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Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals
Kuldeep D More1, Ophélie Lebrasseur1, Jaime Lira Garrido1
1Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France.
Molecular Ecology Resources
|April 9, 2025
Summary
A new DNA sequencing method efficiently targets ancient animal DNA from various sources, reducing costs for genetic analysis. This approach reconstructs animal domestication history and diversity over time, even from challenging samples.
Area of Science:
- Ancient DNA analysis
- Archaeozoology
- Population genetics
Background:
- DNA sequencing of ancient animal remains is crucial for understanding domestication history.
- Limited availability and poor DNA preservation in osteological samples hinder cost-effective genetic analysis.
Purpose of the Study:
- To develop an efficient in-solution target-enrichment method for ancient animal DNA analysis.
- To characterize mitochondrial and Y-chromosomal genetic variation in domesticated and wild species.
Main Methods:
- Utilized 80-mer species-specific RNA probes for target enrichment.
- Applied the assay to ancient osteological remains, soil, and sediments.
- Sequenced enriched DNA libraries to analyze genetic diversity.
Main Results:
- Successfully characterized mitochondrial variation in eight key domestic animal species.
- Retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites.
- Obtained sequences from non-target species like bison and cave hyena, demonstrating assay versatility.
Conclusions:
- The target-enrichment assay significantly minimizes sequencing costs for ancient DNA analysis.
- Enables detailed reconstruction of maternal and paternal lineage diversity across space and time.
- Applicable to a wide range of domestic and wild animal species, including environmental samples.
