 Padian &amp; Horner (2002) offer a coarse-grained example of how a metaphysical commitment overlaps with issues of phylogenetic inference in their defense of treating Aves as the sole living branch of dinosaurs. In this case, they identify “transformationist” thinking against typological thinking. In the former, the identity of taxa is associated with historical continuity, and untethered from the expression of any intrinsic characters. Thus, the transformation of ancient theropod dinosaurs into the the living clade of birds means that birds are dinosaurs, and that this ought to be reflected in our phylogenetic reconstructions. In contrast, they argue, a typological account will treat birds as distinct from dinosaurs, and risks a phylogenetic reconstruction that misrepresents the historical relationship of these taxa. Moreover, they argue that transformationist and typological approaches will differentially categorize features of avian and ancient theropods as evidence and data; what even counts as inferentially relevant is itself at stake. Padian and Horner, here, are identifying metaphysical commitments from phylogenetics to argue how paleontologists ought to reconstruct evolutionary history, what counts as evidence, and what kinds of evidence are important for drawing those inferences, i.e., how characters are coded is treated as a methodological dispute entailed by theoretical commitments. (See Haber 2016b in  Other Internet Resources  for further discussion.)