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Molecular ecology resources2022; 22(6); 2262-2274; doi: 10.1111/1755-0998.13619

Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.

Abstract: Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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Publication Date: 2022-04-29 PubMed ID: 35398984DOI: 10.1111/1755-0998.13619Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article explores the effect of USER-treatment on hyRAD capture when applied to ancient DNA. Findings suggest that though USER-treatment can enhance the quality of ancient DNA sequence data, it might also introduce significant bias and affect capture outcomes.

Explanation of the Study

The research project is aimed at examining the impact of USER-treatment on hyRAD capture in the context of ancient DNA. Due to the fact that ancient DNA extracts generally contain a high amount of molecules from environmental microbes, capture techniques are frequently required to economically obtain homologous sequence data on a population scale.

  • Ancient DNA is derived from subfossil specimens, which offers a unique chance to extract genetic information from the past.
  • The DNA extracts from these specimens are generally dominated by molecules that originate from environmental microbes. This necessitates the use of capture techniques to economically retrieve orthologous sequence data at the population scale.
  • Post-mortem DNA damage, particularly the transformation of cytosine residues into uracils, greatly inflates sequence error rates. The use of the USER enzymatic mix prior to library construction can mitigate this.
  • The researchers applied hyRAD capture to eight ancient equine subfossil specimens. The specimens included horses, donkeys, and their first-generation mule hybrids from France, aged between the 1st and 17th centuries CE.

Findings of the Study

Upon applying the USER-treatment, the researchers found that it could potentially reduce capture efficacy and introduce a significant bias in the experiment.

  • They discovered that the USER-treatment impacted differently on the size distribution of on-target templates following the capture. This was noticeable with two separate hyRAD probe sets. Interestingly, this particular outcome was not driven by differences in probe sizes and DNA methylation levels.
  • The research also showed that the proportions of donkey-specific and horse-specific alleles in mule capture sequence data were unbalanced. This was attributed to a combination of factors, including USER-treatment, probe sets, and reference bias.
  • While USER-treatment can enhance the quality of ancient DNA sequence data, it also has the potential of significantly affecting hyRAD capture outcomes by introducing bias in the sequence data.

Implications of the Study

The researchers suggest that the technical batch effects caused by USER-treatment might be easier to model and correct using capture with synthetic probes of managed sizes and diversity content. This research provides important insights into the methods used in ancient DNA research and throws up possibilities for improving capture outcomes and reducing biases.

Cite This Article

APA
Suchan T, Chauvey L, Poullet M, Tonasso-Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin-Orlando A, Orlando L. (2022). Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour, 22(6), 2262-2274. https://doi.org/10.1111/1755-0998.13619

Publication

Molecular ecology resources
ISSN: 1755-0998
NlmUniqueID: 101465604
Country: England
Language: English
Volume: 22
Issue: 6
Pages: 2262-2274

Researcher Affiliations

Suchan, Tomasz
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
  • W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland.
Chauvey, Lorelei
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Poullet, Marine
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Tonasso-Calvière, Laure
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Schiavinato, Stéphanie
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Clavel, Pierre
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Clavel, Benoit
  • Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, Paris, France.
Lepetz, Sébastien
  • Archéozoologie, Archéobotanique: sociétés, pratiques et environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, Paris, France.
Seguin-Orlando, Andaine
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), Faculté de Santé, Université Paul Sabatier, Toulouse, France.

MeSH Terms

  • Animals
  • Cytosine
  • DNA Damage
  • DNA Methylation
  • DNA, Ancient
  • Equidae / genetics
  • Horses / genetics
  • Sequence Analysis, DNA / methods

Grant Funding

  • University Paul Sabatier IDEX Chaire d'Excellence (OURASI)
  • CNRS Programme de Recherche Conjoint (PRC)
  • CNRS International Research Project (IRP AMADEUS)
  • 681605 / European Union's Horizon 2020 Research and Innovation Programme
  • 797449 / Marie Sku0142odowska-Curie
  • European Research Council (ERC)

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Citations

This article has been cited 3 times.
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