A5066523450- Forensic and Genetic Research
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Forensic Anthropology and Bioarchaeology Studies
- Archaeology and ancient environmental studies
- Identification and Quantification in Food
- Race, Genetics, and Society
- Rangeland Management and Livestock Ecology
- Ancient Near East History
- Indigenous Studies and Ecology
- Wildlife Ecology and Conservation
- Pacific and Southeast Asian Studies
- Algorithms and Data Compression
- Yersinia bacterium, plague, ectoparasites research
- Genetic Mapping and Diversity in Plants and Animals
- Ecology and biodiversity studies
- Quantum Dots Synthesis And Properties
- TiO2 Photocatalysis and Solar Cells
- Language and cultural evolution
- Advanced Photocatalysis Techniques
- Metallurgy and Cultural Artifacts
- Animal Diversity and Health Studies
- Paleopathology and ancient diseases
Middle East Technical University
2020-2025
Laboratoire Interdisciplinaire des Sciences du Numérique
2022-2023
University of Tartu
2022-2023
Trinity College Dublin
2023
Université Paris-Saclay
2022-2023
The social organization of the first fully sedentary societies that emerged during Neolithic period in Southwest Asia remains enigmatic,1Kuijt I. People and Space Early Agricultural Villages: Exploring Daily Lives, Community Size, Architecture Late Pre-Pottery Neolithic.J. Anthropol. Archaeol. 2000; 19: 75-102https://doi.org/10.1006/jaar.1999.0352Crossref Scopus (125) Google Scholar mainly because material culture studies provide limited insight into this issue. However, Anatolian...
Abstract Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, formal documentation only dating few centuries. North European short-tailed (NEST) often assumed to be oldest domestic sheep populations, even thought represent relicts expansions during Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced genomes (up 11.6X) five from Baltic islands...
We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, broad region that experienced earliest Neolithic transition emergence complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 23 present-day published genomes, we found within each steadily increased through Holocene. further observed inferred sources gene flow shifted time. In first half Holocene, Southwest Asian East Mediterranean populations...
Upper Mesopotamia played a key role in the Neolithic Transition Southwest Asia through marked innovations symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Çayönü Tigris basin together with bioarchaeological material culture data. Our findings reveal that was genetically diverse population, carrying mixed ancestry western eastern Fertile Crescent, community received immigrants. results further suggest organized along biological family...
Abstract Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication took place Southwest Asia, although much remains unresolved about precise location(s) and timing(s) earliest domestication, or post-domestication history sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well 14 domestic from Anatolia, two Iran, Iberia, three France,...
The history of human inbreeding is controversial.1 In particular, how the development sedentary and/or agricultural societies may have influenced overall levels, relative to those hunter-gatherer communities, unclear.2-5 Here, we present an approach for reliable estimation runs homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this 411 ancient Eurasian from last 15,000 years.5-34 We show that frequency inbreeding, as measured by ROHs, has...
Abstract The advent of genome-wide ancient DNA analysis has revolutionized our understanding prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges analyzing DNA. READv2, an optimized Python3 implementation most widely used tool for this purpose, addresses while surpassing its predecessor speed and accuracy. For sufficient amounts data, it can classify up third-degree differentiate between two types first-degree...
Abstract The possibility to obtain genome-wide ancient DNA data from multiple individuals has facilitated an unprecedented perspective into prehistoric societies. Studying biological relatedness in these groups requires tailored approaches for analyzing due its low coverage, post-mortem damage, and potential ascertainment bias. Here we present READv2 (Relatedness Estimation Ancient version 2), improved Python 3 re-implementation of the most widely used tool this purpose. While providing...
Abstract There is growing interest in uncovering genetic kinship patterns past societies using low‐coverage palaeogenomes. Here, we benchmark four tools for estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ their input, IBD methods, statistical approaches. We used pedigree ancient genome sequence simulations to evaluate these when only a limited number (1 50 K, minor allele frequency ≥0.01) of shared SNPs are available. The performance all was comparable ≥20 K SNPs....
We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment the linear genome, we show that masking known polymorphic sites graph effectively remove bias, but only starting from raw read files. next study approaches overcome damage: trimming, rescaling, our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine zenodo.org/records/14234666), reads at positions possibly affected by PMD. propose coupled...
Abstract Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central west Anatolian sheep dating Epipaleolithic to late Neolithic, comparatively with modern-day breeds Asian Neolithic/Bronze Age (OBI). Analyzing data, found that Neolithic (ANS) are genetically closest present-day European relative breeds, a conclusion supported by mtDNA haplogroup frequencies. In...
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and Cyprian ophion) were driven to near extinction during 20th century are currently listed as endangered populations by International Union for Conservation of Nature. While exact origins these lineages remain unclear, they have been suggested be close relatives domestic sheep or remnants proto-domestic sheep. Here, we study whole genome sequences n = 5 mouflons 10 terms population history diversity,...
Abstract Arguments have long suggested that the advent of early farming in Near East and Anatolia was linked to a ‘Mother Goddess’ cult. However, evidence for dominant female role these societies has been scarce. We studied social organisation, mobility patterns gendered practices Neolithic Southwest Asia using 131 paleogenomes from Çatalhöyük Mound (7100-5950 BCE), major settlement Central with an uninterrupted occupation apparent egalitarian structure. In contrast widespread genetic...
ABSTRACT Ancient DNA analysis is subject to various technical challenges, including bias towards the reference allele (“reference bias”), postmortem damage (PMD) that confounds real variants, and limited coverage. Here, we conduct a systematic comparison of alternative approaches against PMD. To reduce bias, either (a) mask variable sites before alignment or (b) align data graph genome representing all sites. Compared linear genome, both masking effectively remove allelic when using...
Abstract Western Anatolia has been a crucial yet elusive element in the Neolithic expansion from Fertile Crescent to Europe. Using 30 new palaeogenomes c.8000-6000 BCE we describe early Holocene genetic landscape of Anatolia, which reveals population continuity since late Upper Pleistocene. Our findings indicate that Neolithisation 7 th millennium was multifaceted process, characterised by assimilation practices indigenous groups and influx populations east, their admixed descendants...
Abstract We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced a coverage 0.6–6.4×. Mitochondrial DNA haplotypes individuals clustered with those Equus hydruntinus (or hemionus ), extinct European wild ass, secular name ‘hydruntine’. Further, ass whole genome profiles fell outside genomic diversity other extant and past Asiatic ( E. ) lineages. These observations suggest that asses represent hydruntines, making them...
A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment the candidate reference genomes will only apply when nuclear of comparable quality are available, may still fail coverages low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) between pairs species ancient sequences. MTaxi...
Abstract Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this breed diversity goes, formal documentation only dating few centuries. North European short-tailed often assumed to be oldest domestic sheep populations, even thought represent relicts expansions during Neolithic period reaching Scandinavia less than 6000 years ago. This study sequenced genomes (up 11.6X) five from Baltic islands...
There is growing interest in uncovering genetic kinship patterns past societies using low-coverage paleogenomes. Here, we benchmark four tools for estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ their input, IBD methods, statistical approaches. We used pedigree ancient genome sequence simulations to evaluate these when only a limited number (1K 50K) of shared SNPs (with minor allele frequency ≥0.01) are available. The performance all was comparable ≥20K SNPs. found...
Abstract DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating often struggle when limited, as with paleogenomes and degraded forensic samples. addresses this challenge by leveraging two CNN models trained on simulated classify up the third-degree identify parent-offspring sibling pairs. Our benchmarking shows performs comparably or better than widely used READv2. We validated empirical...
Abstract In this chapter, we investigate the genetics of two Early Chalcolithic Çatalhöyük individuals, U.18333 and U.16835, only burials yet recovered from West Mound. These were neonates buried within same building. Using shotgun-sequenced partial genomes (0.06x 0.02x coverage) identify both as females. Despite being building, find no close genetic kinship between them, in line with previously published results Çatalhöyük. We also that Mound shared gene pool Neolithic other Central...
Abstract Selective funerary practices can inform about social relationships in prehistoric societies but are often difficult to discern. Here we present evidence for an age-specific practice at the Neolithic site of Çatalhöyük Anatolia, dating 7th millennium BCE. Among ancient DNA libraries produced from 362 petrous bone samples, those subadults contained three times higher average human than adults. This difference organic preservation was also confirmed by FTIR analysis. Studying similar...
Abstract Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central west Anatolian sheep dating to Late Glacial early Holocene. We observe loss haplotype diversity around 7500 BCE during Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, haplogroup increases, compatible admixture other domestication centres and/or wild...