iScience (Mar 2023)
DNA methylation-based profiling of horse archaeological remains for age-at-death and castration
- Xuexue Liu,
- Andaine Seguin-Orlando,
- Lorelei Chauvey,
- Gaëtan Tressières,
- Stéphanie Schiavinato,
- Laure Tonasso-Calvière,
- Jean-Marc Aury,
- Aude Perdereau,
- Stefanie Wagner,
- Pierre Clavel,
- Oscar Estrada,
- Jianfei Pan,
- Yuehui Ma,
- Jacob Enk,
- Alison Devault,
- Jennifer Klunk,
- Sébastien Lepetz,
- Benoit Clavel,
- Lin Jiang,
- Patrick Wincker,
- Yvette Running Horse Collin,
- Clio Der Sarkissian,
- Ludovic Orlando
Affiliations
- Xuexue Liu
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Andaine Seguin-Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Gaëtan Tressières
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Laure Tonasso-Calvière
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Évry, Université Paris-Saclay, 91042 Évry, France
- Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Évry, Université Paris-Saclay, 91042 Évry, France
- Stefanie Wagner
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France; INRAE Division Ecology and Biodiversity (ECODIV), Castanet Tolosan, France
- Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Oscar Estrada
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Jianfei Pan
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Jacob Enk
- Daicel Arbor Biosicences, Ann Arbor, MI, USA
- Alison Devault
- Daicel Arbor Biosicences, Ann Arbor, MI, USA
- Jennifer Klunk
- Daicel Arbor Biosicences, Ann Arbor, MI, USA
- Sébastien Lepetz
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d’Histoire Naturelle, CNRS, CP 56, 55 Rue Buffon, 75005 Paris, France
- Benoit Clavel
- Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d’Histoire Naturelle, CNRS, CP 56, 55 Rue Buffon, 75005 Paris, France
- Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Évry, Université Paris-Saclay, 91042 Évry, France
- Yvette Running Horse Collin
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Clio Der Sarkissian
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France
- Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, 31000 Toulouse, France; Corresponding author
- Journal volume & issue
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Vol. 26,
no. 3
p. 106144
Abstract
Summary: 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.
