Genomics is modifying our concepts of evolution in homosporous and heterosporous vascular plants.

Across the tree of life, and particularly within land plants, there is a wide diversity and disparity of genome structure. The most well-studied are angiosperms, comprising mostly small and dynamic genomes, with a history of ancient whole genome duplications. Genome structure and evolution have historically been less clear in ferns and lycophytes, and the origin of their large genomes and high chromosome numbers has been debated for decades, centering on differences in reproductive mode (heterospory and homospory). Klekowski (1973) hypothesized that homosporous ferns and lycophytes were mainly inbreeding and that polyploidy allowed for higher genetic diversity via homoeologous heterozygosity. In contrast, Haufler (1987) and others proposed that homosporous ferns and lycophytes had diploid inheritance and outcrossed frequently, a theory supported by genetic crossing, isozymes, and modern comparative genomic analyses. This article summarizes past and current theories on the mechanisms of genome evolution in homosporous plants, highlights the contributions of comparative genomics to this field in the past two decades, and discusses what we may be able to learn by considering the role of meiosis in heterosporous and homosporous fern and lycophyte genome structure.