Moa bird bones reveal DNA half-life but Jurassic Park remains fiction

13.09.2013 17:26

Moa birds disappeared from New
Zealand following the arrival of
human settlers in the 13th century,
but their fossils now provide us with a
valuable clues about long-term DNA
survival and how DNA decays over
thousands of years.
In a paper published today in
Proceedings of the Royal Society B,
we show that fragments of DNA from
these extinct, flightless birds can be
used to estimate how DNA decays over
time. The findings have implications
in choosing where to look for DNA-
containing fossils and in forensic
casework involving bones.
Sadly, the findings won’t satisfy those
people wanting us to talk about
dinosaur DNA. When telling someone
our day-job involves working with
ancient DNA (aDNA), more often than
not, the response is: “Ahhhh, you
mean like Jurassic Park? ”.
Then we explain how resurrecting the
dinosaurs is not possible and that
the early papers describing isolation
of dinosaur DNA were likely based on
a combination of contaminating
human and chicken DNA.
In other words, when the early aDNA
researchers cranked up the DNA
“photocopier” they copied DNA from
themselves, or what they had for
lunch, rather than dinosaurs. A
number of high-profile (never
retracted) publications citing
dinosaur-era DNA, coupled with
Michael Crichton’s famous novel ,
gave aDNA researchers a serious
headache for a while.
How far back?
So let’s return to the conversation
about our day-job. On explaining
that dinosaur DNA is a pipe dream,
the next question tends to be: “How
far back in time can you go, then?”.
That’s not an easy question to
answer. Questions of DNA survival
and rate of decay have been central
for a long time to scientists engaged
in aDNA research, and also in
forensic cases where old and
degraded DNA is encountered.
But as yet, it has proven extremely
difficult to predict DNA survival, and
there has been little progress towards
understanding the rate of DNA
It was shown in the early 1970s that
free DNA molecules in a solution
would fragment and “disappear” over
time, but this was measured in a
controlled laboratory setting under
artificial conditions and therefore
didn’t resemble the conditions in
fossil bone.
Researchers have since attempted to
predict the decay rates of DNA and
establish theoretical survival times,
but never very convincingly, largely
because there has been a lack of
empirical data on this topic.
Why has it been so difficult to assess?
Well, mainly because fossils with
good DNA preservation are rare. This
means large comparative studies on
this topic are rare too.
Moreover, many studies that have
addressed this question have included
samples from a range of different
burial environments which vary in
soil conditions, temperature, and so
on. All this variation results in a high
degree of variability in DNA
preservation that can mask any true
signal of DNA decay over time.
Our discovery
Our study was different in that we
had access to a very large number of
moa fossil bones from sites within
5km of each other and which
importantly were all subject to
similar environmental conditions.
With funding from the Marsden Fund
of the Royal Society of New
Zealand we were able to uniformly
drill small holes in hundreds of moa
bones and radiocarbon-date them.
The upshot is that the samples, for the
first time, gave us a very solid
framework in which to investigate the
question of DNA decay.
With this unusual setting we could
show that DNA does indeed degrade at
a certain rate and it therefore makes
sense to talk about a half-life of DNA.
That is, the length of time required
before half the original (starting
amount) of DNA is left.
In moa, for the targeted DNA
fragment, we were able to estimate a
half-life of 521 years and propose a
rough, general model that estimates
DNA decay at certain temperatures.
In a perfect world, this would mean
one could predict the amount of DNA
remaining if the age of a bone is
known, or use it as a tool to assess
whether it is worthwhile drilling into
a valuable fossil collections in the
search for aDNA. But our research
also shows that things are,
unfortunately, not that simple.
Despite demonstrating the overall
relationship between age and DNA
preservation, it is evident that time
alone can still only explain about
40% of the variation in DNA content
in these old moa fossils.
So although all these fossils were
preserved under the same
temperature and roughly similar
environmental conditions it is clear
other factors need to be considered if
we want to try and reliably predict
DNA decay. In that sense, our study is
just the first step on the path to better
predictive models.
Beating the survival record
Our study shows that DNA in bone
seems to decay at a rate that is almost
400 times slower than previously
measured for DNA in solution.
Combined with the fact modern DNA
sequencing technology allows us to
target very short fragments of DNA, it
seems likely future research will
identify DNA from permafrozen bone
that is considerably older than
the current DNA survival record of
about half a million years from
Greenlandic ice cores.
Under the best possible scenario,
discovering a million-year-old fossil
DNA sequence seems like a very real
possibility. While this is a long way
short of 65-million-year-old dinosaur
DNA, it would still represent a
considerable achievement.
To illustrate the extreme
improbability of isolating authentic
DNA fragments from 65-million-
year-old dinosaur bones, our model
predicts, under extremely favourable
conditions, all “letters” in the DNA
code (your genome has 3 billion of
them) within bone would be broken
after 6.8 million years.
In other words, the last break to
separate the final two bases in the
DNA code occurs after a maximum of
6.8 million years – and this is indeed
a highly optimistic estimate.
In addition, we know that much
longer DNA fragments are required in
order to be sequenced and
meaningful, and such fragments
would be gone a long time before the
6.8 million year mark.
So dinosaur DNA is still science
fiction … but then again, we all know
now that birds are actually
(theropod) dinosaurs , so in that sense
it is easily argued our entire study is
based on DNA from extinct