Archaeogenomic analysis of genetic and cultural interactions in Neolithic Anatolian societies

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NEOGENE Data Management Plan: The project involves production of human and sheep ancient DNA data (generated by whole genome shotgun sequencing and genotyping) and radiocarbon data. It also includes compiling genetic data and archaeological material culture data from literature surveys and correspondence with research teams. We will ensure that the data remains findable, accessible, interoperable and re-usable in the following ways: - All mapped genome sequencing data (in .bam format) will be made available through the European Nucleotide Archive (https://www.ebi.ac.uk/ena), following the current standard procedure in the archaeogenomics field; - All processed genome datasets (in PLINK flat files format, .map and .ped) and radiocarbon dating results of the biological samples will be available through our local web server at METU; - All raw material culture datasets (in spreadsheet format) will be available through our local web server at METU; - All computer code used in the analyses will be shared through GitHub (github.com), and also through our local web server at METU; - All raw sequencing data (in .fastq format) will be available upon request, following the current standard procedure in the aDNA field (raw aDNA shotgun sequencing reads are usually not submitted to databases as the majority of reads represent microbial contamination, thus hindering data reuse); - All raw sequencing data and radiocarbon dating results will be stored in two physically separate servers at METU for ensuring data safety; - All analysis results will be published in open access journals or choosing the open access option. We will further encourage all archaeology and anthropology teams working with us to openly share their data through “Open Context” (www.opencontext.org; a subproject of Alexandria Archive Institute) and through Digital Archaeology Record (www.tdar.org).

Publications

Intramural burials in Neolithic Anatolia: What do they tell us about social organisation?

Auteurs: Mehmet Somel, N. Ezgi Altınışık, Yılmaz Selim Erdal, Çiğdem Atakuman, Füsun Özer
Publié dans: "Kinship, sex, and biological relatedness: the contribution of archaeogenetics to the understanding of social and biological relations"", ed: Meller, Krause, Haak, Risch.", 2023, Page(s) 137-147, ISBN 978-3-96929-259-4
Éditeur: Landesmuseum für Vorgeschichte
DOI: 10.11588/propylaeum.1280

Peopling the Landscape of Çatalhöyük: Reports from the 2009-2017 Seasons (British Institute at Ankara Monograph) Hardcover – 28 Jan. 2021https://www.amazon.co.uk/Peopling-Landscape-%C3%87atalh%C3%B6y%C3%BCk-2009-2017-Institute/dp/1912090783

Auteurs: Yaka R., Doğu A., Kaptan D., Dağtaş N. D. , Chyleński M., Vural K. B. , Altınışık N. E. , Mapelli I., Koptekin D., Karamurat C., Gemici H. C. , Yorulmaz S., Lagerholm V. K. , Fer E., Işıldak U., Ghalichi A., Kılınç G. M. , Mazzucato C., Juras A., Marciniak A., Larsen C. S. , Pilloud M., Haddow S. D. , Knüsel C. J. , Togan İ., Götherström A., Erdal Y. S. , Sürer E. , Özer F., Ata
Publié dans: Peopling the Landscape of Çatalhöyük, 2021, Page(s) 395-405
Éditeur: The British Institute of Archaeology at Ankara

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Auteurs: Erinç Yurtman, Onur Özer, Eren Yüncü, Nihan Dilşad Dağtaş, Dilek Koptekin, Yasin Gökhan Çakan, Mustafa Özkan, Ali Akbaba, Damla Kaptan, Gözde Atağ, Kıvılcım Başak Vural, Can Yümni Gündem, Louise Martin, Gülşah Merve Kılınç, Ayshin Ghalichi, Sinan Can Açan, Reyhan Yaka, Ekin Sağlıcan, Vendela Kempe Lagerholm, Maja Krzewińska, Torsten Günther, Pedro Morell Miranda, Evange
Publié dans: Communications Biology volume, Numéro 4, Article number: 1279 (2021), 2021, ISSN 2399-3642
Éditeur: NATURE
DOI: 10.1038/s42003-021-02794-8

"A network of mutualities of being"": socio-material archaeological networks and biological ties at Çatalhöyüksubmitted to Journal of Archaeological Method and Theory."

Auteurs: Camilla Mazzucato, Michele Coscia, Ayça Küçükakdağ Doğu, Scott Haddow, Muhammed Sıddık Kılıç, Eren Yüncü, Mehmet Somel
Publié dans: Journal of Archaeological Method and Theory., 2024, ISSN 2331-8422
Éditeur: Cornell University [1991]-
DOI: 10.48550/arxiv.2406.19149

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

Auteurs: Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel
Publié dans: Plos Computational Biology, 2022, ISSN 1553-7358
Éditeur: Plos Computational Biology
DOI: 10.1371/journal.pcbi.1010788

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes

Auteurs: Reyhan Yaka, Igor Mapelli, Damla Kaptan, Ayça Doğu, Maciej Chyleński, Ömür Dilek Erdal, Dilek Koptekin, Kıvılcım Başak Vural, Alex Bayliss, Camilla Mazzucato, Evrim Fer, Sevim Seda Çokoğlu, Vendela Kempe Lagerholm, Maja Krzewińska, Cansu Karamurat, Hasan Can Gemici, Arda Sevkar, Nihan Dilşad Dağtaş, Gülşah Merve Kılınç, Donovan Adams, Mehmet Somel
Publié dans: Current Biology, 2021, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2021.03.050

Techno-typology and provenance of the obsidian chipped stones from Sofular Höyük, an Early Neolithic settlement near the Kızılırmak in Central Anatolia

Auteurs: Murat Karakoç; Hasan Can Gemici; Murat Dirican; Okşan Başoğlu; Çiğdem Atakuman
Publié dans: Documenta Praehistorica, Vol 50 (2023), Numéro 4, 2023, ISSN 1854-2492
Éditeur: Ljubljana: Založba Univerze v Ljubljani
DOI: 10.4312/dp.50.5

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

Auteurs: Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, N. Ezgi Altınışık, Nikolaos Psonis,Natalia Kashuba, Sevgi Yorulmaz, Robert George, Duygu Deniz Kazancı, Damla Kaptan, Kanat Gürün, Kıvılcım Başak Vural, Hasan Can Gemici, Despoina Vassou, Evangelia Daskalaki, Cansu Karamurat, Vendela K. Lagerholm, Ömür Dilek Erdal, Emrah Kırdök, Aurelio Marangoni, Andreas Schachner, Handan Üs
Publié dans: Current Biology, Numéro Volume 33, Numéro 1, 9 January 2023,, 2022, Page(s) Pages 41-57.e15, ISSN 1879-0445
Éditeur: Science Direct
DOI: 10.1016/j.cub.2022.11.034

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Auteurs: N. Ezgi Altınışık; Duygu Deniz Kazancı; Ayça Aydoğan; Hasan Can Gemici; Ömür Dilek Erdal; Savaş Sarıaltun; Kıvılcım Başak Vural; Dilek Koptekin; Kanat Gürün; Ekin Sağlıcan; Daniel Fernandes; Gökhan Çakan; Meliha Melis Koruyucu; Vendela Kempe Lagerholm; Cansu Karamurat; Mustafa Özkan; Gülşah Merve Kılınç; Arda Sevkar; Elif Sürer; Anders Götherström; Çiğdem Atakuman;
Publié dans: Science Advances, Numéro 7, 2022, ISSN 2375-2548
Éditeur: Science Advances
DOI: 10.1126/sciadv.abo3609

Human inbreeding has decreased in time through the Holocene

Auteurs: Ceballos, Francisco C.; Gürün, Kanat; Altınışık, N. Ezgi; Gemici, Hasan Can; Karamurat, Cansu; Koptekin, Dilek; Vural, Kıvılcım Başak; Mapelli, Igor; Sağlıcan, Ekin; Sürer, Elif; Erdal, Yılmaz Selim; Götherström, Anders; Özer, Füsun; Atakuman, Çiğdem; Somel, Mehmet
Publié dans: CURRENT BIOLOGY, Numéro 2, 2021, Page(s) P3925-3934.e8, ISSN 1097-4172
Éditeur: CELL PRESS
DOI: 10.1016/j.cub.2021.06.027

The first complete genome of the extinct European wild ass (<i>Equus hemionus hydruntinus</i>)

Auteurs: Mustafa Özkan; Kanat Gürün; Eren Yüncü; Kıvılcım Başak Vural; Gözde Atağ; Ali Akbaba; Fatma Rabia Fidan; Ekin Sağlıcan; N. Ezgi Altınışık; Dilek Koptekin; Kamilla Pawłowska; Ian Hodder; Sarah E. Adcock; Benjamin S. Arbuckle; Sharon R. Steadman; Gregory McMahon; Yılmaz Selim Erdal; C. Can Bilgin; Eva-Maria Geigl; Anders Götherstrom; Thierry Grange; İnci Togan; Füsun Özer; Meh
Publié dans: Molecular Ecology- Biorvix, Numéro 7, 2023, ISSN 0962-1083
Éditeur: Blackwell Publishing Inc.
DOI: 10.1101/2023.06.05.543765

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

Auteurs: Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel
Publié dans: Molecular Ecology Resources, 2024, ISSN 1755-098X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/1755-0998.13960

MTaxi : A comparative tool for taxon identification of ultra low coverage ancient genomes

Auteurs: Gözde Atağ; Kıvılcım Başak Vural; Damla Kaptan; Mustafa Özkan; Dilek Koptekin; Ekin Sağlıcan; Sevcan Doğramacı; Mevlüt Köz; Ardan Yılmaz; Arda Söylev; İnci Togan; Mehmet Somel; Füsun Özer
Publié dans: Open Research Europe, Numéro 5, 2022, ISSN 2732-5121
Éditeur: Open research Europe
DOI: 10.1101/2022.06.06.491147

Investigating DNA methylation changes associated with food production using paleogenomespublished in Biorxiv and Evolutionary Applications (accepted).

Auteurs: Sevim Seda Çokoğlu; Dilek Koptekin; Fatma Rabia Fidan; Mehmet Somel
Publié dans: Evolutionary Applications, 2023, ISSN 0071-3260
Éditeur: Kluwer Academic/Plenum Publishers
DOI: 10.1101/2023.11.04.565610

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages

Auteurs: Gözde Atağ, Damla Kaptan, Eren Yüncü, Kıvılcım Başak Vural, Paolo Mereu, Monica Pirastru, Mario Barbato, Giovanni Giuseppe Leoni, Merve Nur Güler, Tuğçe Er, Elifnaz Eker, Tunca Deniz Yazıcı, Muhammed Sıddık Kılıç, Nefize Ezgi Altınışık, Ecem Ayşe Çelik, Pedro Morell Miranda, Marianne Dehasque, Viviana Floridia, Anders Götherström, Cemal Can Bilgin, İnci Togan, Tors
Publié dans: Genome Biology and Evolution, Numéro Volume 16, Numéro 5, 2024, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1093/gbe/evae090

Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples

Auteurs: Reyhan Yaka; Maja Krzewińska; Vendela Kempe Lagerholm; Anna Linderholm; Füsun Özer; Mehmet Somel & Anders Götherström
Publié dans: Biotechniques, Numéro Volume 76, 2024 - Numéro 5: BioTechniques, 2023, ISSN 1940-9818
Éditeur: Future Science Ltd
DOI: 10.2144/btn-2023-0107

ARCHAEOGENOMIC ANALYSIS OF POPULATION GENETIC RELATIONSHIPS AND KINSHIP PATTERNS IN THE SEDENTARY SOCIETIES FROM NEOLITHIC ANATOLIASupervisor: Mehmet Somel, Fusun Ozer

Auteurs: Reyhan Yaka
Publié dans: 2020
Éditeur: METU

Female lineages and changing kinship patterns in Neolithic Çatalhöyük

Auteurs: Eren Yüncü, Ayça Küçükakdağ Doğu, Damla Kaptan, MuhammedSıddık Kılıç, Camilla Mazzucato, MerveN. Güler, Elifnaz Eker, Büşra Katırcıoğlu, Maciej Chyleński, Kıvılcım Başak Vural, Arda Sevkar, Gözde Atağ, N. Ezgi Altınışık, Fatma Küçük Baloğlu, Defne Bozkurt, Jessica Pearson, Marco Milella, Cansu Karamurat, Şevval Aktürk, Ekin Sağlıcan, Nisan Yıldız
Publié dans: BioRxiv (awaiting editorial decision from Science), 2024, ISSN 0000-0000
Éditeur: Cold Spring Harbor Labaratory
DOI: 10.1101/2024.06.23.600259

READv2: Advanced and user-friendly detection of biological relatedness in archaeogenomics

Auteurs: Erkin Alaçamlı, Thijessen Naidoo, Şevval Aktürk, Merve N. Güler, Igor Mapelli, Kıvılcım Başak Vural, Mehmet Somel, Helena Malmström, Torsten Günther
Publié dans: bioRxiv, Genome Biology (under second round of revision), 2024, ISSN 1474-760X
Éditeur: London: BioMed Central Ltd, 2001
DOI: 10.1101/2024.01.23.576660

Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean

Auteurs: Dilek Koptekin, Ayca Aydogan, Cansu Karamurat, N. Ezgi Altinisik, Kivilcim Basak Vural, D. Deniz Kazanci, Ayca Kucukakdag Dogu, Damla Kaptan, Hasan Can Gemici, Eren Yuncu, Gulsun Umurtak, Refik Duru, Erkan Fidan, Ozlem Cevik, Burcin Erdogu, Taner Korkut, Christopher J. Knusel, Scott Haddow, Clark Spencer Larsen, Rana Ozbal, Fokke Gerritsen, Eylem Ozdogan, Uygar Ozan Usanmaz, Yasin Cemre Derici, Mi
Publié dans: "bioRxiv- awaiting editorial decision from ""Science""", 2024, ISSN 2692-8205
Éditeur: bioRxiv
DOI: 10.1101/2024.06.23.599747

MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes

Auteurs: Gözde Atağ, Kıvılcım Başak Vural, Damla Kaptan, Mustafa Özkan, Dilek Koptekin, Ekin Sağlıcan, Sevcan Doğramacı, Mevlüt Köz, Ardan Yılmaz, Arda Söylev, İnci Togan, Mehmet Somel, Füsun Özer
Publié dans: Open Research Europe, 2022, ISSN 1539-3704
Éditeur: PUBMED, National Institute of Health
DOI: 10.12688/openreseurope.14936.3

An explanation for the neighbour repulsion phenomenon in Patterson's f-statistics,

Auteurs: Gözde Atağ; Mehmet Somel
Publié dans: bioRxiv, Genetics (under second revision), 2024, ISSN 1943-2631
Éditeur: Genetics
DOI: 10.1101/2024.02.17.580509

Pre-processing of paleogenomes: Mitigating reference bias and postmortem damage in ancient genome dataposted on bioRxiv and under second round of revision in Genome Biology

Auteurs: Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, Ekin Sağlıcan, N. Ezgi Altınışık, Anna-Sapfo Malaspinas, Can Alkan, Mehmet Somel
Publié dans: bioRxiv, Genome Biology (under second round of revision), 2023, ISSN 1474-760X
Éditeur: London BioMed Central Ltd 2001-
DOI: 10.1101/2023.11.11.566695

New insights on commemoration of the dead through mortuary and architectural use of pigments at Neolithic Çatalhöyük, Turkey

Auteurs: Schotsmans, E M J; Busacca, G; Lin, S C; Vasi��, M; Lingle, A M; Veropoulidou, R; Mazzucato, C; Tibbetts, B; Haddow, S D; Somel, M; Toksoy-K��ksal, F; Kn��sel, C J; Milella, M
Publié dans: NATURE-Scientific Reports, Numéro 7, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-07284-3

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