Clock rooting with strong rate shifts - or not

Today at our journal club we discussed Schmitt 2016, "Hennig, Ax, and present-day mainstream cladistics, on polarising characters", published in Peckiana 11: 35-42.

The point of the paper is that early phylogeneticists discussed various ways of figuring out character polarity (i.e. which character state is ancestral and which is derived) first and then using that inference to build a phylogeny, whereas today nearly everybody does the phylogeny building first and then uses outgroup rooting to polarise the resulting network and infer character polarity.

And... that's it, really. There does not appear to be any clear call to action, although one would have expected something on the lines of "and this is bad because...". The paper does end with an exhortation to use more morphological characters instead of only molecular data, and then there is language that may be meant to identify the author as a proponent of paraphyletic taxa without making it explicit (anagenesis!), but neither of those two conclusions appear to be to the point. There is no actual way forward regarding the question of how to polarise characters without outgroup rooting.

The approaches discussed in the paper are the following:

Palaeontological precedence. The character state appearing first in the fossil record is the ancestral one. The problem is, this only works if we assume that the fossil record is fairly complete.

Chorological progression. The character state found more frequently near the edges of a range is the derived one, whereas the ancestral state dominates at the centre of origin. Problem, this is circular because we first need to figure out where the centre of origin is. I am not too convinced of the principle either.

Ontological precedence. Because organisms cannot completely retool their developmental pathways but only change through (1) neoteny or (2) attaching steps to the end of the process, the earlier states in ontogeny are the ancestral ones. The author mentions the problem of a scarcity of ontological data; I might add that this shows a bit of a zoological bias, as it will rarely work in plants and presumably never in microorganisms.

Correlation of transformation series. I must admit I don't quite understand the logic here, and the author isn't very impressed by it either.

Comparison with the stem lineage of the study group. The state found in the ancestral lineage is ancestral. This if very obviously circular, because we would need to know the phylogeny first, and being able to infer that was the whole point of polarising the character.

Ingroup comparison. The state that is more frequent in the study group is ancestral. I see no reason to assume that this is always true, as there can be shifts in diversification rates.

Finally, outgroup comparison. The state that is found in the closest relative(s) of the study group is ancestral in the study group. It is perhaps not totally correct to call this circular, but it has something of turtles all the way down: to find out what the closest relative of your study group is you need to polarise the larger group around it, and then you have the same problem. Still this is the most broadly useful of all these approaches.

Polarising a phylogeny and polarising characters are two sides of the same coin. I have written a thorough post on the former before, which regularly seems to be found by quite a few people doing Google searches. I hope it is still useful. One of the ways I mentioned there for giving the stack of turtles something to stand on is clock rooting, and I found it surprising that the present paper did not mention it at all. It was this, however, that our journal club discussion dwelt on for quite some time.

Admittedly said discussion was a bit meandering, but here are a few thoughts:

The big problem with clock rooting is that it will be thrown off if there are strong rate shifts. Imagine that the true phylogram consists of two sister groups, one with very long branches (short-lived organisms) and the other with very short branches (their long-lived relatives). If we apply a molecular clock model to the phylogenetic analysis, e.g. in MrBayes, it will try to root the tree so that the branches all end at about the same level, the present. The obvious way to do it is to root the tree within the long-branch group. Eh voilà, it has rooted incorrectly.

What to do about this?

The first suggestion was to use an outgroup. In my admittedly limited experience that doesn't work so well. It seems that if the rate shift is strong enough the analysis will simply attach the outgroup to the ingroup in the wrong place.

The next idea was to use a very relaxed clock model, in particular the random local clock model available in BEAST (unfortunately not in MrBayes). But then it was called nice in theory but said to make it hard to achieve stationarity of the MCMC run. I cannot say.

Nick Matzke suggested that a better model could be developed. The hope is that this would allow the analysis to figure out what is going on, recognise the rate shift in the right place, and then root correctly. It would have to be seen how that would work, but at the moment something like that does not appear to be available.

Finally, another colleague said that if the clock models don't work then simply don't use them. Well, but what if we need a time-calibrated phylogeny, a chronogram, to do our downstream analyses, as in biogeographic modelling, studies of diversification rates, or divergence time estimates?

I guess the only way I can think of at the moment is to infer a phylogram whose rooting we trust and then turn it into a chronogram while maintaining topology, as with the software r8s. Maybe there are other ways around the rooting issue with clock models, but I am not ware of them.