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Aim  The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard  Iberolacerta monticola , an endemism considered to be facing a high risk of extinction in several populations.    Location  Northwestern quadrant of the Iberian Peninsula.    Methods  We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome  b  (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species.    Results  According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention.    Main Conclusions  Altogether, the data fit a “refugia within refugia” model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of  Iberolacerta . However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.

Causes and Evolutionary Consequences of Population Subdivision of an Iberian Mountain Lizard, Iberolacerta monticola