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.

Aim: Colonization is a central topic in ecology and one of the cornerstones of island biogeography. Although the evolutionary history of island species is widely studied, the quantification of colonization is particularly challenging because the same area may be colonized multiple times by the same species, whereas initially successful colonization events may eventually be followed by extinction. Nevertheless, an estimation of the actual number of within-archipelago colonization events can be achieved when using adequate sample size and genetic data, which are essential parameters in the inference of colonization success of any species.Location: Canary Islands, Azores and Galápagos Islands.Taxon: Buteo galapagoensis, Croton scouleri, Setophaga petechia aureola and Xylocopa darwini (Galápagos); Canarina canariensis, Cistus monspeliensis, Juniperus cedrus and Olea europaea subsp. guanchica (Canary Islands); and Juniperus brevifolia and Picconia azorica (Azores). Methods:The new R package PAICE uses haplotype (from organelle DNA) sharing and haplotype relationships, and controls for sampling effort to estimate the number of within-archipelago colonization events in island-like systems. PAICE applies a sampling-effort correction based on rarefaction curves of field sampling (number of individuals or populations) and genetic sampling (number of DNA variable positions).The number of colonization events for the 10 insular species were estimated with PAICE and results compared with previous methods.Results: PAICE estimates a number of inter-island colonization events up to an order of magnitude greater than previous methods. Furthermore, PAICE can quantify the colonization events of any study species, in multiple biogeographic contexts and considering sampling size, thus providing a standardized estimate of colonization success. Main conclusions:The new package PAICE provides an estimation of the number of inter-island colonization events (regardless of dispersal routes or rates) based on haplotype data across islands. This new tool will allow gaining new insights on the intensity of long-distance-dispersal events, their drivers and consequences for the assembly of insular faunas and floras.

Aim:To investigate factors that explain the spatial pattern of genetic diversity in three closely related species (Linaria glacialis, Linaria nevadensis and Chaenorhinum glareosum) endemic to a fragile high mountain ecosystem. Location:The alpine belt of Sierra Nevada, Spain. Methods:We analysed the spatial pattern of cpDNA diversity of the three species.To explain the distribution of genetic diversity, we investigated the effect of topographic features and the evolutionary history of the species (demography, habitat availability and colonization dynamics). Results: Genetic diversity was heterogeneous across the landscape. We found moderate positive correlation values between genetic diversity indices of the two Linaria species. We also observed moderate negative correlation values between genetic diversity indices of C. glareosum and those of L. glacialis and L. nevadensis. Topographic variables correlated positively with genetic diversity of the Linaria species and negatively with genetic diversity of C. glareosum. Bayesian skyline plots (BSPs) displayed a shared demographic pattern with a population size stabilization/increase since the LGM (the last 21 kyr) in all three species. Discrete phylogeographical analyses showed similar patterns of westward diffusion for L. nevadensis and C. glareosum. Species distribution models pointed to similar range dynamics in all three species, with a reduction in range size since the LGM.Main conclusions: Different dispersal abilities, demographic trends and colonization patterns can hardly explain the differences in spatial patterns of genetic diversity between the Linaria species and C. glareosum. In contrast, topographic features seem to be an important factor to explain the distribution of genetic diversity in the alpine belt of Sierra Nevada. We point to a relevant role of microniche partitioning in determining patterns of genetic diversity distribution in alpine Mediterranean ecosystems.Furthermore, we highlight the role of microhabitat heterogeneity in the maintenance of distinct lineages, species and genetic diversity in high mountain biodiversity hotspots. K E Y W O R D Scomparative phylogeography, genetic diversity, high mountain, niche partitioning, Quaternary, topography | 75 BLANCO-PASTOR eT AL.