Recent population history in Swedish cattle breeds

In genetic terms, the history of a population can be described by its effective population size over time. We know that domestic cattle have gone through dramatic changes in recent history, including intensifying selection in modern breeding programs and replacement of traditional breeds. 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. We used population genetic simulation to check the inferences.

Our results suggest that the 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. When comparing simulations from the estimated population histories to real data, the proportion of low-frequency variants in real data was different from what was implied by the estimated population histories, and there was somewhat higher genomic inbreeding in real data than implied by the estimated histories.

The estimates of recent population history of cattle 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.