So many people have made admixture analyses, and got results that are inexplicable if compared to uniparental genes. Despite of this very obvious observation very few have tried to resolve why this happens. We can see that for instance the amount and diversity of mitochondrial class H is in obvious contradiction with most admixture analyses. MtDna H is usually connected to ancient farmer populations, to the first farmers in Europe. (update 4.4.15: in a long history mtDna H is probably not solely connected to ancient farming, but the question about different results between admixture tests still remains. Farming in South Europe was probably partly an adaptation, not based on Near-Eastern migrations. And the H was only indicative, same problems exist with other uniparental genes). But admixture results can show almost zero percent of ancient farmer genes (early farmers’ genes typical for example in Sardinia) and the same population can have MtDna H around 40%.
How this happens? The bells should ring between researches’ ears. If observations contradict it is their duty to find out why. I have a theory, not only something from thin air, but observations during reading studies and also making some myself. Studies show that if we use ancient farmer samples from the Neolithic Age we see that uniparental and autosomal results can fit quite well. But when we make our admixture tests based on present-day samples the difference exists. So the reason for this contradiction between uniparental and autosomal results is something in terms of sample sets. This something seems to be the admixture that came among later migrations, after Early European farmers and samples representing them. It looks that formal admixture tools give much more priority to younger admixtures, more than their quantitative proportion in our genomes shows in reality. This error is likely caused by the formal admixture methods giving too much attention to what is different and these differences are there because later migrations have smaller expansion area.