The Great Horned Owl (Bubo virginianus) is a species that shows complex patterns of individual and geographic morphological variation and inhabits myriad habitats throughout the Americas. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger's rule. While untested at the species level, these ecogeographic rules may affect B. virginianus coloration and size. Previous studies have indicated that, despite their morphological variability, little genetic differentiation exists across parts of the range. This study uses reduced representation genome-wide nuclear and mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and assesses the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) south of the Maranon Valley of Peru. We found shallow phylogenetic relationships that loosely follow latitude among populations to the north of the Maranon Valley of Peru, and a deep divergence across this biogeographic barrier, suggesting that B. v. magellanicus may best be treated as a separate species from those northern populations. Differences in relationships between nuclear and mitochondrial data indicate incomplete lineage sorting or hybridization between B. v. magellanicus and northern populations of B. virginianus. Overall, the evidence supports species status for B. v. magellanicus on the basis of differences in morphology, coloration, voice, and genomic divergence, but identifies very shallow divergences within the rest of the range.
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