Abstract
BackgroundAccurate 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.ResultsThis study aims to 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.ConclusionsThis 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.
Highlights
Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution
For VarEff, the main disadvantages are that it cannot infer ancient population changes (e.g., G × μ > 20) and would give a false population decline when a stepwise mutation model (SMM) model was wrongly chosen or when substantial gene flow exists. In view of their advantages and disadvantages, we advocate that researchers should apply MIGRAINE and VarEff in combination when inferring population demography with microsatellite data, which can effectively reduce errors caused by inappropriate model selection and prior parameter settings
Even though whole-genome sequencing is prevalent today, the low mutation rate of SNPs and the limited sampling size are two main hurdles preventing us from inferring recent population dynamics accurately
Summary
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. The SMC methods cannot efficiently reveal the continuous changes of population size within the last ten thousand years [12] and the SFS methods cannot provide an accurate estimation of population demography if the sample size is limited. To accurately predict recent population dynamics is still a major challenge for evolutionary ecologists, which requires molecular markers with much more polymorphisms. Considering there are thousands of studies that have employed microsatellite markers to study species evolution histories in the last two decades, it provides us opportunity to study population demography from these existing data
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
