Dataset Information

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

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.

SUBMITTER: Liu X

PROVIDER: S-EPMC9950528 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Publications

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

Liu Xuexue X Seguin-Orlando Andaine A Chauvey Lorelei L Tressières Gaëtan G Schiavinato Stéphanie S Tonasso-Calvière Laure L Aury Jean-Marc JM Perdereau Aude A Wagner Stefanie S Clavel Pierre P Estrada Oscar O Pan Jianfei J Ma Yuehui Y Enk Jacob J Devault Alison A Klunk Jennifer J Lepetz Sébastien S Clavel Benoit B Jiang Lin L Wincker Patrick P Collin Yvette Running Horse YRH Sarkissian Clio Der C Orlando Ludovic L

iScience 20230205 3

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 anci ...[more]

PMID: 36843848

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Project description:Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region's Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay co-amplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method's reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method's reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method's sensitivity. The method's reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains.

Dataset Information

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

Publications

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration.

Similar Datasets

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