Did Hittites and Other PIE Anatolian Language Speakers Lack Steppe Ancestry?

Iosif Lazaridis, in the pre-print "The evolutionary history of human populations in Europe" (May 4, 2018) casts doubt on the Steppe hypothesis as applied to the Anatolian language family within the Indo-European languages. While I understand the basis for his speculation, I think that this possibility is improbable and that late Bronze Age samples from Hittite individuals will show steppe ancestry.

The most prominent of the languages in this family was the Hittite language of the Bronze Age Hittite people who conquered essentially all of Anatolia and some of the Northern Levant and Northern Mesopotamia in the Bronze Age before collapsing in the Bronze Age collapse.

Contemporaneous historical accounts from Akkadian traders suggest that this conquest started shortly before 1740 BCE. Advocates for an early arrival of Anatolian language speakers (on linguistic grounds) argue that these languages should have been pervasive in Anatolia for more than a thousand years before this expansion, despite evidence that the territory conquered by the Hittites mostly spoke a non-Indo-European Hattic language.

But, the archaeology does not support this conclusion and there are not early historical accounts to support this claim either. Physical anthropology of remains from the region also point to a late arrival of physically distinct people in Anatolian linguistic communities.

The only other pre-Hittite empire Anatolian language which is attested is Luwian, a sister language to Hittite possibly spoken by the Trojans. The other Anatolian languages are only attested after the collapse of the Hittite empire and could have a relationship to it similar to that of Latin to the Romance languages.

They key passage states:

Steppe migrants Steppe populations during the Eneolithic to Bronze Age were a mix of at least two elements[28], the EHG who lived in eastern Europe ~8kya and a southern population element related to present-day Armenians[28], and ancient Caucasus hunter-gatherers[22], and farmers from Iran[24]. Steppe migrants made a massive impact in Central and Northern Europe post5kya[28,43]. Some of them expanded eastward, founding the Afanasievo culture[43] and also eventually reached India[24]. 

These expansions are probable vectors for the spread of Late Proto-Indo-European[44] languages from eastern Europe into both mainland Europe and parts of Asia, but the lack of steppe ancestry in the few known samples from Bronze Age Anatolia[45] raises the possibility that the steppe was not the ultimate origin of Proto-Indo-European (PIE), the common ancestral language of Anatolian speakers, Tocharians, and Late Proto-Indo Europeans. In the next few years this lingering mystery will be solved: either Anatolian speakers will be shown to possess steppe-related ancestry absent in earlier Anatolians (largely proving the steppe PIE hypothesis), or they will not (largely falsifying it, and pointing to a Near Eastern PIE homeland).

Note 45 is a reference to Lazaridis I, et al.: "Genetic origins of the Minoans and Mycenaeans." 584 Nature 214 (2017), which contains three Bronze Age Anatolian samples from Southwest Turkey. The one male and two female Bronze Age Anatolian samples relied upon are as follows (from the Supplemental Materials):

I2495	I2495	A4-1	1240K	2558-2295 caIBCE (3925±35 BP, Poz-81111)	Anatolia_BA	Harmanӧren- Gӧndürle Hӧyük, Isparta	Turkey	37.92	30.71	M	1.981	637146	H	J1a
I2499	I2499	UC1	1240K	2836-2472 caIBCE (4040±35 BP, Poz-82213)	Anatolia_BA	Harmanӧren- Gӧndürle Hӧyük, Isparta	Turkey	37.92	30.71	F	0.285	243348	K1a2
I2683	I2683	G3-95	1240K	2500-1800 BCE	Anatolia_BA	Harmanӧren- Gӧndürle Hӧyük, Isparta	Turkey	37.92	30.71	F	3.695	749308	T2b

The man has Y-DNA J1a, mtDNA H and no steppe ancestry and is from 2558-2295 BCE. One woman is from 2836-2472 BCE, has mtDNA K1a2 and has no steppe ancestry. The other woman is from 2500-1800 BCE, has mtDNA T2b and has no steppe ancestry.

We don't have heaps of information about the archaeological context, but two of the three samples clearly pre-date the Hittite expansion that is attested historically and archaeologically in Anatolia and the third, a woman, could pre-date or post-date that expansion which in every other case was male dominated.

This data is a blow to the theory that the Anatolian languages broke away especially early form the Indo-European languages and were present in Anatolia long before 2000 BCE. 

But, it is not at all in conflict with my longstanding hypothesis that the Anatolian languages arrived in Anatolia with steppe people at a time similar to their arrival in Europe, the Aegean, South Asia and West Asia (i.e. Iran) and that the divergence of the Anatolian languages from other PIE language families is due to stronger and more divergent substrate influences rather than from great antiquity.

If my hypothesis is right, these data are a perfect fit and steppe ancestry should start to become widespread especially in specifically Anatolian language speaking men, and more generally, in late Bronze Age Anatolia. It will take future ancient DNA finds from those periods to determine if this is correct.

I also disagree with his conclusion that an absence of steppe ancestry would imply a Near Eastern PIE homeland. Instead, it would imply that the Anatolian languages arrived in Anatolia largely via elite transmission which could also help explain why it is more divergent than Indo-European languages that arrived with large communities of native speakers via mass migration.

UPDATE May 14, 2018: Davidski does some analysis of the Bronze Age Anatolian genomes discussed above, and agrees with me that these are likely Hattian and not Hittite individuals, albeit for slightly different reasons. He also notes, in data completely consistent with my late Anatolian expansion hypothesis that: "I am actually seeing a minor, but persistent, signal of steppe ancestry in one of the two Old-Hittite Period (~1750–1500 BCE) samples: Anatolia_MLBA MA2203." Also, not inconsistent with the historical record or a late Anatolian expansion hypothesis is his observation that: "None of the other Anatolia_MLBA individuals, three of whom are from the Assyrian Colony Period (~2000–1750 BCE), show such obvious steppe ancestry."