Accuracy of morphology-based phylogenetic fossil placement under maximum likelihood

Abstract—The capability to conduct Maximum Likelihood based phylogenetic (evolutionary) analyses on datasets that con-tain both morphological, as well as molecular data partitions with programs such as RAxML, gives rise to new methodological questions. As we demonstrate on 5 real world datasets that comprise morphological as well as DNA data the trees inferred by separately using the morphological or molecular data partitions are highly incongruent. Since in typical current-day phyloge-nomic alignments, there is significantly more molecular than morphological data available, and hence the final tree shape in a concatenated analysis is dominated by molecular data, the question arises how morphological data can be used within this context. One important application lies in the phylogenetic placement of fossil taxa (for which only morphological data is available) into a fixed, given molecular or otherwise well