Hi Luke,

This is going a bit off-topic, but BEAST2 can definitely work with
multistate characters. I think you need to manually edit the XML file,



2018-02-09 16:05 GMT+01:00 Matthews, Luke <lmatt...@rand.org>:

> This is a reply to the message copied below from Roland Sookias
> Hi Roland,
> This depends slightly on the structure of the data. If you have crocodile
> tails with a set of discrete shape states in the same anatomical part, then
> I would recommend coding it as a multistate characteristic. MrBayes
> provides pretty flexible coding for multi-state characters, and I think
> will handle up to at least 10 states in a single character. There might be
> an implementation in R now that is equivalent but I haven't done this in
> while. Anyone else want to weigh in about an R implementation for
> multistate characters?
> If you really have more than 10 states for a single character I'd be
> concerned about whether multiple observers can consistently code those
> states anyway.
> If instead you have truly inapplicable characters, for example crocodiles
> without tails, and then ones with tails with various shapes, then I think
> the best approach is to have two characters. A presense/absence character
> and a shape character.
> You also can binarize every state as separate characters, but as you say
> it introduces an implicit homology among qualitatively different absence
> states. I've never liked this approach, but there are some articles
> defending it. I think it's validity may depend on a relatively even
> frequency distribution of each state. Also, if you have other anatomical
> parts in the analysis, then you are effectively weighting more heavily
> those parts that you split into more binary characters - they will tend to
> drive the result. Some software allow you to explicitly correct character
> weights so that would solve this, but not all software provide that. Note -
> this binarizing by state is a common approach in phylogeny of language
> cognates - but I believe that has come about because of a tail wagging the
> dog problem. BEAST, unless they changed it recently, didn't support
> multistate character evolution and the language phylo people use BEAST not
> MrBayes.
> There are a bunch of articles about this issue but I'd have to go dig them
> up. I think I cited them in some of my earlier papers that did anatomical
> and cultural phylogenetic work.
> Luke
> Message: 1
> Date: Thu, 8 Feb 2018 17:27:54 +0100
> From: Roland Sookias <r.sook...@gmail.com>
> To: r-sig-phylo@r-project.org
> Subject: [R-sig-phylo] Not inferring homology within "absence" state
>         in phylogenetic analysis
> Message-ID:
>         <CA+PBJbmF2-_VE=4HuXZ610kh_Dtm2i4hK7CZkcfza2yN=1UrOg@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>  Dear all
> Maybe someone has some insight here...
> I am coming up against the problem, when it comes to phylogenetic analysis.
> Basically I want to conduct a parsimony (or other phylogenetic) analysis
> where "inapplicable" scores are treated as separate states *for each taxon*
> .
> I.e. I want to hypothesize shared ancestry for taxa scored with one state
> (let's say state 0), but not hypothesize shared ancestry for the other
> taxa. However, I still want to penalize a change in state from and to state
> 0.
> There are three approaches which I have thought about, but none seems to
> fit the bill:
> -Score all taxa not showing state 0 as separate states. This should do
> what I want, but the problem here is the limit on the number of states in
> most programmes.
> -Scoring binary presence/absence. The problem is here that it could end up
> being parsimonious to group the "absence" state together, when there is no
> reason to infer homology within (i.e. for taxa scored with) this state.
> -Score as 0 and inapplicable. The problem is this does not penalize a
> change from 0 to inapplicable.
> A real life example, is the shape of the ilium in crocodiles. I want to
> say that it is likely that a particular curve in the dorsal margin of the
> ilium in crocodile-line crocodilians is homologous, but I don't want to
> hypothesize homology of those taxa "lacking" this state. They are all
> equally far from each other.
> Thanks very much indeed
> Best
> Roland Sookias
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