Hi Liam, Thanks for getting back to me. You are correct with #2- I have many bifurcations close to the present. The reason for this is that I am comparing between two different habitats of 21 different species. So, essentially, for each species, there are 2 tips (with branch lengths of 0)- 1 for each habitat (lentic and lotic). So, from what you are saying, I can't use the K statistic. Do you (or anyone else on this list) have an idea on a better way to test for phylogenetic significance on a tree where comparisons are made within species (between different habitats) as well as between species? Thank you for your thoughts.
-Daniel > Hi Daniel. > > I can think of two possibilities: > > 1) This is an error. > > 2) Your tree has an extremely unusual shape (for instance, it has many > bifurcations very close to the present day). > > On constant rate Yule trees, substituting 1s for the true branch lengths > does not (on average) bias K in any particular direction. > > If you share your tree and data I would be happy to look at the issue > more closely. > > All the best, Liam > > -- > Liam J. Revell > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > On 1/19/2012 9:53 PM, dwe...@life.illinois.edu wrote: >> Hi, >> I'm using the Picante package in R to calculate the Blomberg K. I'm >> trying to test for a phylogenetic signal in my data. I'm using a >> dataset with the PC score for 21 different species on a tree with >> varying branch lengths. I did this using the code here: >> http://bodegaphylo.wikispot.org/IV._Testing_Phylogenetic_Signal_in_R >> >> I got a K statistic of 0.0006457603 and yet the resultant >> PIC.variance.P >> is 0.001. If I'm correct, the PIC.variance.P is the p-value and >> significant at 0.05. Is that correct? >> I then decided to play with my data and set all branch lengths equal >> to >> 1 to see how that would affect things. I got a K statistic of 2.921763 >> and a PIC.variance.P value of 0.001. My understanding is that K >> statistics close to 0 are not significant and become significant close >> to and above 1. >> I'm confused why I got a significant p-value for both K statistics, >> even >> though one is very close to 0 (0.00065) and the other is above 2. I >> would appreciate any help in explaining Picante and the K statistic. >> Thank you. >> >> >> >> >> -Daniel >> >> ----><((((º> -----><((((º> ----><((((º> ----><((((º> ----><((((º> >> ---- >> >> Daniel P Welsh >> PhD Candidate >> Teaching Assistant >> Department of Animal Biology >> University of Illinois at Urbana-Champaign >> 202 Shelford Vivarium >> 606 E. Healey Street >> Champaign, IL 61821 >> lab phone: (217) 333-5323 >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > ---- ><((((º> ----- ><((((º> ---- ><((((º> ---- ><((((º> ---- ><((((º> ---- Daniel P Welsh PhD Candidate Teaching Assistant Department of Animal Biology University of Illinois at Urbana-Champaign 202 Shelford Vivarium 606 E. Healey Street Champaign, IL 61821 lab phone: (217) 333-5323 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
