In Dienekes' Anthropology Blog, I presented a new method of comparing populations, the population concordance ratio. You can refer to that post for the rationale, definitions, and code, but for the present, I will just say that this ratio estimates the probability that two random individuals from a population A are more similar to each other than either of them is to a random individual from another population B. Its expected value ranges from 0.25 (two very similar populations) to 1 (two very dissimilar populations).
Another common way of comparing populations is by computing an identity-by-state (IBS) similarity matrix. Comparing the genomes of two individuals across many loci, you can get a number (IBS) ranging beteween 0 and 1: in humans 0 is almost never encountered, as two random individuals may share some alleles in common by pure chance, while 1 indicates either monozygotic twins or a clerical error.
I have computed these two statistics over populations of the Dodecad Project with at least 5 individuals. The analysis is based on 282,409 SNPs with a 99%+ genotyping rate over the combined sample.
The results can be found in this spreadsheet.
[NOTE: I have taken down the spreadsheet on Apr 15, in order to investigate a possible error in the Brazilian_D sample]
[NOTE II: The results seem to be correct, so spreadsheet is back up]
For the population concordance ratio each row represents an estimate of the probability that two individuals from that population are more similar to each other than either of them is to a member from a population in each column; this is an asymmetric matrix.
Below are some visualizations of these statistics for the Greek_D sample.
First, the IBS similarity matrix. These ranged between 0.70383 and 0.73689, so I have subtracted 0.7 in order to bring out the scale of the differences.
Second, the population concordance ratio: