[phylocom-user] Opposite results between Blomberg's K and phylogenetic signal in Phylocom (AOT)

K O humblebee at hotmail.co.jp
Thu Jan 16 17:21:53 PST 2014

I've been trying to test for significant phylogenetic conservatism in some plant traits. I used R-package picante (Blomberg's K) and AOT in Phylocom. So far these two methods yield completely opposite results for the same traits, and I'm confused. Is it possible to get such very contrasting outputs from these two methods? In both cases, I am assuming that all the branch lengths = 1.
For example, one trait shows Blomberg's K = 0.2892 (P = 0.001), suggesting that the evolution of this trait overall has not been greatly constrained by phylogenetic relatedness. In contrast, for the same trait AOT yields variance of standardized contrasts across tree = 0.006, significance of contrast variance relative to null model (low rank) = 1, and significance of contrast variance relative to null model (high rank) = 1000 (i.e., P = 0.002), suggesting that treewise phylogenetic conservatism is significantly greater than the expectations of random tip swapping. (if I am correctly understanding)
I've just started looking at these phylogenetic signals, so I may be overlooking something critical. I will greatly appreciate if you could kindly give me directions, thank you very much! 		 	   		  
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