Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.
Overview
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- College of Medical Information and Artificial Intelligence, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
Abstract
Reconstructing ancient population size history is essential for understanding the evolutionary origin of Homo sapiens. We recently developed the fast infinitesimal time coalescent process (FitCoal) and detected a severe population bottleneck occurring approximately 930 thousand years ago. However, two recent studies compared FitCoal and mushi and concluded that the severe bottleneck is a statistical artifact. In this study, we compared the two methods against a benchmark of 10 billion msprime coalescent simulations. We demonstrate that FitCoal achieves both superior speed and accuracy in expected site frequency spectrum (SFS) estimation. Analyses of simulated datasets confirmed that FitCoal reliably recovers the bottleneck, whereas mushi fails under identical conditions. Independent fossil and paleoclimate evidence is consistent with the timing and evolutionary impact of this bottleneck, including associations with hominin dispersals, speciation events, and a subsequent increase in brain size. These findings refine the demographic history of Homo during the Pleistocene and highlight the importance of high-precision SFS computation for revealing critical evolutionary transitions that shaped modern human ancestry.
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Zenodo 19435195
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Data availability
FitCoal version 1.3 is freely available at https://
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 4 keywords, 8 MeSH terms, 3 funders, 64 references.
Cite
This paper
Zhou, S., Zhou, Y., Di Vincenzo, F., Manzi, G., Hu, W., Hao, Z., Shao, Z., Pan, Y.-H., & Li, H. (2026). Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence. Molecular biology and evolution, 43(7), msag157. https://
BibTeX
@article{zhou2026severe,
author = {Zhou, Sumei and Zhou, Yiwen and Di Vincenzo, Fabio and Manzi, Giorgio and Hu, Wangjie and Hao, Ziqian and Shao, Zhen and Pan, Yi-Hsuan and Li, Haipeng},
title = {{Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence}},
journal = {Molecular biology and evolution},
year = {2026},
month = jul,
volume = {43},
number = {7},
pages = {msag157},
publisher = {Oxford University Press},
issn = {0737-4038},
doi = {10.1093/
url = {https://
pmid = {42391510},
pmcid = {PMC13367442}
}
RIS
TY - JOUR
AU - Zhou, Sumei
AU - Zhou, Yiwen
AU - Di Vincenzo, Fabio
AU - Manzi, Giorgio
AU - Hu, Wangjie
AU - Hao, Ziqian
AU - Shao, Zhen
AU - Pan, Yi-Hsuan
AU - Li, Haipeng
TI - Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence
T2 - Molecular biology and evolution
J2 - Mol Biol Evol
PY - 2026
DA - 2026/
VL - 43
IS - 7
SP - msag157
SN - 0737-4038
PB - Oxford University Press
DO - 10.1093/
UR - https://
LA - en
ER -
CSL-JSON
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