Welcome to the Glycine web*


* Actually a page about LASER analyses of Glycine R-gene LTT plots

Comments work like this...

Go get a gmail address, if you don't have one already, so we can share files on Google docs. This will allow each of us to made changes to the file that will be visible to everyone. You can also see the file list on iGoogle if you add the Google docs box to your iGoogle front page.

-- BernardPfeil - 17 Oct 2008

I've added some files on Google docs. Here is a brief description of what's in them:

"Bayes trees ..." text file

- file for Richard to run through LASER

"LASER commands ..." doc

- here is where we put down what each analysis is doing, and the commands in LASER that get us there. Eventually we should be able to cut this down and dump it into a methods section (or supp info) and also use later a reference document to do similar things with other data.

"gamma histograms ..." excel file

- a chart of histograms of the gamma statistic generated in LASER from several sets of trees. These trees come from Phyl-o-gen simulations using the following parameters:

(1) null - b=0.2 d=0.1 with a polyploid event added at ntaxa=30 to ntaxa=45 using b=200 d=0. This was designed to incorporate what we know about the polyploid duplication and see if a constant b and d rate would give an LTT plot similar to the observed RGA LTT plot

(2) 0.12 death rate after polyploidy increased to 0.12

(3) 0.14 death rate " " increased to 0.14

(4) 0.16 as above

(5) 0.18 as above

The increased death rates were to see if greater extinction following polyploidy would make the LTT plots look more like the observed RGA plot. With polyploidy alone, there is a marked step up in the LTT plots not really seen in the observed RGA plot. We had a hard time trying to get a sensible integration of LTT plots over many trees so we are using the gamma statistic instead and looking over representative LTT plots (ones with the polyploid duplication at roughly the same time as the real data).

-- BernardPfeil - 24 Oct 2008

Glycine Web Utilities