Using singleton densities to detect recent selection in Bos taurus.

Matthew Hartfield,Bernt Guldbrandtsen,Nina Aagaard Poulsen,Thomas Bataillon

doi:10.1002/evl3.263

Matthew Hartfield, Bernt Guldbrandtsen + Show 2 more

Open Access

https://doi.org/10.1002/evl3.263

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Abstract

Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the “Singleton Density Score” (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural‐cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans—milk protein content, milk fat content, and stature—have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.

Highlights

Using singleton densities to detect recent selection in Bos taurusThe widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes
Another approach would be to look beyond sequence data and focus on gene networks
We estimated the fixed Ne that would yield the same number of segregating sites in simulations using the standard mutation rate, based on Watterson’s estimator (Watterson, 1975; Hudson, 1990; see Methods for details)

Summary

Using singleton densities to detect recent selection in Bos taurus

The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes We apply one such method, the “Singleton Density Score” (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies. We first performed a genome-wide scan to find individual genetic regions that show signatures of recent selection We identify those relating to cell regulation, catabolic processes, neural-cell adhesion, and immunity.

Evolution Letters

Results

Gene Biotype

Discussion