The pervasive population genomic impacts of genome duplication, gene flow, and selection

Dr Levi Yant
The John Innes Centre 

The outcrossing relatives Arabidopsis arenosa and Arabidopsis lyrata are increasingly the subjects of population genomic studies of adaptive evolution. These works provide case studies for how population genomics can be applied to targeted questions, from understanding the basis of adaptation to whole genome duplication (WGD) to the genomic basis of adaptation to extreme environments, including toxic mines. I present an overview of our studies that allows for a large-scale investigation of within- and between-population evolutionary dynamics in this model genus. We individually resequenced ~500 A. arenosa genomes from 55 diploid and autopolyploid populations, allowing the dating and ordering of successive selective sweeps as lineages follow distinct evolutionary trajectories and diversify across Europe.

We integrate these data with 120 A. lyrata and Arabidopsis halleri genomes for a genus-wide view of the genomic basis of diverse adaptations. In A. arenosa, we observe that the population genomic consequences of WGD are pervasive: following WGD there is evidence of a reduced efficacy of purifying selection, with an increase in non-synonymous polymorphisms, and local reductions in diversity due to linked selection around selective sweeps are less pronounced. Tetraploid diversity is further enriched via local introgression from distantly related diploid populations to the extent that the signal of tetraploid monophyly is largely erased, except at discrete loci resistant to introgression. In addition, the tetraploids specifically exchange compelling candidate alleles for adaptive gene flow with tetraploid A. lyrata. We hypothesise that the combined effects of initial masking of deleterious mutations, a higher proportion of adaptive substitutions and rampant interploidy (and interspecies) introgression likely all conspire to shape the evolutionary potential of polyploids.