Testing natural selection on polygenic trait-associated alleles in anatolia using neolithic and present-day human genomes

Fer, Evrim
The Neolithic transition, which started approximately 10,000 year ago in west Eurasia and introduced sedentary life style and food production, led to major shifts in the human diet. Previous studies have reported strong selection signals on genes related to processing of plant-based diets (Buckley et al., 2017; Harris et al., 2019) or the consumption of dairy products (Schlebusch et al., 2013). With the advent of archeogenomics studies, genetic signatures of such adaptations have also been supported using DNA data from ancient populations (Mathieson et al., 2015). In this study, polygenic adaptations in Anatolia after the Neolithic transition were investigated by comparing Neolithic and modern-day genome sequence data. First, we chose 40 mainly polygenic traits previously subject to selection studies. For 6651 single nucleotide polymorphisms (SNPs) associated with these traits, we compared the genetic distance between Neolithic Anatolian (n=36) and presentday Anatolian (n=16) individuals, measured using the FST statistic, with SNPs in evolutionary neutral regions. Then, frequency changes of alleles that elevating phenotypes were studied, to test for a common direction of allele-frequency change affecting these traits. Finally, a population branch statistic (PBS) approach was applied to detect adaptation signals specific to the modern-day Anatolia in comparison to Neolithic Anatolia and an outgroup population. We found that the frequency of alleles related to GWAS traits broadly linked to lipid metabolism to be more differentiated between Neolithic and present-day Anatolia, than neutrally expected. Directionality analyses also suggested that such traits might have been driven by selection. Consistently, the genes showing the highest differentiation along the modern Anatolia branch in the PBS analysis were frequently associated with lipid metabolism. Our results imply that lipid metabolismrelated traits may have been subject to selective pressures in the last 10,000 years.


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The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather th...
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Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c. 13,790 BP and c. 1,380 BP extending from the Palaeolithic to the Iron Age. Ana...
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The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat (Capra hircus) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat...
Çokoğlu, Sevim Seda; Somel, Mehmet; Department of Biology (2021-9)
As the Neolithic transition dramatically changed human lifestyle and diet, one may expect epigenetic differences between pre-Neolithic Hunter-Gatherers (HGs) and Neolithic farmers (NFs) (Childe, 1940). In this study, we investigate methylation profile differences between the Pre-Neolithic and Neolithic individuals. It is today possible to infer methylation patterns of ancient DNA samples using programs such as epiPALEOMIX, which calculates a methylation score (MS) per CpG position from aDNA data (Hanghoj et...
Citation Formats
E. Fer, “Testing natural selection on polygenic trait-associated alleles in anatolia using neolithic and present-day human genomes,” Thesis (M.S.) -- Graduate School of Informatics. Bioinformatics., Middle East Technical University, 2019.