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We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++

We used ANGSD to calculate Thetas and Tajima D neutrality tests and one of the thetas was a pairwise theta, however I am unsure what this means and how it differs from Tajima's D?

http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests

We then divided the tP over length of each exon to find genetic diversity in the exon level. However, as I am very interested in statistics, if someone could explain what the tP statistic means exactly it would be highly appreciated.

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While I can't explain it to you directly, you might check out the section on theta estimators in Korneliussen et al. (2013) which is cited on the above ANGSD wiki page. The equation for this estimator in this paper traces back to the original Tajima (1989).

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I don't know Theta but Tajima D is a population genetics test that assumes constant sample size. When the number of segregating sites (non-conservative sites in an alignment) significantly differs from pi (Nei's p-distance between a pair of sequence) one possibility is selection given a constant population size.

What Tajima found was cool: under neutrality this relationship conforms to a beta distribution. Just to explain that again so the nucleotide differences between every pair of sequences in an alignment (pi) against the total number of possible mutations conforms to a beta distribution for a constant population size under neutrality.

Its a cool idea - like really cool - but the violations - any level of 'extinction' will skew the distribution, population movement and importantly so could a bias in sampling.

So what you get is a pair-wise matrix at 5% critical probability. If your data entirely conformed to Tajima's D it would be an amazing result, but that is not the result you are looking for. So if Tajima D gave a particular pair <0.05 AND it was supported by other tests THEN (sounds like code) it provides a basis to consider selection as an explanation.

Again I don't know Theta but if both tests were congruent for putative selection I'd say that was reasonable. However, Tajima D alone is not a cool result, its cool theory however but not cool in practice. I hope that explains it?

Note: did any one ever follow this up in trees? Cool if they did because there will be a relationship between the balance of a tree (e.g. Bayesian 'Skyline' plots) and Tajima D.

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