Hi everybody
I want to calculate the genetic distance and similarity for ancestral populations. My data is haplotypes.
I appreciate your help.
Best regards
Hi
Could you use R, GenePOPor GenAlex: genetic distance and STRUCTURE: similarity for ancestral populations
dear Angela Maria Urrea-Rojas thanks for your help.
What is the difference between genetic distance and similarity? Aren't they the same?
Hi Farhad Alizadeh,
I believe they are inverses: things that are more similar are less distant, and things that are less similar are more distant.
What sort of haplotyoes? Y-STR haplotypes? Y-SNP haplotypes? Something else?
As Ive mentioned, people have been using first two principal components as a distance measure, but I doubt this is valid. Multidimensional scaling is another reasonable possibility.
I believe entropy is under-used - in fact, I've never seen it used in population genetics but it is made for purpose.
Mr. Joe Flood
I want to use the haplotypes available on the HapMap. I think they are SNP haplotypes.
Alright, they are whole-genome SNPs, basically (1 or 0) hopefully aligned correctly (this is itself a subject of considerable study).
Out of habit people have tended to use PCA though I have never seen any study of whether it actually works - and I would never use it with samples from different time periods. Take a look at the following for the naive approach..
Article Eigenanalysis of SNP Data with an Identity by Descent Interpretation
As I have suggested, entropy derived from signal processing is probably as good a distance measure as any, we use it in geography and spatial economics, but I dont think they've even heard of it in population genetics. We also use things like indexes of similarity and dissimilarity.
To the best of my knowledge, there is not something like "genetic similarity". At least it is not a defined term. Genetic distance on the other hand is a term that is very often used and there are dozens of different ones. Some of them are fairly naive and many of them make some assumption about the evolutionary history of your samples. Picking one is not really straight forward.
Since you seem to have SNP data, I suggest you have a look at the paper of Joly et al. (2015). They describe a number of SNP based genetic distances and they provide an R package for calculating them.
Once you have chosen and calculated a distance, you can visualize them in a dendrogram.
Additionally to such a distance based dendrogram, you can do a PCA and then compare the results of the PCA and the dendrogram. My population genetics professor used to say to us: "If you are interested in population structure, always use more than one method".
PCA is a rather naive approach. It just looks at the plain numbers without any evolutionary perspective. If you make a PCA and you choose a distance like Nei's genetic distance for your dendrogram (Nei's distance takes into account how DNA evolves over time, at least to some degree), you can look at the genetic structure of your populations from two different ankles. That allows you to draw more informed conclusions.
Joly S., Bryant D., Lockhart P.J. (2015). Flexible methods for estimating genetic distances from single nucleotide polymorphisms. Methods in Ecology and Evolution 6(8). Article Flexible methods for estimating genetic distances from singl...
dear Timo Hellwig thank you for your help. the paper of Joly et al. (2015) seems to be appropriate.
Dear Tim,
Your answer given is true!!!
It is not just done by a simple calculus without knowing the exact use of the chosen nucleotide polymorphisms and the sort of haplotypes. The question itself is kept far too general.
As a result there are too many open questions to be cleared front-end.
Best rgds
Jim Verstege
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