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AIC-c as a measure of recombination rate? (Read 1571 times)
michiel
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AIC-c as a measure of recombination rate?
May 22nd, 2011 at 6:14am
 
Dear fellow datamonkeys,

I am looking for a method that quantifies recombination rate in my many single gene alignments (I am not interested in specific breakpoints etc). Could I plot the AIC-c score as a proxy for recombination rate?

Many thanks for any suggestions you might have!

Best Wishes, Michiel
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Sergei
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Re: AIC-c as a measure of recombination rate?
Reply #1 - May 23rd, 2011 at 10:48am
 
Hi Michiel,

Unfortunately, AIC-c would not be useful as a quantifiable measure of recombination rate because it conflates the size of the recombination effect (rate) with evolutionary change (divergence) -- and some other effects as well.

Sergei
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michiel
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Re: AIC-c as a measure of recombination rate?
Reply #2 - May 23rd, 2011 at 12:40pm
 
Dear Sergei,

thank you for your rapid reply. I suspected an effect of divergence (more polymorphisms > more power to detect recombination). However, since I have a large datset, perhaps I could statistically correct for this effect (e.g. using an ANCOVA)? Or is there something I am overlooking?

Best Wishes, Michiel
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