The Neolithic Transition

2025

1. Female Lineages and Changing Kinship Patterns in Neolithic Çatalhöyük

   Eren Yüncü, Ayça Küçükakdağ Doğu, Damla Kaptan, and 44 more authors

   Science, Jun 2025

   Abs DOI Bib

   Combining 131 paleogenomes with bioarchaeological and archaeological data, we studied social organization and gendered practices in Çatalhöyük East Mound (7100 to 5950 BCE), a major Neolithic settlement in Central Anatolia. In early Çatalhöyük, burials in the same building were frequently close genetic relatives, suggesting that houses were used by biological family members. In later periods, however, individuals buried in the same building were often genetically unrelated, despite sharing similar diets. We found no indication of sex-biased mobility into Çatalhöyük. Meanwhile, in all periods, within-building genetic connections were predominantly maternal rather than paternal. Burials of female subadults also received a higher frequency of gifts than male subadults. Our results reveal how kinship practices changed while specific practices prioritizing female lines persisted for 1000 years at Neolithic Çatalhöyük.

   @article{Yuncu2025-zg,
     title = {Female Lineages and Changing Kinship Patterns in {Neolithic} {Çatalhöyük}},
     author = {Yüncü, Eren and Doğu, Ayça Küçükakdağ and Kaptan, Damla and Kılıç, Muhammed Sıddık and Mazzucato, Camilla and Güler, Merve N. and Eker, Elifnaz and Katırcıoğlu, Büşra and Chyleński, Maciej and Vural, Kıvılcım Başak and Sağlıcan, Ekin and Atağ, Gözde and Bozkurt, Defne and Pearson, Jessica and Sevkar, Arda and Altınışık, N. Ezgi and Milella, Marco and Karamurat, Cansu and Aktürk, Şevval and Yurttaş, Emre Deniz and Yıldız, Nisan and Koptekin, Dilek and Yorulmaz, Sevgi and Kazancı, Duygu Deniz and Aydoğan, Ayça and Gürün, Kanat and Schotsmans, Eline M. J. and Anvari, Jana and Rosenstock, Eva and Byrnes, Jennifer and Biehl, Peter F. and Orton, David and Lagerholm, Vendela Kempe and Gemici, Hasan Can and Vasic, Milena and Marciniak, Arkadiusz and Atakuman, Çiğdem and Erdal, Yılmaz Selim and Kırdök, Emrah and Pilloud, Marin and Larsen, Clark Spencer and Haddow, Scott D. and Götherström, Anders and Knüsel, Christopher J. and Özer, Füsun and Hodder, Ian and Somel, Mehmet},
     journal = {Science},
     publisher = {American Association for the Advancement of Science},
     volume = {388},
     number = {6754},
     pages = {eadr2915},
     month = jun,
     year = {2025},
     doi = {10.1126/science.adr2915},
   }

2. Out-of-Anatolia: Cultural and Genetic Interactions during the Neolithic Expansion in the Aegean

   Dilek Koptekin, Ayça Aydoğan, Cansu Karamurat, and 32 more authors

   Science, Jun 2025

   Abs DOI Bib

   West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Holocene West Anatolia using 30 new paleogenomes. We show that Neolithization in West Anatolia was a multifaceted process, characterized by the assimilation of Neolithic practices by local foragers, the influx of eastern populations, and their admixture, with their descendants subsequently establishing Neolithic Southeast Europe. We then coanalyzed genetic and cultural similarities across early Holocene Anatolian and Aegean Neolithic villages using 58 material culture elements. Cultural distances among villages correlate with their spatial distances but not with their genetic distances after controlling for geography. This suggests that cultural change was often decoupled from genetically visible mobility.

   @article{Koptekin2025-zk,
     title = {{Out-of-Anatolia}: Cultural and Genetic Interactions during the {Neolithic} Expansion in the {Aegean}},
     author = {Koptekin, Dilek and Aydoğan, Ayça and Karamurat, Cansu and Altınışık, N. Ezgi and Vural, Kıvılcım Başak and Kazancı, D. Deniz and Doğu, Ayça Küçükakdağ and Kaptan, Damla and Gemici, Hasan Can and Yüncü, Eren and Moots, Hannah M. and Umurtak, Gülsün and Duru, Refik and Fidan, Erkan and Çevik, Özlem and Erdoğu, Burçin and Korkut, Taner and Knüsel, Christopher J. and Haddow, Scott and Larsen, Clark Spencer and Özbal, Rana and Gerritsen, Fokke and Özdoğan, Eylem and Akbaba, Ali and Usanmaz, Uygar Ozan and Derici, Yasin Cemre and Uçmazoğlu, Mine and Jay, Flora and Özdoğan, Mehmet and Götherström, Anders and Erdal, Yılmaz Selim and Malaspinas, Anna-Sapfo and Atakuman, Çiğdem and Özer, Füsun and Somel, Mehmet},
     journal = {Science},
     publisher = {American Association for the Advancement of Science},
     volume = {388},
     number = {6754},
     pages = {eadr3326},
     month = jun,
     year = {2025},
     doi = {10.1126/science.adr3326},
   }

3. Pre-processing of Paleogenomes: Mitigating Reference Bias and Postmortem Damage in Ancient Genome Data

   Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, and 5 more authors

   Genome Biology, Jan 2025

   Abs DOI Bib

   We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine and zenodo.org/records/14234666), masking reads only at positions possibly affected by PMD. We propose graph alignment coupled with bamRefine as a simple strategy to minimize data loss and bias, and urge the community to publish FASTQ files.

   @article{Koptekin2025-cv,
     title = {Pre-processing of Paleogenomes: Mitigating Reference Bias and Postmortem Damage in Ancient Genome Data},
     author = {Koptekin, Dilek and Yapar, Etka and Vural, Kıvılcım Başak and Sağlıcan, Ekin and Altınışık, N. Ezgi and Malaspinas, Anna-Sapfo and Alkan, Can and Somel, Mehmet},
     journal = {Genome Biology},
     publisher = {Springer Nature},
     volume = {26},
     number = {1},
     pages = {6},
     month = jan,
     year = {2025},
     doi = {10.1186/s13059-024-03462-w},
   }

2024

1. Benchmarking Kinship Estimation Tools for Ancient Genomes Using Pedigree Simulations

   Şevval Aktürk, Igor Mapelli, Merve N. Güler, and 13 more authors

   Molecular Ecology Resources, Jul 2024

   Abs DOI Bib

   There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.

   @article{Akturk2024-un,
     title = {Benchmarking Kinship Estimation Tools for Ancient Genomes Using Pedigree Simulations},
     author = {Aktürk, Şevval and Mapelli, Igor and Güler, Merve N. and Gürün, Kanat and Katırcıoğlu, Büşra and Vural, Kıvılcım Başak and Sağlıcan, Ekin and Çetin, Mehmet and Yaka, Reyhan and Sürer, Elif and Atağ, Gözde and Çokoğlu, Sevim Seda and Sevkar, Arda and Altınışık, N. Ezgi and Koptekin, Dilek and Somel, Mehmet},
     journal = {Molecular Ecology Resources},
     publisher = {Wiley},
     volume = {24},
     number = {5},
     pages = {e13960},
     month = jul,
     year = {2024},
     doi = {10.1111/1755-0998.13960},
   }

2023

1. Spatial and Temporal Heterogeneity in Human Mobility Patterns in Holocene Southwest Asia and the East Mediterranean

   Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, and 52 more authors

   Current Biology, Jan 2023

   Abs DOI Bib

   We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.

   @article{Koptekin2023-xn,
     title = {Spatial and Temporal Heterogeneity in Human Mobility Patterns in {Holocene} {Southwest Asia} and the {East Mediterranean}},
     author = {Koptekin, Dilek and Yüncü, Eren and Rodríguez-Varela, Ricardo and Altınışık, N. Ezgi and Psonis, Nikolaos and Kashuba, Natalia and Yorulmaz, Sevgi and George, Robert and Kazancı, Duygu Deniz and Kaptan, Damla and Gürün, Kanat and Vural, Kıvılcım Başak and Gemici, Hasan Can and Vassou, Despoina and Daskalaki, Evangelia and Karamurat, Cansu and Lagerholm, Vendela K. and Erdal, Ömür Dilek and Kırdök, Emrah and Marangoni, Aurelio and Schachner, Andreas and Üstündağ, Handan and Shengelia, Ramaz and Bitadze, Liana and Elashvili, Mikheil and Stravopodi, Eleni and Özbaşaran, Mihriban and Duru, Güneş and Nafplioti, Argyro and Rose, C. Brian and Gencer, Tuğba and Darbyshire, Gareth and Gavashelishvili, Alexander and Pitskhelauri, Konstantine and Çevik, Özlem and Vuruşkan, Osman and Kyparissi-Apostolika, Nina and Büyükkarakaya, Ali Metin and Oğuzhanoğlu, Umay and Günel, Sevinç and Tabakaki, Eugenia and Aliev, Akper and Ibrahimov, Anar and Shadlinski, Vaqif and Sampson, Adamantios and Kılınç, Gülşah Merve and Atakuman, Çiğdem and Stamatakis, Alexandros and Poulakakis, Nikos and Erdal, Yılmaz Selim and Pavlidis, Pavlos and Storå, Jan and Özer, Füsun and Götherström, Anders and Somel, Mehmet},
     journal = {Current Biology},
     publisher = {Elsevier},
     volume = {33},
     number = {1},
     pages = {41--57.e15},
     month = jan,
     year = {2023},
     doi = {10.1016/j.cub.2022.11.034},
   }

2022

1. A Genomic Snapshot of Demographic and Cultural Dynamism in Upper Mesopotamia during the Neolithic Transition

   N. Ezgi Altınışık, Duygu Deniz Kazancı, Ayça Aydoğan, and 22 more authors

   Science Advances, Nov 2022

   Abs DOI Bib

   Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.

   @article{Altinisik2022-pd,
     title = {A Genomic Snapshot of Demographic and Cultural Dynamism in {Upper Mesopotamia} during the {Neolithic} Transition},
     author = {Altınışık, N. Ezgi and Kazancı, Duygu Deniz and Aydoğan, Ayça and Gemici, Hasan Can and Erdal, Ömür Dilek and Sarıaltun, Savaş and Vural, Kıvılcım Başak and Koptekin, Dilek and Gürün, Kanat and Sağlıcan, Ekin and Fernandes, Daniel and Çakan, Gökhan and Koruyucu, Meliha Melis and Lagerholm, Vendela Kempe and Karamurat, Cansu and Özkan, Mustafa and Kılınç, Gülşah Merve and Sevkar, Arda and Sürer, Elif and Götherström, Anders and Atakuman, Çiğdem and Erdal, Yılmaz Selim and Özer, Füsun and Erim Özdoğan, Aslı and Somel, Mehmet},
     journal = {Science Advances},
     publisher = {American Association for the Advancement of Science},
     volume = {8},
     number = {44},
     pages = {eabo3609},
     month = nov,
     year = {2022},
     doi = {10.1126/sciadv.abo3609},
   }

2021

1. Variable Kinship Patterns in Neolithic Anatolia Revealed by Ancient Genomes

   Reyhan Yaka, Igor Mapelli, Damla Kaptan, and 54 more authors

   Current Biology, Jun 2021

   Abs DOI Bib

   The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic, mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings, household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük, and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.

   @article{Yaka2021-jq,
     title = {Variable Kinship Patterns in {Neolithic} {Anatolia} Revealed by Ancient Genomes},
     author = {Yaka, Reyhan and Mapelli, Igor and Kaptan, Damla and Doğu, Ayça and Chyleński, Maciej and Erdal, Ömür Dilek and Koptekin, Dilek and Vural, Kıvılcım Başak and Bayliss, Alex and Mazzucato, Camilla and Fer, Evrim and Çokoğlu, Sevim Seda and Lagerholm, Vendela Kempe and Krzewińska, Maja and Karamurat, Cansu and Gemici, Hasan Can and Sevkar, Arda and Dağtaş, Nihan Dilşad and Kılınç, Gülşah Merve and Adams, Donovan and Munters, Arielle R. and Sağlıcan, Ekin and Milella, Marco and Schotsmans, Eline M. J. and Yurtman, Erinç and Çetin, Mehmet and Yorulmaz, Sevgi and Altınışık, N. Ezgi and Ghalichi, Ayshin and Juras, Anna and Bilgin, C. Can and Günther, Torsten and Storå, Jan and Jakobsson, Mattias and de Kleijn, Maurice and Mustafaoğlu, Gökhan and Fairbairn, Andrew and Pearson, Jessica and Togan, İnci and Kayacan, Nurcan and Marciniak, Arkadiusz and Larsen, Clark Spencer and Hodder, Ian and Atakuman, Çiğdem and Pilloud, Marin and Sürer, Elif and Gerritsen, Fokke and Özbal, Rana and Baird, Douglas and Erdal, Yılmaz Selim and Duru, Güneş and Özbaşaran, Mihriban and Haddow, Scott D. and Knüsel, Christopher J. and Götherström, Anders and Özer, Füsun and Somel, Mehmet},
     journal = {Current Biology},
     publisher = {Elsevier},
     volume = {31},
     number = {11},
     pages = {2455--2468.e18},
     month = jun,
     year = {2021},
     doi = {10.1016/j.cub.2021.03.050},
   }

2. Human Inbreeding Has Decreased in Time through the Holocene

   Francisco C. Ceballos, Kanat Gürün, N. Ezgi Altınışık, and 12 more authors

   Current Biology, Sep 2021

   Abs DOI Bib

   The history of human inbreeding is controversial. In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear. Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROHs, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to small population size instead of consanguinity. Cases of high consanguinity were rare and only observed among members of farming societies in our sample. Despite the lack of evidence for common consanguinity in our ancient sample, consanguineous traditions are today prevalent in various modern-day Eurasian societies, suggesting that such practices may have become widespread within the last few millennia.

   @article{Ceballos2021-zm,
     title = {Human Inbreeding Has Decreased in Time through the {Holocene}},
     author = {Ceballos, Francisco C. and Gürün, Kanat and Altınışık, N. Ezgi and Gemici, Hasan Can and Karamurat, Cansu and Koptekin, Dilek and Vural, Kıvılcım Başak and Mapelli, Igor and Sağlıcan, Ekin and Sürer, Elif and Erdal, Yılmaz Selim and Götherström, Anders and Özer, Füsun and Atakuman, Çiğdem and Somel, Mehmet},
     journal = {Current Biology},
     publisher = {Elsevier},
     volume = {31},
     number = {17},
     pages = {3925--3934.e8},
     month = sep,
     year = {2021},
     doi = {10.1016/j.cub.2021.06.027},
   }