From RonO@21:1/5 to All on Tue Jan 24 06:21:18 2023
There were several talks on ancient DNA at this years Plant Animal
Genome meeting. One Plenary talk was on the recent ancient DNA from
Greenland, and how they were proceeding with the work. They can get
some usuable DNA directly out of the sediments, but there isn't very
much of it that they are interested in. Most of it is microbial DNA, so
they have to do a lot of sequencing before they find enough bits to
identify any specific species of plant or animal that may have lived at
that time. So what they do is make probe arrays that capture the DNA
that they want. The issue with this is that you need to make the probe
DNA similar enough to what you want to identify that it hybridizes with
your probe above random sequence. You need to have some idea of what
you expect to find and make probes for that DNA to hybridize with and
get pulled out of the mess of unwanted DNA. These fragments of DNA are
only around 70 base-pairs long, so the probes have to be fairly
specific. If you use some conserved sequence you can mostly expect a
lot of the same conserved sequence unless there are polymorphisms
flanking the conserved sequence that are informative.
She put up something that she called a "smile" graphic that showed that
there were more cytosine deaminations in the ancient DNA than
contaminating modern human DNA at the ends of the DNA fragments.
Cytosine deamination spontaneously occurs more often in single stranded
DNA and that is more often found at the ends of her short ancient DNA fragments. So she claimed that it put a smile on her face when she saw
the "smile" created by having more cytosine deaminations at the ends of
the fragments that they were sequencing.