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Archaeogenomic analysis of genetic and cultural interactions in Neolithic Anatolian societies


Data Management Plan

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 (, 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 (, 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” (; a subproject of Alexandria Archive Institute) and through Digital Archaeology Record (


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

Author(s): 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
Published in: Communications Biology volume, Issue 4, Article number: 1279 (2021), 2021, ISSN 2399-3642
Publisher: NATURE
DOI: 10.1038/s42003-021-02794-8

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

Author(s): Arda Söylev; Sevim Seda Çokoglu; Dilek Koptekin; Can Alkan; Mehmet Somel
Published in: Crossref, Issue 1, 2022, ISSN 1553-7358
DOI: 10.1101/2021.12.17.473150


Author(s): Reyhan Yaka
Published in: 2020
Publisher: METU

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

Author(s): 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
Published in: Current Biology, Issue Volume 33, Issue 1, 9 January 2023,, 2022, Page(s) Pages 41-57.e15, ISSN 1879-0445
Publisher: 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

Author(s): 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;
Published in: Crossref, Issue 7, 2022, ISSN 2375-2548
Publisher: Science Advances
DOI: 10.1126/sciadv.abo3609

Human inbreeding has decreased in time through the Holocene

Author(s): 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
Published in: CURRENT BIOLOGY, Issue 2, 2021, Page(s) P3925-3934.e8, ISSN 1097-4172
Publisher: CELL PRESS
DOI: 10.1016/j.cub.2021.06.027

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

Author(s): 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
Published in: Open Research Europe, Issue 5, 2022, ISSN 2732-5121
Publisher: Open research Europe
DOI: 10.1101/2022.06.06.491147

Peopling the Landscape of Çatalhöyük: Reports from the 2009-2017 Seasons (British Institute at Ankara Monograph) Hardcover – 28 Jan. 2021

Author(s): 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
Published in: Peopling the Landscape of Çatalhöyük, 2021, Page(s) 395-405
Publisher: The British Institute of Archaeology at Ankara

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