Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches –allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL. We then expand this model-selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for ...