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Dataset associated with “Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America”




Gaines, T.
Slavov, G.
Hughes, D.
Kuepper, A.
Sparks, C.
Oliva, J.
Vila-Aiub, M.
Garcia, M. A.
Merotto, A.
Neve, P.

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The global invasion, and subsequent spread and evolution of weeds provides unique opportunities to address fundamental questions in evolutionary and invasion ecology. Amaranthus palmeri is a widespread glyphosate-resistant (GR) weed in the USA. Since 2015, GR populations of A. palmeri have been confirmed in South America, raising questions about introduction pathways and the importance of pre- versus post-invasion evolution of GR traits. We used RAD-Seq genotyping to characterize genetic structure of populations from Brazil, Argentina, Uruguay and the USA. We also quantified gene copy number of the glyphosate target, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS) and the presence of an extra-chromosomal circular DNA (eccDNA) replicon known to confer GR in USA populations. Populations in Brazil, Argentina, and Uruguay were only weakly differentiated (pairwise FST  0.043) in comparison to USA populations (mean pairwise FST = 0.161, range = 0.068-0.258), suggesting a single major invasion event. However, elevated EPSPS copy number and the EPSPS replicon were identified in all populations from Brazil and Uruguay, but only in a single Argentinean population. These observations are consistent with independent in situ evolution of glyphosate resistance in Argentina, followed by some limited recent migration of the eccDNA based mechanism from Brazil to Argentina. Taken together, our results are consistent with an initial introduction of A. palmeri into South America sometime before the 1980s, and local evolution of GR in Argentina, followed by a secondary invasion of GR A. palmeri with the unique eccDNA based mechanism from the USA into Brazil and Uruguay during the 2010’s.


VCF file from UNEAK on RAD-Seq data containing 4,659 SNPs that can be used to reproduce all analyses, with a bit of formatting for STRUCTURE, smartpca, PLINK, and BA3.
Department of Agricultural Biology

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Palmer amaranth
Amaranthus palmeri
herbicide resistance
population genomics


Associated Publications

Gaines, T. A., Slavov, G. T., Hughes, D., Küpper, A., Sparks, C. D., Oliva, J., Vila-Aiub, M. M., Garcia, M. A., Merotto, A., & Neve, P. (2021). Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America. Molecular Ecology, 30, 5360– 5372.