Sometimes DNA and RNA provide great insight into phylogenetic relationships.
Other times… not so much.
Ultimately molecule analyses have to be supported by morphological studies that enable us to see the gradual accumulation of traits in lineages. If we can’t see those gradual evolutionary changes, then we must assume there are agents in the DNA that are obfuscating relationships, rather than illuminating relationships.
Two cases in point:
Hedges & Poling (1999) argued that Sphenodon was more closely related to archosaurs than to squamates. This would require independent acquisition of a wide range of specialized features and takes no account of the fossil histories of the groups in question, according to Evans (2003).
Wiens et al., (2012) produced a molecule study of extant taxa that rearranged prior squamate trees, nesting Dibamus and gekkos at the base while nesting Anguimorpha and Iguania as derived sister clades. For those who don’t know Dibamus too well, it has no legs and a very odd skull morphology. In the large reptile tree it nests with other legless scincomorphs, with which it shares a long list of character traits.
Unfortunately these DNA studies, like ALL DNA studies, ignore fossil taxa.
But we need them.
Not sure where to draw the line. Be careful out there.
Evans SE 2003. At the feet of the dinosaurs: the early history and radiation of lizards. Biological Reviews 78:513–551.
Hedges SB and Poling LL 1999. A molecular phylogeny of reptiles. Science 283, 998–1001.
Wiens JJ, et al. 2012. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters. 2012 8, doi: 10.1098/rsbl.2012.0703.