Can I estimate recombination rate based on LD

Question

[wang.yiguan]

Hi, I am using some tools (VCTtools, or PopLDdecay) to calculate LD decay of drosophila, and I am thinking can I use the results of LD decay to estimate the recombination rate. (Knowing the recombination rate can help me do some simulations.) There seems some relationship between LD and recombination rate, but I am not sure. Thanks very much!

[natasha.sernova]

There was a paper about relationship between LD and recombination rate 15 years ago.

http://genomics.princeton.edu/AndolfattoLab/Publications_files/Andolfatto_Wall.pdf

It has 69 citations. Look at them.

https://scholar.google.ru/scholar?cites=8007281401593842176&as_sdt=2005&sciodt=0,5&hl=ru

For example, see this recent one:

http://www.genetics.org/content/genetics/early/2016/04/18/genetics.115.184002.full.pdf

Abstract fragment: "This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation."

They observed:

"Slow decay of linkage disequilibrium in the Zambian and Raleigh populations relative to neutral expectations"

"Elevation of haplotype homozygosity in the Zambian and Raleigh populations relative to neutral expectations" etc.