The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Abstract

Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind‐pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native‐range populations has been described as rapid evolution. However, a recent study demonstrated major human‐mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native‐range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine‐scale population genetic structure across the species' native range, we characterized diallelic SNP loci via a reduced‐representation genotyping‐by‐sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.

Parallel clines in native and introduced ragweed populations are likely due to adaptation

“…Population differentiation in neutral markers as measured by FST was low for both the native (0.0639) and invasive (0.0566) ranges. Past work on ragweed has found similarly 307 low FST values (Genton et al 2005 North American ragweed, and found that a solitary genetic cluster was the most likely population 310 structure (Martin et al 2016). Our STRUCTURE analyses showed the highest likelihoods for 311 multiple clusters, but there was not a geographic pattern to the ancestral groupings, especially for 312 the European populations.…”

Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation

“…We excluded snps with a minor allele count lower than 4 (equivalent to 2.2%) or with data missing in greater than 20% of samples. These thresholds were average to conservative based on those used in previous studies (Beck & Semple, 2015; Huang, Poland, Wight, Jackson, & Tinker, 2014; Ilut et al, 2015; Martin, Olsen, Samaniego, Zimmer, & Gilbert, 2016; McGrath, 2014; Mondon, Owens, Poverene, Cantamutto, & Rieseberg, 2017; Sawler et al, 2015; Taylor, Curry, White, Ferretti, & Lovette, 2014). We set the significance threshold for Hardy–Weinberg equilibrium at 1e‐5, which was the midpoint used in a review of past studies (Anderson et al, 2010).…”

Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia

“…We set uniform priors on all model parameters (Table S3) with the exception of timing of admixture in the native range. As native admixture increased rapidly in more recent years following deforestation and intensification of agriculture (Martin, Olsen, Samaniego, Zimmer, & Gilbert, 2016;Martin et al, 2014), prior sampling followed a log-uniform distribution to favour lower values. We specified prior lower bounds for ancestral divergence and upper bounds for the admixture in the native range based on pollen records, which are consistent with southeast and northwest native genetic units prior to 500 years before present (Williams, Shuman, Webb, Bartlein, & Leduc, 2004).…”