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Cladistics/phenetics was Re: Mice given bat-like forelimbs through gene switch

AFAIK, the only application for phenetics these days is in morphological comparisons.

There are still a few people who consciously use neighbour-joining on molecular data... and there are lots of people who use it without knowing it. For example, the guide trees of ModelTest and Clustal are NJ trees.

As to whether molecular phylogenetic analyses qualify as "cladistic", I've heard differing points of view. I tend to limit the term "cladistic" to those analyses that use a parsimony-based approach (as morphology-based analyses do). But most molecular phylogenetic analyses tend to use statistics-based evolutionary models to analyze sequence data (e.g., maximum likelihood, Bayesian inference) rather than a parsimony-based approach.

IMHO that's just an extension of parsimony: we know that back-mutations all the way to saturation happen and can lead to long-branch attraction, so it's not parsimonious to ignore this fact. A few papers that use Bayesian analysis on morphological data (with a flat prior) have been published.

I don't want to get bogged down into a debate over whether Hennig came up with the concept of parsimony for assessing evolutionary relationships; but in any case the fact remains parsimony has become the foundation for cladistic analysis, and other approaches (e.g., maximum likelihood, Bayesian inference) are regarded as "non-Hennigian".

I've read that the term "cladistics" was invented by Mayr and was intended to be derogatory, like "Big Bang" by Sir Fred Hoyle. Hennig seems to have always called it "phylogenetic systematics" (he doesn't seem to have imagined doing phylogenetics for any other purpose than classification), though admittedly I've hardly read any of his work.