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Parental relatedness through time revealed by runs of homozygosity in ancient DNA

Author

Listed:
  • Harald Ringbauer

    (Max Planck Institute for Evolutionary Anthropology
    University of Chicago)

  • John Novembre

    (University of Chicago
    University of Chicago)

  • Matthias Steinrücken

    (University of Chicago
    University of Chicago)

Abstract

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.

Suggested Citation

  • Harald Ringbauer & John Novembre & Matthias Steinrücken, 2021. "Parental relatedness through time revealed by runs of homozygosity in ancient DNA," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25289-w
    DOI: 10.1038/s41467-021-25289-w
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    Cited by:

    1. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Selina Carlhoff & Wibhu Kutanan & Adam B. Rohrlach & Cosimo Posth & Mark Stoneking & Kathrin Nägele & Rasmi Shoocongdej & Johannes Krause, 2023. "Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    3. Javier G. Serrano & Alejandra C. Ordóñez & Jonathan Santana & Elías Sánchez-Cañadillas & Matilde Arnay & Amelia Rodríguez-Rodríguez & Jacob Morales & Javier Velasco-Vázquez & Verónica Alberto-Barroso , 2023. "The genomic history of the indigenous people of the Canary Islands," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Kendra A. Sirak & Daniel M. Fernandes & Mark Lipson & Swapan Mallick & Matthew Mah & Iñigo Olalde & Harald Ringbauer & Nadin Rohland & Carla S. Hadden & Éadaoin Harney & Nicole Adamski & Rebecca Berna, 2021. "Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    5. Druet, Tom & Gautier, Mathieu, 2022. "A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors," Theoretical Population Biology, Elsevier, vol. 145(C), pages 38-51.

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