
However, such experiments are highly problematic because present-day
human DNA frequently contaminates bones [1,2]. For example, in a
recent study of mitochondrial (mt) DNA from Neolithic European
skeletons, sequence variants were only taken as authentic if they were
absent or rare in the present population, whereas others had to be
discounted as possible contamination [3,4]. This limits analysis to
EMH individuals carrying rare sequences and thus yields a biased view
of the ancient gene pool. Other approaches of identifying
contaminating DNA, such as genotyping all individuals who have come
into contact with a sample, restrict analyses to specimens where this
is possible [5,6] and do not exclude all possible sources of
contamination. By studying mtDNA in Neandertal remains, where
contamination and endogenous DNA can be distinguished by sequence, we
show that fragmentation patterns and nucleotide misincorporations can
be used to gauge authenticity of ancient DNA sequences. We use these
features to determine a complete mtDNA sequence from a =E2=88=BC30,000-year=
-
old EMH from the Kostenki 14 site in Russia.

http://www.cell.com/current-biology/abstract/S0960-9822%2809%2902139-3