BRYANT David's profile
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BRYANT David

  • Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
  • Combinatorics, Computational complexity, Design and analysis of algorithms, Evolutionary Biology, Genetics and population Genetics, Genomics and Transcriptomics, Graph theory, Probability and statistics
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Areas of expertise
1994-1997 PhD, University of Canterbury, withMike Steel 1998-2000 Postdoc, CRM, Universite de Montreal, with David Sankoff 2000-2001 Postdoc, LIRMM, France, with Olivier Gascuel 2001-2005 Asst. Prof. at McGill, Montreal, in Mathematics & Statistics and Computer Science. Tenured in Mathematics in 2005. 2005-2010 Assoc. Prof At University of Auckland, Department of Mathematics 2010- Professor, University of Otago, Department of Mathematics & Statistics

Review:  1

22 Jul 2024
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Genetic Evidence for Geographic Structure within the Neanderthal Population

Decline in Neanderthal effective population size due to geographic structure and gene flow

Recommended by based on reviews by David Bryant and Guillaume Achaz

Published PSMC estimates of Neanderthal effective population size (𝑁e) show an approximately five-fold decline over the past 20,000 years [1]. This observation may be attributed to a true decline in Neanderthal 𝑁e, statistical error that is notorious with PSMC estimation, or geographic subdivision and gene flow that has been hypothesized to occur within the Neanderthal population. Determining which of these factors contributes to the observed decline in Neanderthal 𝑁e is an important question that can provide insight into human evolutionary history.

Though it is widely believed that the decline in Neanderthal 𝑁e is due to geographic subdivision and gene flow, no prior studies have theoretically examined whether these evolutionary processes can yield the observed pattern. In this paper [2], Rogers tackles this problem by employing two mathematical models to explore the roles of geographic subdivision and gene flow in the Neanderthal population. Results from both models show that geographic subdivision and gene flow can indeed result in a decline in 𝑁e that mirrors the observed decline estimated from empirical data. In contrast, Rogers argues that neither statistical error in PSMC estimates nor a true decline in 𝑁e are expected to produce the consistent decline in estimated 𝑁e observed across three distinct Neanderthal fossils. Statistical error would likely result in variation among these curves, whereas a true decline in 𝑁e would produce shifted curves due to the different ages of the three Neanderthal fossils.

In summary, Rogers provides convincing evidence that the most reasonable explanation for the observed decline in Neanderthal 𝑁e is geographic subdivision and gene flow. Rogers also provides a basis for understanding this observation, suggesting that 𝑁e declines over time because coalescence times are shorter between more recent ancestors, as they are more likely to be geographic neighbors. Hence, Rogers’ theoretical findings shed light on an interesting aspect of human evolutionary history.

References

[1] Fabrizio Mafessoni, Steffi Grote, Cesare de Filippo, Svante Pääbo (2020) “A high-coverage Neandertal genome from Chagyrskaya Cave”. Proceedings of the National Academy of Sciences USA 117: 15132- 15136. https://doi.org/10.1073/pnas.2004944117

[2] Alan Rogers (2024) “Genetic evidence for geographic structure within the Neanderthal population”. bioRxiv, version 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2023.07.28.551046

avatar

BRYANT David

  • Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
  • Combinatorics, Computational complexity, Design and analysis of algorithms, Evolutionary Biology, Genetics and population Genetics, Genomics and Transcriptomics, Graph theory, Probability and statistics
  • recommender

Recommendations:  0

Review:  1

Areas of expertise
1994-1997 PhD, University of Canterbury, withMike Steel 1998-2000 Postdoc, CRM, Universite de Montreal, with David Sankoff 2000-2001 Postdoc, LIRMM, France, with Olivier Gascuel 2001-2005 Asst. Prof. at McGill, Montreal, in Mathematics & Statistics and Computer Science. Tenured in Mathematics in 2005. 2005-2010 Assoc. Prof At University of Auckland, Department of Mathematics 2010- Professor, University of Otago, Department of Mathematics & Statistics