Protocol for Projecting Allele Frequency Change under Future Climate Change at Adaptive-Associated Loci

Meghan Blumstein; Andrew Richardson; David Weston; Jin Zhang; Wellington Muchero; Robin Hopkins

doi:10.1016/j.xpro.2020.100061

Protocol for Projecting Allele Frequency Change under Future Climate Change at Adaptive-Associated Loci

Meghan Blumstein, Andrew Richardson, David Weston, Jin Zhang, Wellington Muchero, Robin Hopkins

Plant Systems Biology

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

We describe how to predict population-level allele frequency change at loci associated with locally adapted traits under future climate conditions. Our method can identify populations that are at higher risk of local extinction and those that might be prime targets for conservation intervention. We draw on previously developed community ecology statistical methods and apply them in novel ways to plant genomes. While a powerful diagnostic tool, our method requires a wealth of genomic data for use. For complete details on the use and execution of this protocol, please refer to Blumstein et al. (2020).

Original language	English
Article number	100061
Journal	STAR Protocols
Volume	1
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2020.100061
State	Published - Sep 18 2020

Funding

This material is based on work supported by the U.S. Department of Energy , Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program, and by the National Science Foundation Graduate Research Fellowship under grant no. DGE1745303 . The SCGSR program is administered by the Oak Ridge Institute for Science and Education (ORISE) for the DOE. ORISE is managed by ORAU under contract number DE-SC0014664. This material is based on work supported by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program, and by the National Science Foundation Graduate Research Fellowship under grant no. DGE1745303. The SCGSR program is administered by the Oak Ridge Institute for Science and Education (ORISE) for the DOE. ORISE is managed by ORAU under contract number DE-SC0014664. M.B. and R.H. developed statistical protocols. D.W. J.Z. and W.M. provided genomic information and loci of interest GWAS results. A.R. helped design trait sampling, used to produce actual and example data. The authors declare no competing interests.

Funders	Funder number
Office of Science Graduate Student Research
SCGSR
National Science Foundation	DGE1745303
U.S. Department of Energy
Office of Science
Workforce Development for Teachers and Scientists
Oak Ridge Associated Universities	DE-SC0014664
Oak Ridge Institute for Science and Education

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Protocol for Projecting Allele Frequency Change under Future Climate Change at Adaptive-Associated Loci

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