Friday, January 28, 2011
Do they even understand the matrix they're coding?
You may remember my prior criticism of Hone and Benton (2008), who merged matrices when examining pterosaur relationships, but didn't combine equivalent OTUs. They had both Lepidosauromorpha AND the lepidosauromorphs Gephyrosaurus, Sphenodontia and Squamata. And they had both Choristodera AND the choristoderes Lazarussuchus, Cteniogenys and Champsosaurus. Disturbingly, each more inclusive OTU did not clade with its exemplars in their trees.
Well now we have another example of using matrices without taking equivalent OTUs into account. Yates (2004) had a sauropodomorph matrix where he tried two sets of outgroups. One was Herrerasaurus and (Neo)Theropoda, another was Ornithischia and an expanded Theropoda including Herrerasaurus. In the recent description of Chuxiongosaurus, Lu et al. (2010) used Yates' matrix but just ran the whole thing without noticing this. Thus we have a cladogram with "Neotheropoda" sister to "Theropods"... :| Herrerasaurus is the outgroup, probably because it is listed first in Yates' matrix, and Lu et al. didn't realize PAUP makes the first listed OTU the outgroup automatically. Thus Ornithischia (which really should be the outgroup) is sister to the double-theropod clade. What makes it especially sad is even if Lu et al. didn't read Yates' text, Yates labels the OTUs "Herrerasaurus ischigualastensis", "Theropoda (excluding Herrerasaurus)" and "Theropoda (including Herrerasaurus)" in his matrix. How can you copy codings from that and not realize those aren't all independant taxa?!
As an aside, I'd like to see Chuxiongosaurus compared to Yunnanosaurus and Jingshanosaurus. Thanks to Brad McFeeters for alerting me to this mess.
Coming soon, more Zhao taxa and part 2 of my recommended theropod clade definitions.
References- Hone and Benton, 2008. Contrasting supertree and total-evidence methods: the origin of the pterosaurs. Zitteliana. 28, 35-60.
Lu, Kobayashi, Li and Zhong, 2010. A new basal sauropod dinosaur from the Lufeng Basin, Yunnan Province, Southwestern China. Acta Geologica Sinica. 84(6), 1336-1342.Yates, 2004. Anchisaurus polyzelus (Hitchcock): The smallest known sauropod dinosaur and the evolution of gigantism among sauropodomorph dinosaurs. Postilla. 230, 58 pp.