Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

Department of Botany Faculty of Science Charles University Benátská 2 128 01 Prague Czech Republic

Department of Cell and Developmental Biology John Innes Centre Norwich NR4 7UH UK

Department of Genetics and Genome Biology University of Leicester Adrian Building University Road Leicester LE1 7RH UK

Future Food Beacon of Excellence and the School of Life Sciences University of Nottingham Nottingham UK

Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3FL UK

The Czech Academy of Sciences Zámek 1 252 43 Průhonice Czech Republic

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