Avoidable false PSMC population size peaks occur across numerous studies

We detected and solved a common artifact in PSMC and related methods: recent population peaks followed by population collapses. Combining real and simulated genomes, we show that these peaks do not represent true population dynamics. Instead, ill-set default parameters cause false peaks in our own and published data, which can be avoided by adjusted parameter settings. Furthermore, we show that certain population structure changes can cause similar patterns. Newer methods like Beta-PSMC do not always avoid this artifact. Our results suggest testing multiple parameters before interpreting recent population peaks followed by collapses, and call for the development of robust methods.