Population Genomics of Copy Number Variation in a Natural Population of Teosinte

Understanding genetic diversity in natural populations has long been a central theme for biologists. However, so far most efforts have focused on single nucleotide polymorphisms (SNPs) to characterize genetic diversity, demography, introgression and gene flow. Yet considerable evidence suggests an important evolutionary role for structural variation in shaping genetic and phenotypic diversity. Here, we use high depth whole genome sequencing data from a single natural population of the maize wild relative teosinte to study population genomics of copy number variants (CNVs). We find that a large proportion of the genome shows evidence of segregating CNVs, and that CNV segregation dramatically skews frequencies of the underlying SNPs. While most CNVs appear to be deleterious, we shows that segregating CNVs are found even in regions of the genome shown to be functionally relevant for phenotype, and a small number of CNVs appear to be targeted by positive selection. Taken together, our results begin to shed light on the importance of structural variation in the evolution of large plant genomes.