Reconstruct recent multi-population migration history by using identical-by-descent sharing

Wenxiao Zhang; Kai Yuan; Ru Wen; Haifang Li; Xumin Ni

doi:10.1016/j.jgg.2024.02.006

Volume 51 Issue 6

Jun. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(6): 642-651

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Reconstruct recent multi-population migration history by using identical-by-descent sharing

doi: 10.1016/j.jgg.2024.02.006

a. School of Mathematics and Statistics, Beijing Jiaotong University, Beijing 100044, China;
b. The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
c. Baidu Incorporated, Beijing 100085, China

Funds:

This study was supported by the Fundamental Research Funds for the Central Universities (2023JBMC011), the National Natural Science Foundation of China (NSFC) Grant (12271026), the Beijing Natural Science Foundation Grant (L222051), and the Stanley Center for Psychiatric Research at Broad Institute. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.

Received Date: 2023-10-24
Accepted Date: 2024-02-20
Rev Recd Date: 2024-02-19

Available Online: 2025-06-06

Publish Date: 2024-02-27

Abstract

Abstract

Identical-by-descent (IBD) is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction. However, limited by the nature of IBD, which could only capture the relationship between two individuals/haplotypes, existing IBD-based history inference is constrained to two populations. In this study, we propose a framework by leveraging IBD sharing in multi-population and develop a method, MatrixIBD, to reconstruct recent multi-population migration history. Specifically, we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations. Within our model, we establish a theoretical connection between migration history and IBD sharing. Our method is rigorously evaluated through simulations, revealing its remarkable accuracy and robustness. Furthermore, we apply MatrixIBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia. By taking into account the IBD sharing across multiple populations simultaneously, MatrixIBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics, providing a holistic perspective on intricate patterns embedded within the recent population migration history.
- Population genetics,
- IBD sharing,
- Migration history,
- Structured coalescent theory,
- Gene flow

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References(24)

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