Section: Mathematical & Computational Biology
Topic: Evolution, Genetics/genomics

Genetic Evidence for Geographic Structure within the  Neanderthal Population

Rogers, Alan R.1  
1 University of Utah

10.24072/pcjournal.448 - Peer Community Journal, Volume 4 (2024), article no. e68.

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PSMC estimates of Neanderthal effective population size (Ne) exhibit a roughly 5-fold decline across the most recent 20~ky before the death of each fossil. To explain this pattern, this article develops new theory relating genetic variation to geographic population structure and local extinction. It argues that the observed pattern results from subdivision and gene flow. If two haploid genomes are sampled from the same subpopulation, their recent ancestors are likely to be geographic neighbors and therefore coalesce rapidly. By contrast, remote ancestors are likely to be far apart, and their coalescent rate is lower. Consequently, Ne is larger in the distant past than in the recent past. New theoretical results show that modest rates of extinction cause substantial reductions in heterozygosity, Wright's FST, and Ne.

Published online:
DOI: 10.24072/pcjournal.448
Type: Research article
Keywords: Neanderthals; ancient DNA; geographic population structure; extinction; population history

Rogers, Alan R. 1

1 University of Utah
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Rogers, Alan R. Genetic Evidence for Geographic Structure within the  Neanderthal Population. Peer Community Journal, Volume 4 (2024), article  no. e68. doi : 10.24072/pcjournal.448. https://peercommunityjournal.org/articles/10.24072/pcjournal.448/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100232

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Assis, R. Decline in Neanderthal effective population size due to geographic structure and gene flow, Peer Community in Mathematical and Computational Biology (2024) | DOI

[2] Baumdicker, F.; Bisschop, G.; Goldstein, D.; Gower, G.; Ragsdale, A. P.; Tsambos, G.; Zhu, S.; Eldon, B.; Ellerman, E. C.; Galloway, J. G.; Gladstein, A. L.; Gorjanc, G.; Guo, B.; Jeffery, B.; Kretzschumar, W. W.; Lohse, K.; Matschiner, M.; Nelson, D.; Pope, N. S.; Quinto-Cortés, C. D.; Rodrigues, M. F.; Saunack, K.; Sellinger, T.; Thornton, K.; van Kemenade, H.; Wohns, A. W.; Wong, Y.; Gravel, S.; Kern, A. D.; Koskela, J.; Ralph, P. L.; Kelleher, J. Efficient ancestry and mutation simulation with msprime 1.0, Genetics, Volume 220 (2021) no. 3 | DOI

[3] Bladt, M.; Nielsen, B. F. Matrix-Exponential Distributions in Applied Probability, Probability Theory and Stochastic Modelling, Springer US, Boston, MA, 2017 | DOI

[4] Carmelli, D.; Cavalli-Sforza, L. Some models of population structure and evolution, Theoretical Population Biology, Volume 9 (1976) no. 3, pp. 329-359 | DOI

[5] Chikhi, L.; Rodríguez, W.; Grusea, S.; Santos, P.; Boitard, S.; Mazet, O. The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice, Heredity, Volume 120 (2017) no. 1, pp. 13-24 | DOI

[6] Cox, D.; Miller, H. The Theory of Stochastic Processes, Chapman and Hall, 1965

[7] Hudson, R. R. Gene Genealogies and the Coalescent Process, In: Oxford Surveys in Evolutionary Biology. Ed. by Douglas Futuyma and Janis Antonovics. Vol. 7., Volume 7, Oxford University Press, Oxford, 1990, pp. 1-44

[8] Jacobs, G. S.; Hudjashov, G.; Saag, L.; Kusuma, P.; Darusallam, C. C.; Lawson, D. J.; Mondal, M.; Pagani, L.; Ricaut, F.-X.; Stoneking, M.; Metspalu, M.; Sudoyo, H.; Lansing, J. S.; Cox, M. P. Multiple Deeply Divergent Denisovan Ancestries in Papuans, Cell, Volume 177 (2019) no. 4 | DOI

[9] Kalbfleisch, J.; Prentice, R. The statistical analysis of failure time data. By . New York, 1980. xi + 321 pp. U.S. $31.50, C $40.35. ISBN 0‐471‐05519‐0, Canadian Journal of Statistics, 10, John Wiley & Sons, Inc., New York, 1980 no. 1 | DOI

[10] Kelleher, J.; Etheridge, A. M.; McVean, G. Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes, PLOS Computational Biology, Volume 12 (2016) no. 5 | DOI

[11] Kimura, M.; Weiss, G. H. The stepping stone model of population structure and the decrease of genetic correlation with distance, Genetics, Volume 49 (1964) no. 4, pp. 561-576 | DOI

[12] Laporte, V.; Charlesworth, B. Effective Population Size and Population Subdivision in Demographically Structured Populations, Genetics, Volume 162 (2002) no. 1, pp. 501-519 | DOI

[13] Li, H.; Durbin, R. Inference of human population history from individual whole-genome sequences, Nature, Volume 475 (2011) no. 7357, pp. 493-496 | DOI

[14] Mafessoni, F.; Grote, S.; de Filippo, C.; Slon, V.; Kolobova, K. A.; Viola, B.; Markin, S. V.; Chintalapati, M.; Peyrégne, S.; Skov, L.; Skoglund, P.; Krivoshapkin, A. I.; Derevianko, A. P.; Meyer, M.; Kelso, J.; Peter, B.; Prüfer, K.; Pääbo, S. A high-coverage Neandertal genome from Chagyrskaya Cave, Proceedings of the National Academy of Sciences, Volume 117 (2020) no. 26, pp. 15132-15136 | DOI

[15] Maruyama, T.; Kimura, M. Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent, Proceedings of the National Academy of Sciences, Volume 77 (1980) no. 11, pp. 6710-6714 | DOI

[16] Maruyama, T. On the rate of decrease of heterozygosity in circular stepping stone models of populations, Theoretical Population Biology, Volume 1 (1970) no. 1, pp. 101-119 | DOI

[17] Maruyama, T. Stochastic Problems in Population Genetics, Springer-Verlag., New York, 1077

[18] Mazet, O.; Rodríguez, W.; Grusea, S.; Boitard, S.; Chikhi, L. On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?, Heredity, Volume 116 (2015) no. 4, pp. 362-371 | DOI

[19] Mazet, O.; Noûs, C. Population genetics: coalescence rate and demographic parameters inference, Peer Community Journal, Volume 3 (2023) | DOI

[20] Nei, M.; Takahata, N. Effective population size, genetic diversity, and coalescence time in subdivided populations, Journal of Molecular Evolution, Volume 37 (1993) no. 3 | DOI

[21] Rodríguez, W.; Mazet, O.; Grusea, S.; Arredondo, A.; Corujo, J. M.; Boitard, S.; Chikhi, L. The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure, Heredity, Volume 121 (2018) no. 6, pp. 663-678 | DOI

[22] Rogers, A. R. Legofit: estimating population history from genetic data, BMC Bioinformatics, Volume 20 (2019) no. 1 | DOI

[23] Rogers, A. R. An efficient algorithm for estimating population history from genetic data, Peer Community Journal, Volume 2 (2022) | DOI

[24] Rousset, F. Genetic Structure and Selection in Subdivided Populations, Princeton University Press, 2004 | DOI

[25] Schiffels, S.; Durbin, R. Inferring human population size and separation history from multiple genome sequences, Nature Genetics, Volume 46 (2014) no. 8, pp. 919-925 | DOI

[26] Sexton, J. P.; Hangartner, S. B.; Hoffmann, A. A. Genetic isolation by environment or distance: which pattern of gene flow is most common?, Evolution, Volume 68 (2013) no. 1, pp. 1-15 | DOI

[27] Slatkin, M. Gene flow and genetic drift in a species subject to frequent local extinctions, Theoretical Population Biology, Volume 12 (1977) no. 3, pp. 253-262 | DOI

[28] Slatkin, M. The average number of sites separating DNA sequences drawn from a subdivided population, Theoretical Population Biology, Volume 32 (1987) no. 1, pp. 42-49 | DOI

[29] Slatkin, M. Inbreeding coefficients and coalescence times, Genetical Research, Volume 58 (1991) no. 2, pp. 167-175 | DOI

[30] Strobeck, C. Average Number of Nucleotide Differences in a Sample From a Single Subpopulation: A Test for Population Subdivision, Genetics, Volume 117 (1987) no. 1, pp. 149-153 | DOI

[31] Sukhov, Y.; Kelbert, M. Probability and Statistice by Example: II: Markov Chains: A Primer In Random Processes and their Applications, Cambridge University Press, Cambridge, 2008

[32] Tavaré, S. Line-of-descent and genealogical processes, and their applications in population genetics models, Theoretical Population Biology, Volume 26 (1984) no. 2, pp. 119-164 | DOI

[33] Terhorst, J.; Kamm, J. A.; Song, Y. S. Robust and scalable inference of population history from hundreds of unphased whole genomes, Nature Genetics, Volume 49 (2016) no. 2, pp. 303-309 | DOI

[34] Wakeley, J. Nonequilibrium Migration in Human History, Genetics, Volume 153 (1999) no. 4, pp. 1863-1871 | DOI

[35] Whitlock, M. C.; Barton, N. H. The Effective Size of a Subdivided Population, Genetics, Volume 146 (1997) no. 1, pp. 427-441 | DOI

[36] Whitlock, M. C.; McCauley, D. E. Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups, Evolution, Volume 44 (1990) no. 7, pp. 1717-1724 | DOI

[37] Wilkinson-Herbots, H. M. Genealogy and subpopulation differentiation under various models of population structure, Journal of Mathematical Biology, Volume 37 (1998) no. 6, pp. 535-585 | DOI

[38] Wright, S. Breeding Structure of Populations in Relation to Speciation, The American Naturalist, Volume 74 (1940) no. 752, pp. 232-248 | DOI

[39] Wright, S. Isolation by distance, Genetics, Volume 28 (1943) no. 2, pp. 114-138 | DOI

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