Protocol for reconstructing ancestral genomes from present-day samples by applying local ancestry inference

Xiaoxi Zhang; Baonan Wang; Jia Wen; Yang Gao; Yuwen Pan; Shuhua Xu

doi:10.1016/j.xpro.2024.103580

Protocol for reconstructing ancestral genomes from present-day samples by applying local ancestry inference

STAR Protoc. 2025 Jan 17;6(1):103580. doi: 10.1016/j.xpro.2024.103580. Online ahead of print.

Authors

Xiaoxi Zhang¹, Baonan Wang², Jia Wen², Yang Gao², Yuwen Pan³, Shuhua Xu⁴

Affiliations

¹ Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
² State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
³ Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
⁴ State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China. Electronic address: [email protected].

PMID: 39826116
DOI: 10.1016/j.xpro.2024.103580

Abstract

The genome of the most recent common ancestor is generally not available but can greatly facilitate the inference of demographic history and the detection of local adaptations. Here, we present a protocol for applying local ancestry inference in present-day samples to reconstruct ancestral genomes. We describe steps for estimating haplotypes, inferring local ancestry, and assembling ancestral haplotypes. This protocol describes the analytic steps of reconstructing ancestral genomes using the example data of the Miao and She target populations. For complete details on the use and execution of this protocol, please refer to Gao et al.¹.

Keywords: Bioinformatics; Evolutionary biology; Genetics; Genomics.