The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.

Long–term, concurrent measurement of population dynamics and associated top–down and bottom–up processes are rare for unmanipulated, terrestrial systems. Here, we analyse populations of moose, their predators (wolves, Canis lupus), their primary winter forage (balsam fir, Abies balsamea) and several climatic variables that were monitored for 40 consecutive years in Isle Royale National Park (544 km²), Lake Superior, USA. We judged the relative importance of top–down, bottom–up and abiotic factors on moose population growth rate by constructing multiple linear regression models, and calculating the proportion of interannual variation in moose population growth rate explained by each factor. Our analysis indicates that more variation in population growth rate is explained by bottom–up than top–down processes, and abiotic factors explain more variation than do bottom–up processes. Surprisingly, winter precipitation did not explain any significant variation in population growth rate. Like that detected for two Norwegian ungulate populations, the relationship between population growth rate and the North Atlantic Oscillation was nonlinear. Although this analysis provides significant insight, much remains unknown: of the models examined, the most parsimonious explain little more than half the variation in moose population growth rate.