Background Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. Results This study aims

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... o reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (pGSM) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. Conclusions This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting.