. 2024 Jun 21;5(2):102985.

doi: 10.1016/j.xpro.2024.102985. Epub 2024 Apr 30.

Protocol for a comprehensive pipeline to study ancient human genomes

Kongyang Zhu¹, Haifeng He¹, Le Tao¹, Hao Ma¹, Xiaomin Yang², Rui Wang¹, Jianxin Guo³, Chuan-Chao Wang⁴

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
² Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China.
³ Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: jxguo@xmu.edu.cn.
⁴ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China. Electronic address: wang@xmu.edu.cn.

PMID: 38691462
PMCID: PMC11070629
DOI: 10.1016/j.xpro.2024.102985

Protocol for a comprehensive pipeline to study ancient human genomes

Kongyang Zhu et al. STAR Protoc. 2024.

. 2024 Jun 21;5(2):102985.

doi: 10.1016/j.xpro.2024.102985. Epub 2024 Apr 30.

Authors

Kongyang Zhu¹, Haifeng He¹, Le Tao¹, Hao Ma¹, Xiaomin Yang², Rui Wang¹, Jianxin Guo³, Chuan-Chao Wang⁴

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
² Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China.
³ Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China. Electronic address: jxguo@xmu.edu.cn.
⁴ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University Xiamen 361005, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen, Fujian 361005, China. Electronic address: wang@xmu.edu.cn.

PMID: 38691462
PMCID: PMC11070629
DOI: 10.1016/j.xpro.2024.102985

Abstract

Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.¹.

Keywords: Genetics; Genomics; Sequence analysis; Sequencing.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

**Figure 1**
Map of electrophoresis Ancient DNA bands should range from 120–200 bp. The size of the markers (M) corresponds to library molecules (loaded on lanes L). DNA band should not be observed in the Negative control (NC) lane; otherwise, the samples may be contaminated by exogenous DNA. The brightness of this graph has been entirely adjusted to present a clear DNA marker.

**Figure 3**
Screenshot of the sample1 output of part 1

**Figure 2**
Screenshot of the sample1 output of AdapterRemoval

**Figure 4**
Ancient DNA damage pattern of sample1 Nucleotide misincorporation patterns caused by C- > T deamination in both ends of ancient DNA sequences.

**Figure 5**
Genetic kin relationships estimated by READ

**Figure 6**
Visualization of first two PCs of the output of smartPCA

**Figure 7**
Admixture ancestry estimation based on the model-based ADMIXTURE analysis

**Figure 8**
The top and bottom five results of outgroup-f₃ statistics show the close relationship between Upper Yellow River populations and the test population

**Figure 9**
The top and bottom five results of f₄-statistics show the close genetics profiles between CDG and JHC

**Figure 10**
Screenshot of the output of the qpAdm provided in CDG.result and JHC.result

See this image and copyright information in PMC

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References

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Protocol for a comprehensive pipeline to study ancient human genomes

Affiliations

Protocol for a comprehensive pipeline to study ancient human genomes

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