Program in Bioinformatics and Integrative Biology
Bioinformatics | Genetics | Genomics | Integrative Biology | Population Biology
Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.
Rights and Permissions
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI of Published Version
PLoS One. 2014 Nov 10;9(11):e110579. doi: 10.1371/journal.pone.0110579. eCollection 2014. Link to article on publisher's site
Poh Y, Domingues VS, Hoekstra HE, Jensen JD. (2014). On the prospect of identifying adaptive loci in recently bottlenecked populations. Open Access Articles. https://doi.org/10.1371/journal.pone.0110579. Retrieved from https://escholarship.umassmed.edu/oapubs/2468
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.