Background: We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. Results: Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n = 7) and wolves (n = 18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci were highly correlated. Conclusion: With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.

The relative contributions of genetic and social factors in shaping the living world are a crucial question in ecology. The annual migration of birds to their wintering grounds and back provides significant knowledge in this field of research. Migratory movements are predominantly genetically determined in passerine birds, while in large soaring birds, it is presumed that social (cultural) factors play the largest role. In this study, we show that genetic factors in soaring birds are more important than previously assumed. We used global positioning system (GPS)-telemetry to compare the autumn journeys and wintering ranges of two closely related large raptorial bird species, the greater spotted eagleClanga clangaand the lesser spotted eagleClanga pomarina, and hybrids between them. The timing of migration in hybrids was similar to that of one parental species, but the wintering distributions and home range sizes were similar to those of the other. Tracking data were supported by habitat suitability modelling, based on GPS fixes and ring recoveries. These results suggest a strong genetic influence on migration strategy via a trait-dependent dominance effect, although we cannot rule out the contribution of social interactions.