Paper developing a new approach to phylogenetic tree shape


#1

If any of you are interested in phylogenetic tree shape, this paper takes an actually new approach as compared to more formulas:

I think it’s pretty neat!


#2

Indeed. Pretty neat. Quantifying tree shape is a good thing. However, I’m inclined to believe that effective population size already does a pretty good job of this. Generally, ladder-like trees have low Ne and star-like trees have high Ne. Quantifying Ne in this fashion corrects for temporal sampling patterns (you’ll get a star-like tree for flu if you just sample one season). In figure 5, we could go left-to-right from HIV to dengue to flu with decreasing Ne. Additionally, Ne has an advantage of being more readily interpretable than this kernel measure.

However, I could be convinced that this kernel metric adds something Ne does not (like clade clustering). But I think comparing it to tree imbalance statistics is a poor choice.


#3

I like your argument for Ne. However, I was thinking about multivariate collections of tree statistics, which this gives and effective population size does not. This was something I thought about during my PhD.


#4

Interesting. I absolutely agree that Ne doesn’t cover everything. At the minimum you’d need something like Tajima’s D to quantify departure of intervals from coalescent expectation and tree imbalance. Probably others as well (maybe clade structure). The Poon et al. analysis is cool, I just didn’t like Ne being ignored when discussing ladder-like and star-like trees.


#5

A true population geneticist. Just throw Ne and D into the station wagon and head for the beach!