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A recent comparison of medieval mitochondrial DNA from a Byzantine cemetery with modern populations in Southwest Turkey shows what we have assumed in our population analyses of atDNA 2.0. The integration of historical with archaeological information proves that the little South Anatolian town of Sagalassos has a clearly structured Balkan/Greek maternal population with some ancient Persians and Italians in the mix but no Central Asian (Turkic) contributions discernible. The inference is that when the Turks conquered Anatolia and eventually took control of the Byzantine capital (modern-day Constantinople) they remained largely a ruling class with little penetration into the ancient settlements scattered through Turkey. Even though the general populace accepted their conquerors' religion, Islam, their bedrock DNA did not significantly alter, at least not in the female lines. 

Claudio Ottoni et al., "Mitochondrial Analysis of a Byzantine Population Reveals the Differential Impact of Multiple Historical Events in South Anatolia," Eur. J. of Hum. Genet. (2011) 19:571-76.

Abstract
The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th–13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained.