Spotted owls (SOs, Strix occidentalis) are a flagship species inhabiting old-growth forests in western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here, we use an updated SO genome assembly along with 51 high-coverage whole-genome sequences to examine population structure, hybridization, and recent changes in population size in SO and BO. We found that potential hybrids identified from intermediate plumage morphology were a mixture of pure BO, F1 hybrids, and F1 × BO backcrosses. Also, although SO underwent a population bottleneck around the time of the Pleistocene–Holocene transition, their population sizes rebounded and show no evidence of any historical (i.e., 100–10,000 years ago) population decline. This suggests that the current decrease in SO abundance is due to events in the past century. Finally, we estimate that western and eastern BOs have been genetically separated for thousands of years, instead of the previously assumed recent (i.e., <150 years) divergence. Although this result is surprising, it is unclear where the ancestors of western BO lived after the separation. In particular, although BO may have colonized western North America much earlier than the first recorded observations, it is also possible that the estimated divergence time reflects unsampled BO population structure within central or eastern North America.


  • Spotted owls (SOs, Strix occidentalis) occupy forests in western North America

  • The longer scaffolds in our new genome assembly combined with high-coverage whole-genome sequence data enabled us to more accurately estimate past population sizes in both SO and BO, which showed that SO experienced a moderate population bottleneck that may have been coincident with the end of the last Ice Age

  • Given our limited sampling of eastern barred owls (EBOs) individuals, it is possible that there is a substantial amount of genetic variability within EBO, and that there exists an unsampled EBO population that is directly ancestral to extant western barred owls (WBO) individuals

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Spotted owls (SOs, Strix occidentalis) occupy forests in western North America. The listing of NSO has led to changes in forest management practices across the Pacific Northwest, which have had an ongoing economic effect on the West Coast timber industry (Courtney et al 2004). This act was initially motivated by concerns over habitat loss (Forsman et al 1984; Anderson and Burnham 1992), it is clear that competition with the congeneric, invasive barred owl (BO, Strix varia) poses an additional and perhaps greater threat (Diller et al 2016; Dugger et al 2016). BOs continue to expand their range southward, currently overlapping with CSOs as far south as Kern County, near Bakersfield, California


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