As to the first, there is quite a number now of these studies (several more have emerged since this blog post), conducted by different researchers on independently-collected genotypic data, and many find a strong correlation between genetic and geographic distance. This signal is fairly robust. I disagree with your broad claim that there were somehow major methodological problems with any of the several PLoS Genetics studies, but would be interested to learn more about what specifically you found to be farcical or biased about them.

As to your position in Global Similarity: Advanced, this does depend on the reference genotypes that are available to the analysis. At the moment we have fewer Southern (and Eastern) European reference individuals (the colored squares in the plots) than we would like. This is something that we hope to address as more data become available. Were we to come into a number of Croatian samples it would be informative to see where you fall with respect to them. If you moved towards the Croatians, that would indicate that your present position was inaccurate due to the absence of relevant reference data. If you stayed about where you are, that would suggest that you might have some northern European ancestry of which you were not previously aware.

I submitted a sputum sample to 23andme and was PC plotted in Northern Europe with Germans and Austrians however my ancestors are from Croatia (southern Europe). Moreover, my closest genome matches are from a male from Wales, Belgium, Germany and Scandinavia.

It just goes to show that autosomal DNA is not the be all and end all in determining genetic similarity.

I still think the PLOS genetics study is a farce and very bias. If I were a reviewer of the manuscript I would have torn it to shreds and asked for a major review.

It is sometimes hard to believe how good the concordance is between genes and geography in Europe, but it’s worth noting that this is what you would expect: neighbors are more likely to mate with each other than people on opposite sides of the continent. Thus, over time, neighbors will be more likely to be similar to one another than to people from far away.

Your example of Y-chromosome haplogroup I is worth bringing up. However, on more precise examination there are different lineages within haplogroup I in different parts of Europe. I1 is found further north, on average, and I2 is found at higher frequencies in the Balkans. Most markers across the genome provide very little information (less than the Y-chromosome haplogroup I SNPs, for example) about ancestry, but combined, hundreds of thousands of markers do tell quite a lot. If you are a customer at 23andMe or have a demo account, you can see it for yourself. The new Advanced Global Similarity feature puts you in this same sort of display:
https://www.23andme.com/you/globalsim/advanced/
check it out!

Take for example the Y-chromosome haplogroup I. Its frequency among the male population between regions of southern europe and northern europe are remarkably similar. More specifically, in the north west balkans the frequency of the “I” haplogroup matches or exceeds frequencies of that found in areas of far northern europe. Perhaps this is why this region of europe was left out of the study?