Origin: A Genetic History of the Americas

looking good.
Amplification and sequencing of mitochondrial fragments is a bit of an oldschool
way of studying ancient DNA. As I mentioned before, although
mitochondrial DNA can tell us a lot about a population, it does have some
limitations. When methods for reading the DNA sequences of complete
nuclear genomes—all 3 billion base pairs—became available, the ancient
DNA community quickly realized their potential. It took time to optimize
the DNA extraction methods for these approaches. Talented researchers
identified the skeletal elements that were likeliest to contain enough DNA
preserved for whole genome sequencing, which turned out to be teeth and a
small pyramid-shaped section of bone at the bottom of the skull that
contains the inner ear bones (called the petrous or rocklike portion, in
recognition of its density). Other researchers perfected the extraction
method that I used, allowing the smallest DNA fragments to be captured
and cleaned.
Having ascertained that there was ancient mitochondrial DNA preserved
in the tiny drops of liquid at the bottom of my tube, I was back in the lab a
few weeks later to make a genomic library. Sitting at the benchtop inside
the highest-pressure room, I slipped my arms into the hood and began to
carefully mix a small amount of my DNA extraction with water. Keeping
all the tubes inside a chilled rack to prevent the reaction from starting
before I was ready, I added a few drops of a buffer and a tiny amount of a
powerful (and outrageously expensive) solution and pipetted the solution a
few times to make sure it was completely mixed. I then placed the tube
inside the thermocycler we keep inside the ancient lab and pressed a few
buttons. After returning the reagents to the freezer, I settled back in my
chair to wait.
For the next 45 minutes or so, as I was absorbed in a podcast, the
machine slowly warmed the solution, first to room temperature and then to
a blisteringly hot 145°F (63°C). Inside the tube many millions of random
DNA fragments that had been extracted from the sample were having their
ends “repaired.” i Think of each tubeful of DNA as containing millions of
tiny little snippets of ribbons that you want to use for an art project, but they
have been chewed up by a rodent. Looking at the ribbons under a powerful