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Abstract Temporal population genetic studies have investigated evolutionary processes, but few have characterized reproductive system variation. Yet, temporal sampling may improve our understanding of reproductive system evolution through the assessment of the relative rates of selfing, outcrossing, and clonality. In this study, we focused on the monoicous, haploid‐diploid freshwater red algaBatrachospermum gelatinosum. This species has a perennial, microscopic diploid phase (chantransia) that produces an ephemeral, macroscopic haploid phase (gametophyte). Recent work focusing on single‐time point genotyping suggested high rates of intragametophytic selfing, although there was variation among sites. We expand on this work by genotyping 191 gametophytes sampled from four sites that had reproductive system variation based on single‐snapshot genotyping. For this study, we sampled at multiple time points within and among years. Results from intra‐annual data suggested shifts in gametophytic genotypes throughout the season. We hypothesize that this pattern is likely due to the seasonality of the life cycle and the timing of meiosis among the chantransia. Interannual patterns were characterized by consistent genotypic and genetic composition, indicating stability in the prevailing reproductive system through time. Yet, our study identified limits by which available theoretical predictions and analytical tools can resolve reproductive system variation using haploid data. There is a need to develop new analytical tools to understand the evolution of sex by expanding our ability to characterize the spatiotemporal variation in reproductive systems across diverse life cycles. 

Abstract The freshwater red algaBatrachospermum gelatinosumhas a well‐documented distribution spanning historically glaciated and unglaciated eastern North America. This alga has no known desiccation‐resistant propagule; thus, long‐distance dispersal events are likely rare. We predicted strong genetic structure among drainage basins and admixture among sites within basins. We predicted greater genetic diversity at lower latitude sites because they likely serve as refugia and the origin of northward, post‐Pleistocene range expansion. We used 10 microsatellite loci to investigate genetic diversity from 311 gametophytes from 18 sites in five major drainage basins: South Atlantic Gulf, Mid‐Atlantic, Ohio River, Great Lakes, and Northeast. Our data showed strong genetic partitioning among drainage basins and among sites within basins, yet no isolation by distance was detected. Genetic diversity varied widely among sites and was not strictly related to latitude as predicted. The results fromB. gelatinosumprovide strong support that each stream site contributes to the unique genetic variation within the species, potentially due to limited dispersal and the prevailing reproductive mode of intragametophytic selfing. Simulations of migration suggested post‐Pleistocene dispersal from the Mid‐Atlantic.Batrachospermum gelatinosumpotentially persisted in refugia that were just south of the ice margins rather than in the southernmost part of its range. Research of other taxa with similar ranges could determine whether these results are generally applicable for freshwater red algae. Nevertheless, these results fromB. gelatinosumadd to the growing literature focused on the patterns and genetic consequences of post‐Pleistocene range expansion by eastern North American biota.