UPGMA starting tree not compatible with topological constraints (?)

[Ingo Michalak]

In set up my xml file with Beauti 1.8.3 to start the analysis from a UPGMA tree. The anlysis fails because a specified taxon does not appear in the starting tree. What am I missing (code snippets below)? 

<!-- Construct a starting tree that is compatible with specified clade heights-->

<rescaledTree id="startingTree" height="50.0">

<!-- Construct a rough-and-ready UPGMA tree as an starting tree              -->

<upgmaTree>

<distanceMatrix correction="JC">

<patterns>

<!-- To generate UPGMA starting tree, only use the 1st aligment, which may be 1 of many aligments using this tree.-->

<alignment idref="alignment1"/>

</patterns>

</distanceMatrix>

</upgmaTree>

<clade>

<taxa idref="taxA"/>

</clade>

<clade>

<taxa idref="taxB"/>

</clade>

<clade>

<taxa idref="taxC"/>

</clade>

<clade>

<taxa idref="taxD"/>

</clade>

</rescaledTree>

and

<!-- Taxon Sets                                                              -->

<tmrcaStatistic id="tmrca(taxA)" includeStem="false">

<mrca>

<taxa idref="taxA"/>

</mrca>

<treeModel idref="treeModel"/>

</tmrcaStatistic>

<monophylyStatistic id="monophyly(taxA)">

<mrca>

<taxa idref="taxA"/>

</mrca>

<treeModel idref="treeModel"/>

</monophylyStatistic>

<tmrcaStatistic id="tmrca(taxB)" includeStem="false">

<mrca>

<taxa idref="taxB"/>

</mrca>

<treeModel idref="treeModel"/>

</tmrcaStatistic>

<monophylyStatistic id="monophyly(taxB)">

<mrca>

<taxa idref="taxB"/>

</mrca>

<treeModel idref="treeModel"/>

</monophylyStatistic>

<tmrcaStatistic id="tmrca(taxC)" includeStem="false">

<mrca>

<taxa idref="taxC"/>

</mrca>

<treeModel idref="treeModel"/>

</tmrcaStatistic>

<monophylyStatistic id="monophyly(taxC)">

<mrca>

<taxa idref="taxC"/>

</mrca>

<treeModel idref="treeModel"/>

</monophylyStatistic>

<tmrcaStatistic id="tmrca(taxD)" includeStem="false">

<mrca>

<taxa idref="taxD"/>

</mrca>

<treeModel idref="treeModel"/>

</tmrcaStatistic>

<monophylyStatistic id="monophyly(taxD)">

<mrca>

<taxa idref="taxD"/>

</mrca>

<treeModel idref="treeModel"/>

</monophylyStatistic>

when I run the file in BEAST 1.8.3 I get:

Creating Jukes-Cantor distance matrix

dr.xml.XMLParseException: Error parsing '<rescaledTree>' element with id, 'startingTree':

Clade defined by taxon Set, taxA, is not found in the guide tree

at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

Feb 17, 2016 5:28:45 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, TetrOUT_1.xml:

Error parsing '<rescaledTree>' element with id, 'startingTree':

Clade defined by taxon Set, taxA, is not found in the guide tree

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

What did I do wrong (given I set this all up in BEAUTi) and what can I improve in the xml manually? The respective online tutorials seem to be down...

Thanks

[Bárbara Leal]

Hi Ingo,

I know it's been a while... but, did you find a solution? I'm facing the same problem.

Thanks in advance for any tips!

Bárbara