Has Molecular Data Replaced Morphological Data in Phylogeny Reconstruction

The phylogenetic positioning of taxa within a tree has long been of interest to systematicists such that the evolutionary history of life can be studied. However, due to the timescales involved, direct observation of this phenomenon is not possible and as such, evolutionary history must be inferred from observable characters. Traditionally, morphological features have been used to invoke ancestral and present relationships existent between taxa, but with recent technological advantages in genomics, more weight is being given to molecular data. So, the question arises as to whether this novel method is superior in the results yielded and regarding whether it can potentially replace traditional methods completely.
Morphology has provided the primary source of data throughout the historical study of phylogenetics and has yielded the majority of the trees that are used today. It is rare in the literature to find examples where molecular studies have completely usurped the original tree, albeit examples are found to exist. This suggests a high degree of congruence between the two applied methods which implies that neither can be considered significantly superior. …