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Equation 26 · Part 1 · Evolutionary Biology and Ecology in Practice: An Advanced Technical Guide

Symbol N_e

NeN_e
NeN_e

What this part means

the downward in inferred.

Its job in the formula

NeN_e is a part of this expression. Its role is fixed by the surrounding article and by the operations shown in the formula.

Where the article explains it

Physically linked loci must be excluded or flagged , because the method’s entire logic depends on treating background disequilibrium as drift-generated between unlinked loci; loci close together on the same chromosome carry disequilibrium from physical linkage that has nothing to do with NeN_e and will bias the estimate upward in apparent LD, downward in inferred NeN_e .

The passage around this formula

…pairs of loci observed in the sample, and S is the sample size, with the 1/S term correcting for the sampling bias that a finite number of genotyped individuals introduces into r^2\hat{r}^2 even when the true population NeN_e is large. The practical consequence practitioners have to internalize: r^2\hat{r}^2 is estimated with noise from a finite sample, and that noise itself creates apparent linkage disequilibrium indistinguishable from drift-generated LD unless it is explicitly subtracted — which is exactly what the…

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