Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

Transposable elements (TEs) represent a large and dynamic portion of most eukaryotic genomes, yet little is known about their mutation rates or the correspondence between rates and long-term patterns of accrual. We compare TE activity over long and short time periods by quantifying TE profiles and mutation rates (with and without minimizing selection) among 9 genotypes from three populations of Daphnia magna sampled along a latitudinal gradient. The patterns of genome-wide variation observed in nature mirror direct estimates of rates and spectra observed in a multi-year laboratory mutation accumulation experiment, where net rates range from -11.98 to 12.79 x 10-5 per copy per generation across genotypes. Overall, gains outnumber losses and both types of events are highly deleterious based on comparing lines with and without selection minimized. The rate and spectrum of TE mutations vary widely among genotypes and across TE families/types, even within the same population. We compare TE mutation rates to previously published rates of base substitution, microsatellite mutation, and gene conversion for the same genotypes, and show a correlation only with the latter. Our study provides strong evidence for the notion that TEs represent a highly mutagenic force in the genome. Furthermore, the variation we observe underscores the need to expand the repertoire of mutations studied to include a wider array of mutation types with different underlying mechanisms in order to better understand the evolution of the mutation rate and the ways in which genetic variation is generated genome wide.