Population-specific selective sweeps contribute to the maintenance of genetic structure in Chlamydomonas reinhardtii

Microbial eukaryotes often exhibit large effective population sizes and broad dispersal, yet the extent of population structure and the forces shaping it remain poorly understood. While biogeographic structure is often attributed to limits on dispersal, the role of natural selection in maintaining differentiation has received less attention. We investigated population structure and adaptive evolution in the cosmopolitan soil alga Chlamydomonas reinhardtii. In addition to the 35 available North American genome sequences we have sequenced 38 new isolates from Ontario (Canada). Population genetic structure analyses demonstrate that these new isolates from Ontario represent a second well-sampled genetically distinct cluster, and that this structure persists despite the presence of recent migrants. Using this data set we were able to conduct genome-wide scans for selective sweeps across the species and within each population. Our results conservatively identify 151 species-wide sweeps and 325 population-specific signals, showing that positive selection is widespread and common. The continued presence of the two distinct genetic clusters as well as loci under differential selection, provide evidence that local adaptation persists despite ongoing gene flow. Together, our results demonstrate that selection plays a central role in reinforcing geographic structure in this highly dispersive microbe.