Unexpected grouping in the output tree of BEAST
I used BEAST to perform divergence time estimation. My ingroups consist of 46 taxa of fungi from several different phyla. My outgroups consist of 3 taxa of plants/animals. I have set the “Monophylogenetic” flag to my ingroup including all the 46 fungal taxa on the prior in the prior panles in BEAUti. Expectedly, in the output tree by BEAST, the three outgroup taxa grouped together to form a clade. However, the outgroup clade clustered somewhere within my ingroup taxa instead of clustering basal to my ingroup. Do you have any suggestions/solutions for an expected grouping in BEAST?
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