Phylonet in 2018

In 2007 Agnar Helgason published a paper which I found to be just brilliant. He was combining known damage patterns in ancient DNA with phylogenetic networking to authenticate ancient DNA. This was actually the first time I had seen that been done in any useful way. The idea is that if you have enough data from the same DNA fragment and individual, you should be able to detect an ancient sequence and separate it from contaminants. And with the NGS on the way in, this came at just the right time. For a few years I used the technique a lot.

Flying over Texas


Now, a decade later, the way we authenticate ancient DNA have developed. It is still based on Agnars old idea, that damage patterns is the best marker. But it is used in a slightly different way now. But I got a possibility to re-visit the old “Phylonet” techniques today (Phylonet was the software Agnar developed to the technique). As I am spending a few days in Texas with Anna Linderholm, writing up stuff based on data she produced a long time ago, using techniques that were cutting edge a long time ago, Phylonet was all of a sudden relevant to us again. And while adding it to the manuscript today, I was wondering if this is going to be the last time I cite the software which I still think was such an important step forward for this field when it was published.

Anna working on our (mostly her though) old dataset