The genetic similarity here is estimated within the cohort; the Framingham cohort is by design ethnically homongeous to try to eliminate that sort of population structure confound. This way, the homophily is not picking up on the obvious stuff like ethnic groups. If they studied people from multiple ethnic groups, the results would be trivial and uninteresting. (This is why astazangasta's criticism in another comment is so amusing - this is meaningful because the sample is so 'biased'. This also holds for all the other studies done on Framingham.) But because only one highly homogeneous sample is studied, the chance genetic similarities of friends aren't due to just similar ethnic backgrounds, but are being caused by the genetic influence on things like SES and personality and intelligence and religiosity and hobbies and things like that. These similarities would probably also hold when considering a more unusual and cosmopolitan group, but it would be difficult to spot the increased similarity on a genome-wide basis because of all the racial differences in genomes (most of which would be nonfunctional and irrelevant to anything).
They only apply population stratification from Figure 2 including onwards:
>The results so far do not control for population stratification because we wanted to characterize overall similarity. However, it is important to remember that some of the similarity in genotypes can be explained by simple assortment into relationships with people who have the same ancestral background. The Framingham Heart Study is composed of mostly whites (e.g., of Italian descent), so it is possible that a simple preference for ethnically similar others could explain the results in Fig. 1. However, in the following results, we applied strict controls for population stratification to ensure that any correlation we observed was not due to such a process.
I don't understand why they did not do this for Figure 1 (or why they do not show that figure) - I assume that the difference disappeared, but who knows.
I just realized that this paper is from 2014, first published on arxiv in 2013. I can't find any study replicating it in the 34 citations since so I would be careful (but this type of dataset for replication is hard to come by) https://scholar.google.com.au/scholar?cites=7301900347564089...
