The problem for the Anatolian sample is not only recent immigration by the Turks. As non-Indo-Europeans, the Etruscans in Anatolia would already have been a small and marginalized population there in 1000 BC, potentially genetically isolated from their neighbors for several thousand years. Then from 1000 BC to the modern era, there was continuous additional immigration into Anatolia, of which the Ottoman conquest was only one chapter. It's also possible that the entire Etruscan ethnic group (perhaps meaning a few hundred refugees) could have left Anatolia to resettle in Italy.

So any ancient Etruscan DNA in Anatolia could well be extinct or quite rare in the modern population of Turkey. In fact this is supported by the authors' own premise. They found Etruscan mtDNA in a modern Italian population because they looked in Volterra, not Florence or Palermo, and this is after 2000 years. So a small and general DNA sample from Turkey as a whole, after 3000 years, can't be counted on to identify an isolated ancient minority population up in the hills somewhere. If they ever existed. If they didn't disappear long ago.

What this study has shown is that ancient Etruscan mtDNA is at least not common in Turkey today, and that's certainly useful to know. A future large-scale database of DNA from modern Turkey, or DNA from Bronze Age Anatolian burials, might positively prove Etruscan origins there. But a lack of DNA will never positively disprove it from silence, given the possibility of a small ethnic group totally disappearing from the detectable record.

Regarding continuity of the ancient to modern Tuscans, an essential issue is class. The DNA in elaborate Etruscan tombs is of the aristocracy. This could be quite distinct from that of the large majority of the ancient Etruscan population -- certainly if the upper class was a thin layer of foreign settlers/conquerers. This applies really even with an "indigenous" model, if by this we mean the Villanovan culture -- which was just another elite that had arrived from Central Europe a few hundred years earlier.

What is unexpected about this study is that it examined only mtDNA. Perhaps there is a technical explanation for this or it is simply the researchers' current undertaking, among others. Settlement in Italy could easily have been by Etruscan-speaking males only. One possibility is that Etruscan men arrived neither in a migration, nor as conquerors, but as foreign merchants setting up trading depots in Italy, and becoming a bourgeoise ruling class due to their wealth, intermarrying with the Indo-European Villanovan women. Everyone will agree that Etruscan culture is fundamentally influenced by Aegean culture, and the essential thing is that pots don't fly. They, or at least their designs, are brought by men. In all cases, the "Etruscans" in the initial sense can be a very small group which superimposes its language and culture on the region much more than its genes.

I will also mention that modeling of Etruscan origins should definitely not be limited to the three options of indigenous, Anatolian, or Alpine/Central European (Rhaetian). Other strong contenders are Corsica, Iberia, Crete, and the Caucasus Mountains. Given the Etruscans' highly-developed nautical skills they could even have come from more exotic locations beyond the Mediterranean. Historians are oddly quiet even about the fact that they traded for tin in Britain.

Finally indigenous origin for the Etruscans is not a default that wins if no other conclusive proof can be established. There is no explanation for the Villanovans simultaneously adopting Greek culture, while switching to inhumation, which is both un-Villanovan and utterly un-Greek. Advocates of indigenous origin must positively prove it with Bronze Age DNA of their own in Italy, which is directly ancestral to the (male) Etruscans in the tombs. And this should be easy for them, if there was really a single ethnic group living on the same piece of land for 5000 years.

I thank the authors for their hard work on this fascinating subject and apologize for some tangents from the present study.