Selection leads to false inferences of introgression using popular methods.

Autor:	Smith ML; Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA.; Department of Biology, Indiana University, Bloomington, IN 47405, USA., Hahn MW; Department of Biology, Indiana University, Bloomington, IN 47405, USA.; Department of Computer Science, Indiana University, Bloomington, IN 47405, USA.
Jazyk:	angličtina
Zdroj:	Genetics [Genetics] 2024 Aug 07; Vol. 227 (4).
DOI:	10.1093/genetics/iyae089
Abstrakt:	Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g. of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum. Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium-divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed. Competing Interests: Conflicts of interest The author(s) declare no conflict of interest. (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
Databáze:	MEDLINE
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