I can do quote mining too. The difference is that this quote isn't out of
context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
is attempting to cast doubt on the efficacy of molecular systematics, by
pointing out how silly some of the results are:

"Even when different molecules can be combined to give a single tree, the
result is often bizare: A 1996 study using 88 protein sequences grouped
rabbits with primates instead of rodents; a 1998 analysis of 13 genes in
19 animal species placed sea urchins among the chordates; and another 1998
study based on 12 proteins put cows closer to whales than to horses."

Of course the last example is the funniest, given the wealth of molecular
and fossil data showing that cows and whales are indeed related.

See:

Gatesy, J., P. O'Grady, and R. H. Baker. 1999. Corroboration among data
sets in simultaneous analysis: Hidden support for phylogenetic
relationships among higher level artiodactyl taxa. Cladistics 15:271-313.

Matthee, C. A., J. D. Burzlaff, J. F. Taylor, and S. K. Davis. 2001.
Mining the mammalian genome for artiodactyl systematics. Syst. Biol.
50:367-390.

Naylor, G. J. P., and D. C. Adams. 2001. Are the fossil data really at
odds with the molecular data? Morphological evidence for Cetartiodactyla
phylogeny reexamined. Syst. Biol. 50:444-453.

Gingerich, P. D., M. ul Haq, I. S. Zalmout, I. H. Khan, and M. S. Malkani.
2001. Origin of whales from early artiodactyls: Hands and feet of Eocene
Protocetidae from Pakistan. Science 293:2239-2242.

and older references therein.

Of the other two examples, the first (rabbits) is a real example of
improper results arising from poor methodology, which I will gladly
explain to anyone who asks. The second, though, just like the whale-cow
example, is correct; the study didn't find sea urchins to be nested within
chordates, it found them to be the sister group of chordates, which of
course they are.

Wells read a lot of the primary literature for his book, but not enough.
He was just quote-mining on a large scale, and didn't grab enough context
to realize the cow-whale claim wasn't bizarre, even in 1998.

For the record, Wells was citing these:

Graur, D., L. Duret, and M. Gouy. 1996. Phylogenetic position of the order
Lagomorpha (rabbits, hares and allies). Nature 379:333-335.

Naylor, G. J. P., and W. M. Brown. 1998. Amphioxus mitochondrial DNA,
chordate phylogeny, and the limits of inference based on comparisons of
sequences. Systematic Biology 47:61-76.

Cao, Y., A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N.
Okada, S. Paabo, and M. Hasegawa. 1998. Conflict among individual
mitochondrial proteins in resolving the phylogeny of eutherian orders.
Journal of Molecular Evolution 47:307-322.

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