Uncovering the genomic basis of an extraordinary plant invasion

Abstract

Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant’s remarkable success as an invasive species.

Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia

“…Genome resequencing of A. artemisiifolia herbarium samples 11 allowed comparisons between historic and modern populations. We grouped historic samples based on their age and proximity to a modern population sample, resulting in five North American and seven European historic-modern population pairs (Supplementary Table 8 ), which were scanned for signatures of local selective sweeps by identifying windows with extreme shifts in allele frequency and extreme reductions in diversity over time.…”

“…Here we present a new, chromosome-level phased diploid genome assembly for A. artemisiifolia . Using this high-quality reference and over 600 historic and modern A. artemisiifolia re-sequenced genomes from North America and Europe 11 , we were able to uncover, at unprecedented temporal and spatial resolution, the evolutionary-genetic changes accompanying the recent and rapid invasion of Europe by this noxious pest. Previous work leveraged these re-sequenced genomes to understand population structure, invasion history as well as the microbial community of the species 11 .…”

“…Using this high-quality reference and over 600 historic and modern A. artemisiifolia re-sequenced genomes from North America and Europe 11 , we were able to uncover, at unprecedented temporal and spatial resolution, the evolutionary-genetic changes accompanying the recent and rapid invasion of Europe by this noxious pest. Previous work leveraged these re-sequenced genomes to understand population structure, invasion history as well as the microbial community of the species 11 . In this study, we have exposed dramatic genomic signals of parallel climate adaptation and discovered large structural variants that have played a significant adaptive role during this species’ recent range expansion.…”

“…Here, we develop a chromosome-level phased diploid reference assembly, and examine genome-wide variation in over 600 modern and historic A. artemisiifolia samples from throughout North America and Europe 11 . Using these data of unparalleled spatial and temporal resolution, we first identify regions of the genome experiencing climate-mediated selection in the native North American and introduced European ranges leveraging landscape genomic approaches and genome-wide association studies of adapting traits such as flowering time.…”

Forest health in the Anthropocene: the emergence of a novel tree disease is associated with poplar cultivation

“…Phenotypic plasticity as well as rapid adaptation may facilitate the emergence and success of an introduced species into a new environment [7]. Once introduced, pathogens may evolve by acquiring adaptive genes through gene exchange with local species or horizontal gene transfer, or adapt their lifestyle to local new host through host jump.…”