Confused about Effective Population size

Question

[andreagarcia871]

I am newbie in bioinformatics, I started to read about Effective Population size (Ne) being an important genetic estimation for population studies (my goal is to run SHAPEIT software with the proper effective population size parameter), and I have this kind of basic theoretical question:

Let's say I have 5 cattle populations, like Hereford, Braford, Angus, etc. Is there a kind of "universal" Effective Population size for all the Hereford? Or should I calculate Ne for MY own Hereford sampled populations?

[Petr Ponomarenko]

Depends on the way your population was sampled from Hereford population, sizes of your and Hereford sets of species and what difference in the effective population sizes for the same allele variance is considered to be negligible for your goals. More important is that effective population size is not only function of population structure, but also a function of the phenotype you are testing

In case of random sampling from huge (size >> 10 samples) dataset variance is going to be almost the same as in the big original dataset

[andreagarcia871]

Thank you Petr, maybe you could reply in the Answer input?

So, from what I understand, it almost makes no sense to use an "universal" Ne size when I have my own samples.

Also one also should have an estimate population count of a breed for the particular geographical region implicated in the study.

[Petr Ponomarenko]

Effective population size has almost nothing to do with real population size, so there is no need to estimate the later (other than real population size is usually bigger).