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Re: Prolacertiformes and Protorosauria

On May 19, 2009, at 7:27 PM, David Peters wrote:

The data set in question is 14x larger than any prior published data set covering the same taxonomic spectrum. With it I can reduce the dataset to the size of the smaller ones and often (not always) get their topology.

I'm not sure if you mean 14x by taxon number, character number, or the product of the two (i.e. total matrix size), but in any case, having a much larger matrix has its advantages. However, it is worth noting that increased taxon sampling does not necessarily provide a better answer - Scotland et al. (2003) discussed this property, and simulation tests have demonstrated this somewhat counter-intuitive result. That's not to say that you don't have an interesting result: you have shown an important taxon sampling effect. The question that remains is: what exactly about the inclusion sets is driving the topology changes? Can get some measure of confidence between the two? The larger set is more practically useful *if* the topology is stronger.

Adding taxa to see if the tree shifts has also been a good test of tree topology. At some point in the addition process, tree shifts become less and less possible because you're reaching a saturation point where the weight of the rest of the tree is becoming harder to shake.

That saturation effect is not altogether unexpected, and it is interesting - I'm not sure what it really says about topology confidence, though. I'd have to see some simulation results to have a better feel for the empirical ramifications. I do like the sensitivity analysis approach, though, for what that's worth. I'd be quite curious to hear what the theoretical phylogenetics crowd has to say about these effects.

If the lack of confidence and lack of resolution are the result of taxon exclusion, then PAUP offers a clue that some or all of those excluded taxa are better off included. All I've ever asked for is inclusion. If someone excludes pertinent and previously taxa to protect a precious hypothesis, then they're doing a disservice to their own studies.

If that is the reason for exclusion, I agree. But if an author excludes a taxon because they don't feel confident in coding it - it is fragmentary, or they have not had sufficient access to the specimen, for example - then it might be justified.

One reason is that it often happens that a taxon can occupy two equally parsimonious places in the tree, _no matter how robust the rest of the tree is_. (Especially when it's incompletely known and/ or there are just too few characters in the matrix.)

>>>>>> Should be right next to the same sister taxa, though. They're never widely separated (given the above parameters). Important distinction left unsaid. And this is due to the fact that some sisters are really different, or not much is known of one or the other or both.

They don't have to remain with the same sister taxon - it is quite plausible (and reasonably common) for a taxon to move substantially throughout the tree, without any change in total calculated parsimony (i.e. total tree length is constant).



Michael Habib, M.S. PhD. Candidate Center for Functional Anatomy and Evolution Johns Hopkins School of Medicine 1830 E. Monument Street Baltimore, MD 21205 (443) 280-0181 habib@jhmi.edu