Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

Genomic datasets generated by next-generation sequencing are increasingly
prevalent in phylogenetics, but morphological data are required to
phylogenetically place fossils, corroborate molecular hypotheses, and date
phylogenies. Combined-evidence analyses provide an integrative assessment
of tree topology. However, no attempt has been made to simultaneously
analyze next-generation genomic datasets and morphological data, and the
future of morphology in the context of genomic data is uncertain. I
conducted combined-evidence analyses that include genomic and
morphological datasets, specifically, with ultraconserved elements and two
morphological matrices. In unweighted maximum likelihood and Bayesian
combined-evidence analyses, morphological signal was dwarfed by the
ultraconserved elements, and some node support values were reduced
relative to ultraconserved element-only analyses. Increasing the weight of
morphological characters allowed those data to influence the tree, but
weighting subjectivity should be considered in future analyses. More
attempts should be made to simultaneously analyze genomic and
morphological datasets.