Abstract: Accurate inference in phylogeography requires appropriate sampling strategies. Complex questions demand a large sample size at both the population and genetic levels to obtain precise reconstructions. This is the case of the phylogeographic history of Cistus monspeliensis, a plant that displays low plastid (cpDNA) diversity in the Mediterranean Basin but high diversity in the Canary Islands. Here, we aimed to identify Mediterranean refugial areas and to accurately quantify inter‐island colonization events in the Canaries. Using a previous study as starting point, we increased sample size in two ways: (i) additional sampling of plastid genetic markers (from 1041 to 1899 bp); and (ii) additional sampling of populations (from 47 to 69) in long‐term persistence areas suggested by species distribution modeling (SDM). The synergy between SDM and extended population sampling helped find higher genetic diversity. Our deeper phylogeographic sampling of C. monspeliensis revealed the following: (i) potential refugia in long‐term persistence areas with high cpDNA diversity in western Europe and the Canary Islands; and (ii) a significant increase (from 7 to 12) in the number of inferred inter‐island colonization events across the archipelago. Our results stress the usefulness of SDM to identify the genetic signature associated with potential refugial areas. We herein propose a field sampling approach based on SDM that, in combination with a larger cpDNA sampling, can help answer a wide array of phylogeographic questions, such as the location of Quaternary refugia and number of colonizations across archipelagos.

Key words: Canary Islands, Cistaceae, Cistus monspeliensis, ecological niche modeling, Mediterranean Basin, phylogeography, Quaternary refugia, sampling strategy, species distribution modeling