Severe bottleneck of ancient Homo populations: Insights from computational modeling and relevant fossil evidence

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ID: 319443
2026
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Abstract
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 ten 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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openalex_W7167065833 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Sumei Zhou, Yi Zhou, Fabio Di Vincenzo, G M Giovanna Manzi, Wangjie Hu, Zi-Qian Hao, Zhen Shao, Yi-Hsuan Pan, Haipeng Li
Journal molecular biology and evolution
Year 2026
DOI
10.1093/molbev/msag157
URL
https://doi.org/10.1093/molbev/msag157
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