I need to reconstruct the nodal position of some fossil taxa on molecular tree with morphological data about extant species. My data have quite complex structure; categorical are multistate (sometimes contain ambiguities) moreover other are continuous. I want to ask if EPA implemented in RAxML:
1) Will deal with ambiguous states? In other sofrware I have often had a problem when trait encoded as e.g. "1/2" was reconstructed as a separate state.
2) Will deal with continuous data? Do they require categorization? I will have to that arbitrally, because there are no natural categories in some of traits (basing on analyses of their distribution).
Hi Jakub,
Unfortunately I am not able to answer your question directly, but I want to point out another caveat. The differences in tip dates between fossil and extant taxa need to be taken into account in such an analysis in order to get meaningful estimates of the evolutionary rates of each character, and in turn get reliable placements of the fossils. As far as I know RAxML can't handle tip dates, but dating softwares (BEAST) can. I am not sure how to analyse such complex datasets though, but you'll probably need to define different partitions that are analysed under different site models but under the same clock. You might want to check if BEAST2 can do that for you.
Cheers,
Thomas
Dear Jakub,
In the same way that you are including morphological data for extant species and coding those character, I would code those data for some fossil candidates that you believe in this moment to be basal. Test your assumption(s) on this. However, if a priority you know that you are dealing with some ambiguities, I suggest to omit them from your analysis.
With my best wishes.
Thank You for Your answers! I have dug through litearture and currently there is practically no way to deal with compund morphological data. Albeit polymorphisms can be simply encoded as dummy variables, there are completely different models for continuous and categorical data. I have decided to use Gower's dissimilarity index - just a simple phenetic but there is no other option if You are unwilling to categorize Your data.
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