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Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls

Naoko T. Fujito, View ORCID ProfileZachary R. Hanna, Michal Levy-Sakin, Rauri C. K. Bowie, Pui-Yan Kwok, John P. Dumbacher, Jeffrey D. Wall
doi: https://doi.org/10.1101/2020.02.18.954685
Naoko T. Fujito
aInstitute for Human Genetics, University of California San Francisco, San Francisco, CA 94143
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  • For correspondence: naoko.fujito@gmail.com jeff.wall@ucsf.edu
Zachary R. Hanna
aInstitute for Human Genetics, University of California San Francisco, San Francisco, CA 94143
bMuseum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720
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  • ORCID record for Zachary R. Hanna
Michal Levy-Sakin
cCardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143
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Rauri C. K. Bowie
bMuseum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720
dDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA 94720
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Pui-Yan Kwok
aInstitute for Human Genetics, University of California San Francisco, San Francisco, CA 94143
cCardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143
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John P. Dumbacher
eDepartment of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA 94118
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Jeffrey D. Wall
aInstitute for Human Genetics, University of California San Francisco, San Francisco, CA 94143
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  • For correspondence: naoko.fujito@gmail.com jeff.wall@ucsf.edu
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Abstract

Spotted owls (SO, Strix occidentalis) are a keystone 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 (subspecies S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurina and occidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.

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Posted February 19, 2020.
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Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls
Naoko T. Fujito, Zachary R. Hanna, Michal Levy-Sakin, Rauri C. K. Bowie, Pui-Yan Kwok, John P. Dumbacher, Jeffrey D. Wall
bioRxiv 2020.02.18.954685; doi: https://doi.org/10.1101/2020.02.18.954685
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Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls
Naoko T. Fujito, Zachary R. Hanna, Michal Levy-Sakin, Rauri C. K. Bowie, Pui-Yan Kwok, John P. Dumbacher, Jeffrey D. Wall
bioRxiv 2020.02.18.954685; doi: https://doi.org/10.1101/2020.02.18.954685

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