Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well‐documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome‐wide diversity, with 18% higher heterozygosity and 81% lower F_ROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.

Comprehensive population parameter data are useful for assessing effective conservation actions. The Fennoscandian arctic fox Alopex lagopus is critically endangered and the population size is estimated at 120 individuals that are fragmented into four isolated populations. Here, we use molecular tracking and visual observations to estimate population size and survival in one of the populations on the Swedish mountain tundra during a year of low food availability. We collected 98 arctic fox faecal samples during the winter of 2006 and recorded visual observations of ear‐tagged individuals during the summer of 2005 and 2006. The faecal samples were analysed for variation in nine microsatellite loci and matched to the genetic profiles of previously ear‐tagged individuals from 2001 to 2005. During winter 2006, the minimum number alive was 12 individuals using visual observations, 30 using molecular tracking and 36 by combining the datasets. Population size was estimated through mark–recapture for the molecular tracking and visual observation datasets and through rarefaction analyses for molecular tracking data. The mark–recapture estimate for visual observations was uninformative due to the large confidence interval (CI) (i.e. 6–212 individuals). Based on the molecular tracking dataset combined with the minimum number alive for visual observations and molecular tracking, we concluded a consensus population size of 36–55 individuals. We also estimated the age‐specific finite survival rate during 1 year (July 2005 to July 2006) by combining molecular tracking with visual observations. Juvenile survival on a yearly basis was 0.08 (95% CI 0.02–0.18) while adults had a survival of 0.59 (95% CI 0.39–0.82). Juveniles displayed a lower survival than the adults during autumn (P<0.01) whereas no age‐specific survival difference during spring was found. The risk of negative effects due to the small population size and low juvenile survival is accordingly considerable.