Phylogenetic analyses are inconsistent (Talk.Origins)

Claim CB821:

Modern versions of the phylogenetic "tree of life" are based on DNA and other molecular analyses. Inconsistent and bizarre results based on different molecular analyses "have now plunged molecular phylogeny into a crisis" (Wells 2000, 51).

Source:
 * Wells, Jonathan, 2000. Icons of Evolution, Washington DC: Regnery Publishing Inc., pp. 49-54.

CreationWiki response:

Nice theory, but Wells's entire point is that such cases are not rare but rather make up the general pattern of results.

Except for the fact that Wells offers several references showing that the larger the number of genes or molecules, the bigger the problem.

Wells clearly deals with this as well. It turns out that their frequency and statistics eliminate methodological and interpretive mistakes as a general explanation.

While this is theoretically possible, Wells does not do this. Yes, he cites a few examples, but they are intended only as illustrations.

Wells's case rests on more than just a few examples, and those he used were just illustrations. Given the fact that theories tend to change from time to time, it is likely that some previous inconsistencies will become consistent.

Sea urchins may be grouped in a broader category with chordates, but they are still not chordates, though some genetic similarities suggest that they are. Talk Origins is grasping at straws here.

Talk Origins gives absolutely no basis for cows being closer to whales than to horses. What evidence are they referring to?

The claim that morphological evidence puts a cow closer to a whale than a horse is absurd, to say the least. There are clearly far more morphological differences between a cow and a whale than a cow and a horse.