This isn't the topic I brought up last week, but it will sound like the same discussion.
So, it strikes me that despite all the extrinsic vs. intrinsic noise made by several of the papers we read this week, what we'd really like to do is test such hypotheses using a tree-painting approach, like in the multi-OU, multi-BM type models that we explored earlier in the class. Why can't we take a tree, paint a scenario of extrinsic increase of diversification (say, increase speciation due to the formation of a large island archipelago) with two clades having their own intrinsic key innovations that further boosts their diversification, use maximum likelihood to estimate the diversification factors and BANG get our AICc and AIC-W values and actually say to ourselves based on the best fitting model "Gee, looks like the breakup of Pangaea was pretty important (x1.5 speciation rate), but developing specialized leaves seems to have greatly decreased clade A's extinction rate (x0.001 extinction rate)."
Isn't that really what we should want?
Obviously, this would require a heck of tree, with a number of fossil lineages on it, particularly as I think we SHOULD ask questions about how speciation and extinction rate changes over time. But it seems like that's where the field will be heading now anyway.
Or maybe I'm obsessed with pipe dreams.
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