From Bones to Bonds

Building the genomic basis for Roman kinship studies (2025–2027)

From Bones to Bonds: Building the Genomic Basis for Roman Kinship Studies


Role	Principal Investigator
Funding	TÜBİTAK 2247-B European Research Council (ERC) Support Program
Duration	24 months, 2025–2027
Host institution	Department of Anthropology, Hacettepe University

Overview

How were families and communities organised in Roman Anatolia, and how did kinship, mobility and social structure shape one another? Ancient DNA makes it possible to address these questions directly from the people themselves, but doing so reliably requires well-preserved genomes and kinship methods that remain accurate on degraded, low-coverage data. This project builds that foundation, as preparatory work for a larger ERC Starting Grant research programme on kinship, mobility and social organisation in Roman Anatolia.

Objectives

Assessing DNA preservation. We screen around 50 newly selected Roman-period skeletal remains from different regions of Anatolia, to identify the individuals best suited for high-coverage sequencing and to guide future sampling strategies.

Deepening existing genomes. We deep-sequence previously prepared libraries from 22 individuals that gave promising initial results. Higher-resolution genomes allow more reliable inference of both genetic relatedness and ancestry.

Benchmarking kinship inference. Using simulated ancient-like genomes embedded in known pedigrees, we test how accurately current methods classify relatives, and how they can be adapted to the low coverage and post-mortem damage typical of ancient DNA. The aim is a reproducible, validated framework for kinship inference in archaeological contexts. This work builds on our earlier benchmarking of kinship estimation tools and the development of DeepKin (Aktürk et al., 2024; Güler et al., 2025), as well as our studies of genetic and social kinship in Neolithic Anatolia (Yaka et al., 2021; Yüncü et al., 2025).

Methods and open science

All genomic data are produced in clean-room laboratories dedicated to ancient DNA, using double-stranded library preparation and strict contamination controls, and analysed with established bioinformatic pipelines. Data will be shared publicly following publication, in line with open data principles. The project supports a doctoral fellow and a postdoctoral researcher.

References

2025

DeepKin: Predicting Relatedness from Low-Coverage Genomes and Palaeogenomes with Convolutional Neural Networks

Merve N. Güler, Ardan Yılmaz, Büşra Katırcıoğlu, and 6 more authors

Molecular Ecology Resources, Nov 2025

Abs DOI Bib

DeepKin is a novel tool designed to predict relatedness from genomic data using convolutional neural networks (CNNs). Traditional methods for estimating relatedness often struggle when genomic data is limited, as with palaeogenomes and degraded forensic samples. DeepKin addresses this challenge by leveraging two CNN models, which are trained solely on simulated genomic data, to classify relatedness up to the third degree and to identify parent-offspring and sibling pairs. Our benchmarking shows DeepKin performs comparably or better than the widely used tool READv2. We validated DeepKin, which uses PLINK’s .map and .ped files as input, on empirical palaeogenomes from three archaeological sites, demonstrating its robustness and adaptability across different genetic backgrounds, with accuracy > 90% above 10 K shared SNPs. By capturing information across genomic segments, DeepKin offers a new methodological path for relatedness estimation in settings with highly degraded samples, with applications in ancient DNA, as well as forensic and conservation genetics.
@article{Guler2025-bc, title = {{DeepKin}: Predicting Relatedness from Low-Coverage Genomes and Palaeogenomes with Convolutional Neural Networks}, author = {Güler, Merve N. and Yılmaz, Ardan and Katırcıoğlu, Büşra and Kantar, Sarp and Ünver, Tara Ekin and Vural, Kıvılcım Başak and Altınışık, N. Ezgi and Akbas, Emre and Somel, Mehmet}, journal = {Molecular Ecology Resources}, publisher = {Wiley}, volume = {25}, number = {8}, pages = {e70032}, month = nov, year = {2025}, doi = {10.1111/1755-0998.70032}, }

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},
}

2024

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}, }

2021

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}, }