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Sawyer S, Gelabert P, Yakir B, Llanos-Lizcano A, Sperduti A, Bondioli L, Cheronet O, Neugebauer-Maresch C, Teschler-Nicola M, Novak M, Pap I, Szikossy I, Hajdu T, Moiseyev V, Gromov A, Zariņa G, Meshorer E, Carmel L, Pinhasi R. Improved detection of methylation in ancient DNA. Genome Biol 2024; 25:261. [PMID: 39390557 PMCID: PMC11465500 DOI: 10.1186/s13059-024-03405-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 09/26/2024] [Indexed: 10/12/2024] Open
Abstract
Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.
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Affiliation(s)
- Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Benjamin Yakir
- Department of Statistics, The Faculty of Social Science, The Hebrew University Mount Scopus, Jerusalem, Israel
| | - Alejandro Llanos-Lizcano
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Facultad de Química y Farmacia, Universidad del Atlántico, Barranquilla, Colombia
| | - Alessandra Sperduti
- Museo Delle Civiltà, Servizio Di Bioarcheologia, Rome, Italy
- Dipartimento di Asia, Africa e Mediterraneo, Università degli Studi di Napoli "L'Orientale", Naples, Italy
| | - Luca Bondioli
- Università Di Padova, Dipartimento Dei Beni Culturali, Padua, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Christine Neugebauer-Maresch
- Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
- Institute of Prehistory and Early History, University of Vienna, Vienna, Austria
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia
| | - Ildikó Pap
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
- Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary
| | | | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), RAS, Saint Petersburg, Russia
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Riga, Latvia
| | - Eran Meshorer
- The Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
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DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience 2023; 26:106144. [PMID: 36843848 PMCID: PMC9950528 DOI: 10.1016/j.isci.2023.106144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
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