article published yes Nicholas H Barton author 4880FE40-F248-11E8-B48F-1D18A9856A870000-0002-8548-5240 Arcadio Navarro author Natural populations are structured spatially into local populations and genetically into diverse ‘genetic backgrounds’ defined by different combinations of selected alleles. If selection maintains genetic backgrounds at constant frequency then neutral diversity is enhanced. By contrast, if background frequencies fluctuate then diversity is reduced. Provided that the population size of each background is large enough, these effects can be described by the structured coalescent process. Almost all the extant results based on the coalescent deal with a single selected locus. Yet we know that very large numbers of genes are under selection and that any substantial effects are likely to be due to the cumulative effects of many loci. Here, we set up a general framework for the extension of the coalescent to multilocus scenarios and we use it to study the simplest model, where strong balancing selection acting on a set of n loci maintains 2n backgrounds at constant frequencies and at linkage equilibrium. Analytical results show that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. However, simulation results reveal that the structured coalescent approach breaks down when the number of backgrounds approaches the population size, because of stochastic fluctuations in background frequencies. A new method is needed to extend the structured coalescent to cases with large numbers of backgrounds. Cambridge University Press2002 eng 0016-6723 1207355110.1017/S0016672301005493 792129 - 139 yes Barton, N. H., &#38; Navarro, A. (2002). Extending the coalescent to multilocus systems: the case of balancing selection. <i>Genetical Research</i>. Cambridge University Press. <a href="https://doi.org/10.1017/S0016672301005493">https://doi.org/10.1017/S0016672301005493</a> Barton, Nicholas H., and Arcadio Navarro. “Extending the Coalescent to Multilocus Systems: The Case of Balancing Selection.” <i>Genetical Research</i>, vol. 79, no. 2, Cambridge University Press, 2002, pp. 129–39, doi:<a href="https://doi.org/10.1017/S0016672301005493">10.1017/S0016672301005493</a>. N. H. Barton and A. Navarro, “Extending the coalescent to multilocus systems: the case of balancing selection,” <i>Genetical Research</i>, vol. 79, no. 2. Cambridge University Press, pp. 129–139, 2002. Barton, Nicholas H, and Arcadio Navarro. “Extending the Coalescent to Multilocus Systems: The Case of Balancing Selection.” <i>Genetical Research</i>. Cambridge University Press, 2002. <a href="https://doi.org/10.1017/S0016672301005493">https://doi.org/10.1017/S0016672301005493</a>. Barton NH, Navarro A. 2002. Extending the coalescent to multilocus systems: the case of balancing selection. Genetical Research. 79(2), 129–139. N.H. Barton, A. Navarro, Genetical Research 79 (2002) 129–139. Barton NH, Navarro A. Extending the coalescent to multilocus systems: the case of balancing selection. <i>Genetical Research</i>. 2002;79(2):129-139. doi:<a href="https://doi.org/10.1017/S0016672301005493">10.1017/S0016672301005493</a> 42622018-12-11T12:07:55Z2023-06-06T11:23:19Z