Biology Reference
In-Depth Information
If your sample will be coming directly from an excavation, the ideal situation is for only
one person to excavate the sample in protective gear to minimize any skin or hair exposure.
The gear is to protect the sample from you (and your DNA), not the reverse. If you are
sampling already excavated and curated remains, you should at least wear a facemask,
hair cover, and gloves. Make sure to also take DNA samples (cheek swab samples are fine)
from anybody who has been in contact with the remains to control for the presence of their
DNA on the sample as possible contaminants.
The primary sample should be stored in a DNA-free bag or container (use full-strength
household bleach to clean the inside of a plastic bag, rinse with DNA-free sterile water,
and dry; or use DNA-free tubes). Transfer the sample to the clean room lab.
Just inside the clean room lab, the external part of the storage receptacle will need to be
decontaminated (use a solution of 10
e
30% household bleach). By this point you will be
encased in protective gear and will remove the sample from the receptacle and prepare to
take your secondary sample. If you have sampled a bone, the first step is to decontaminate
the external surface. As per above, this can be done mechanically by physically removing
the outer layer as well as any trabeculae (trabecular bone is notoriously hard to clean and
decontaminate), followed by a rinse in 10
e
30% household bleach, followed by sterile,
DNA-free water. If you are dealing with a tooth, the tooth can be submerged in household
bleach for about ten minutes, then rinsed with sterile DNA-free water. You may decide to
use the entire tooth, or just a section of it.
Most ancient DNA protocols ask for between a quarter and one gram of sample in a typical
extraction (see for example
Rohland and Hofreiter, 2007
).
Please keep in mind that the intention here is to give very general indications for how to
conduct an analysis of degraded DNA. In practice, these steps are much more specific and
detailed. They also tend to be sample specific. You should consult optimized protocols for
extraction of degraded DNA, which can be found in the methods section of any published
paper on ancient or forensic DNA. The scientific journals
Forensic Science International,
Genetics
,
BioTechniques
, and
Electrophoresis
, to list some examples, tend to publish useful
methods articles on a regular basis. All protocols will tend to use some variation of the stan-
dard protocols that are either silica- or phenol-chloroform-based (or both), as mentioned
earlier in the chapter.
At this point you are ready to reduce your sample in preparation for DNA extraction (as
per earlier discussion).
What Kind of Questions can I Feasibly Address Using Degraded DNA?
In most analyses relying on degraded DNA, you will be dealing with small sample sizes,
meaning few individual specimens will yield any DNA at all, and for those that do, fragment
sizes will be very small. This means that sequence lengths will be short, and you may need to
further limit your analysis to very informative SNPs.
Despite its limitations, working with degraded DNA has a huge advantage: it enables the
access of
direct
information about individual and populational genetic variation, past or
present. Below we discuss some typical kinds of studies, all of which represent successful
examples of the utility of degraded DNA analysis for anthropology.
