Akademik Veri Yönetim Sistemi
SOMEL M. (Yürütücü)
TÜBİTAK Projesi, 2017 - 2020
The transition from the hunter-gatherer life style to farming and herding was one of the most fundamental changes in human history. This Neolithic Transition first took place in Eastern Mediterranean and Mesopotamia, and led to increase in population size, the emergence of towns and cities, an increased rate of technological innovation, complex social institutions, and major changes in nutrition and health. The social dynamics behind this change, as well as the dynamics it produced, has been a constant source of interest.
Recent ancient DNA (aDNA) and genome studies on the Neolithic Period have mainly focused on one contested question in archaeology, whether farming reached Europe via migration or cultural transmission. These studies have shown that the first farmers of Europe were genetically distinct from contemporaneous European hunter-gatherers; this implying that farming reached Europe by migration. As part of an ongoing TÜBİTAK 3501 Project we have further shown that the first European farmers' ancestors were most likely related to Anatolian farmers or their close relatives. Overall, this suggests that farming spread westward by a migration wave routed in the Near East.
However, ancient genome studies hitherto (including our 3501 project) have not studied Neolithic population structure and dynamics. Questions that have been neglected include how the Neolithic Transition unfolded in the Near East, the characteristics of social structures that emerged from this process, and which changed over time, including the family structure, and also genetic continuity among Neolithic sites.
One reason for this has been technical limitations in sequencing large numbers of genomes, which have been overcome with the hybridization-capture and sequencing method. Another limitation has been access to archaeological material. But intense archaeological work in Turkey has long produced the necessary collections to address these questions. Human remains collected at three sites in Central Anatolia region present a perfect opportunity in this regard. Boncukluhöyük is an early Neolithic site settled between 10,000 and 9,000 BP; Çatalhöyük is a subsequent Neolithic site settled between roughly 9,000 and 8,000 BP and Aşıklı Höyük is another early Neolithic site settled between 10,000 and 9,000 BP. A major question for archaeologists working in the region is whether these sites were following each other.
The tradition of in-house burials in Central Anatolian Neolithic sites presents another opportunity for ancient genome studies. Thanks to these in-house burials, an individual’s remains are recovered with information on his/her social interaction network. Thus, it becomes possible to test genetic relatedness within the household. As part of this study, we will be studying human remains found in the Çatalhöyük site, belonging to different houses and periods, with respect to relatedness. A study of tooth morphology suggested that in Çatalhöyük, the household was not genetically more closely related to each other than to other households. However, this analysis has been limited in resolution and the results await verification by aDNA work.
Another question involves the observed cultural continuity between Çatalhöyük houses built on top of each other in different periods, or "house series". Was the cultural continuity based on genetic continuity between households? The question has not yet been addressed. Determining genetic relatedness using aDNA among these individuals can significantly further the understanding of social structures that emerged during the Neolithic Transition.
The proposal has two major aims: (1) Testing genetic continuity among populations of Boncukluhöyük, Çatalhöyük and Aşıklı Höyük sites to describe the demographic dynamics of the Neolithic; (2) testing genetic relatedness among contemporaneous houses and house series in Çatalhöyük and Aşıklı Höyük, and to describe the social structure of these populations.
The optimal method to test relatedness within a population is using genotyping at known SNPs (which is different from whole genome shotgun sequencing used in the current 3501 Project). The following steps will be taken: (1) Through a simulation based on published modern and ancient genome data, we will determine the set of 25,000 SNPs that are most efficient in capturing relatedness among Neolithic Near Eastern farmers; (2) ordering a kit containing oligonucleotides that will target these SNPs; (3) aDNA extraction from ancient bone and tooth samples and sequencing DNA from 60 of these with low coverage on the Illumina HiSeq platform; (4) aligning the reads to the human genome, and determining contamination rates based on aDNA-specific postmortem damage patterns and human DNA content; (5) selecting 30 samples that have relatively higher human DNA ratios and do not show any sign of contamination; (6) DNA capture from those 30 samples by hybridizing the DNA libraries with designed oligos; (7) deep sequencing of the captured DNA; (8) aligning the reads to the human genome and genotype calling of individuals based on thousands of SNPs; (9) calculating population genetics statistics (Fst, f3 and f4-statistics) using the genotype data produced, to test the hypotheses of genetic continuity among populations of these archaeological sites; (10) testing relatedness among individuals buried within and among contemporaneous houses and among individuals buried in house series at Çatalhöyük and Aşıklı Höyük.
Our preliminary work has shown that aDNA extraction can be highly successful from human bones and teeth from the Anatolian Neolithic. Within this study, for the first time to our knowledge, we will be applying the aDNA capture and sequencing method on human samples in Turkey, and also for the first time that the method will be used to decipher the social structure of a historical site. The results will create a unique resource to complement archaeological studies of the Neolithic.