# [Taxacom] Likelihoodism versus probabilism

Richard Zander Richard.Zander at mobot.org
Wed Oct 7 17:29:34 CDT 2020

```Are you, as a systematist, a likelihoodist or a probabilist? Here is a test:

Q.: What does the support measure of 1.00 BPP mean in a molecular cladogram?

A.: A probabilist would say it means that exactly that molecular cladogram represents what happened in nature because there is no evidence of support for any other cladogram. In other words, it is statistically certain that the probability distribution is entirely taken up by the chance of that cladogram modeling what happened in past evolution.

A likelihoodist would say that exactly that molecular cladogram is most likely to have generated that molecular data. And that considering a probability distribution of the chance of other cladograms generating that data is irrelevant.

The probabilist is wrong, having not been alert to a major shift in systematics.

A very simple example of using MCMC Bayesian methods (which involve likelihood ratios) is as follows.

Consider a die of six sides, which is weighted such that one side comes up more often than any of the other sides. Roll the die, which is like Monte Carlo sampling. Keep track of how often each side comes up. Discard, as you roll the die, any data on the sides that come up if lower than the data on the side that comes up most often. The data converge on the side that comes up most often. The data converge on the "truth" of the side of maximum likelihood. If done a large number of times, the Bayesian Posterior Probability of 1.00 is given that side. This does not tell you how often that side came up out of all those rolls of the die. It could be anywhere from almost all the time or only a little bit more than 1/6 of the time. This is why molecular cladograms may have all the branches supported at 1.00 BPP.

Molecular systematists are likelihoodists. The actual probability that a molecular cladogram with branches all of 1.00 BPP does represent what actually happened in nature is almost certainly near zero. The actual probability that a 1.00 BPP three-taxon split (two branches more closely related than a third) is "correct" as opposed to a simple nearest-neighbor interchange (switch one branch of a sister group with the next lowest branch) may not be much more than 50:50

By "correct" a probabilist means the hypothesis which probably happened in nature given the fact that all possible hypotheses do probabilistically explain the data, not what the likelihoodist means by "correct," which is that the one cladogram is definitely the best hypothesis that explains the data in spite of the chances that other hypotheses are also possible.

Likelihoodists say we systematists are all likelihoodists now.  Are we? Did you take the test? I think it should be intolerable that classification changes be based on likelihood and optimality alone. Likelihood and MCMC Bayesian analysis should never be used as a basis on which to make changes in classifications given the low probability that the results are retrodictions of the evolutionary past.

Am I right? I hope Taxacom probabilists and likelihoodists might weigh in on this problem, which I think is a fundamental difficulty with modern systematics.

[For more info, Wikipedia has good treatments of likelihood, and literature by A.F.W. Edwards, the phylogeneticist who popularized likelihood as a replacement for probability, is available on the Web, as are additional criticisms. Likelihood ratios and the similar Bayes factors have utility when there are only two hypotheses or when the number of possible hypotheses is unknown. Log likelihoods are added in likelihood analyses just as Shannon informational bits are added in macroevolutionary analysis, but the similarity in dealing with trait differentials ends there.]

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Richard H. Zander
Missouri Botanical Garden - 4344 Shaw Blvd. - St. Louis - Missouri - 63110 - USA
richard.zander at mobot.org<mailto:richard.zander at mobot.org> Ofc: +1 314 577-0276