Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California

We analyzed whole-genome data of four spotted owls ( Strix occidentalis ) to provide a broad-scale assessment of the genome-wide nucleotide diversity across S. occidentalis populations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all California S. occidentalis populations. We found no evidence of genetic differentiation between northern spotted owl ( S. o. caurina ) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl ( S. o. occidentalis ) than between populations of S. o. occidentalis and S. o. caurina in northern California. The San Diego County S. o. occidentalis population was substantially diverged from the other three S. occidentalis populations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.