Population history of Swedish cattle breeds: estimates and model checking

In this work, we use linkage disequilibrium-based methods to estimate recent population history from genotype data in Swedish cattle breeds, as well as international Holstein and Jersey cattle data for comparison. Our results suggest that these breeds have been effectively large up until recently, when they declined around the onset of systematic breeding. The inferred trajectories were qualitatively similar, with a large historical population and one decline. We used population genetic simulation to check the inferences. When comparing simulations from the inferred population histories to real data, the proportion low-frequency variants in real data was different than was implied by the inferred population histories, and there was somewhat higher genomic inbreeding in real data than implied by the inferred histories. The inferred population histories imply that much of the variation we see today is transient, and it will be lost as the populations settle into a new equilibrium, even if efforts to maintain effective population size at current levels are successful.