Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia

Abstract

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

Genomic and dietary transitions during the Mesolithic and Early Neolithic in Sicily

“…Interestingly, whereas a Near Eastern-related ancestry component is discerned in many of the Mesolithic HGs from the Iron Gates and other areas in the Balkan, Baltic or Scandinavia, this is not the case for any of the Villabruna cluster individuals. In contrast to previous statements that the Villabruna cluster individuals form a genetically homogenous group ( 16, 25 ), here the individuals show rather diverse ancestry profiles with various combinations of Sicily EM, EHG and GoyetQ2 -related ancestry. Since the Sicily LM HG gene pool contains the distinct Near Eastern-related ancestry but not the GoyetQ2 -related ancestry, it is unlikely that the diversity of this group originated solely from genetic drift from these Villabruna cluster individuals.…”

“…The assigned ancestry components confirm both the substantial continuation of the local Sicily EM ancestry, and the influx of a non-local ancestry frsm (south-)eastern Europe, in Sicily during the Mesolithic. Moreover, the Upper Palaeolithic Pınarbaşı-related ancestry in the Sicily LM HGs is striking, and underlines previous indications for a pre-Neolithic genetic connection between the Near East and European HGs by at least 12,000 calBCE ( 16, 17, 25 ).…”

“…Subsequently, using qpAdm-based admixture models ( 36 ) we aimed to more explicitly model the gene pool of the Sicily LM HGs. We found that a three-way ancestry combination of 75.0±1.6% Sicily EM, 15.5±2.4% EHG and 9.5±2.8% Pınarbaşı, a ∼13,300 calBCE HG from central Anatolia ( 25 ), results in a good fit (P = 0.123, Table 1). Notably, replacing the Sicily EM ancestry with that of Loschbour resulted in poorly fitting models (P Adm = 4.27E-09, Table 1).…”

“…S6.2). However, southeastern European HGs and early farmers from Anatolia Barcin and the Balkan share a part of their ancestry ( 17, 25 ). The excess genetic attraction for southeastern European HGs might hence be driven by the farmer, rather than HG, ancestry component in Sicily EN.…”

“…At the MPI-EVA, 30uL undiluted extract aliquot was converted into double-indexed single-stranded (ss-) libraries ( 86 ) with minor modifications detailed in ( 87 ), without UDG treatment (‘ss non-UDG’) (Data file 1). At the MPI-SHH, all the ds- and ss-libraries were shotgun sequenced to check for aDNA preservation, and subsequently enriched using in-solution capture probes following a modified version of ( 19 ) (described in ( 25 )) for ∼1240k single nucleotide polymorphisms (SNPs) in the nuclear genome ( 17, 18, 54 ) and independently for the complete mitogenome. Then the captured libraries were sequenced on an Illumina 224 HiSeq4000 platform using either a single end (1×75bp reads) or paired end configuration (2×50bp reads).…”