Inferring seed bank from hidden Markov models: new insights into metapopulation dynamics in plants

Summary1. Capturing metapopulation dynamics of plants that have seed banks is challenging, because of thedifficulty in characterizing the seed bank in the field.2. To account for the presence of a seed bank, we developed a hidden Markov model, where thefocus species can be present in two forms, both above-ground and below-ground, the latter beingunobservable. We generated patch histories of presence–absence for a species with a one-year seedbank under different colonization–extinction dynamics and metapopulation sizes, using a mechanisticmodel that accounts for three different sources of seedlings (seed bank, newly locally producedseeds and migrant seeds) as well as a disturbance process reflecting extinction. Using the program E - SURGE , we analysed these simulated data to evaluate the statistical performance of the hiddenMarkov model in detecting the presence of a seed bank and providing accurate estimates of themodel parameters for different sets of parameter values.3. Our simulation tests showed that the absence of a seed bank was very well detected when datasets were simulated with no seed bank, regardless the size of the metapopulation. Similarly, thepresence of a seed bank was well detected when data sets were simulated with a seed bank. In thislatter case, detection of the seed bank improved with increasing size of the metapopulation.4. The quality of the estimates of the model parameters increased with the size of the metapopula-tion but still remained high for small metapopulation sizes. The two parameters reflecting the coloni-zation process and seed dormancy were those best estimated. In addition, we showed that ignoringthe presence of a seed bank unvaryingly led to overestimations of colonization and extinction rates.5. Synthesis. Hidden Markov models offer a reliable way to estimate colonization and extinctionrates for plant metapopulations with a seed bank using time series of presence–absence data. There-fore, these models have the potential to provide valuable insights into the metapopulation dynamicsof many plant and animal species with an unobservable life form that have remained poorly studiedbecause of methodological constraints.Key-words: colonization, E-Surge, extinction, hidden Markov model, metapopulation dynamics,multievent model, patch occupancy, plant metapopulation, plant population and community dynamics,seed bankIntroduction

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