Supplemental Material for Hanna et al., 2018 (in review)

Figure S1. Image of barred owls from Siskiyou County. This image displays the ventral plumage of three Strix varia collected in Siskiyou County, California. Owl A is specimen CAS:ORN:92981. Owl B is CAS:ORN:92979. Owl C is CAS:ORN:97181. Author Z.R.H. took this photograph.

Figure S2. Plot of outlier window proportion versus outlier window length for each sample. The x-axis plots the lengths of outlier windows in increments of 50,000 nucleotides (nt). The y-axis displays the number of outlier windows of a given length as a proportion of all analyzed windows. The z-axis separates individual samples, which we grouped by population.

Figure S3. Plot of number of outlier windows versus analyzed windows. The number of spotted owl ancestry windows of length ≥50,000 nt that were outliers relative to the genome-wide average ancestry for those samples is on the y-axis. The x-axis represents the total number of windows analyzed for each sample. We required the presence of data for at least ten variant sites in order to analyze a window for a given sample. Samples with lower sequence coverage tended to have fewer windows that could be analyzed.

Table S1. Specimen institution data. This table provides information regarding the collections that archive the Strix specimens utilized in this study.

Table S2. Additional specimen data. We here provide additional data for each sample, including the taxonomic identification, the county and state of the collection locality, and the date of collection. The column “Pre or Post Contact” documents whether, based upon the date of collection, a sample’s population was in contact with the other species.

Table S3. Population assignment, ancestry, and site coverage values for each sample. The “Category” column provides the population into which we grouped each sample. The spotted owl ancestry values are averages of the ancestry at each variant site across all sites with data for an individual. The site coverage is the average sequence coverage across all sites examined. “SD” stands for “standard deviation”.

Table S4. Mean and standard deviation spotted owl ancestry by population. We provide the mean and standard deviation of spotted owl ancestry for each population. The “All Western Barred Owls” population was a superset of the Siskiyou and Western Barred Owl populations. The “All Barred Owls” population is a combination of all of the Strix varia samples and the “All Spotted Owls” population is a combination of all of the S. occidentalis samples. “SD” stands for “standard deviation”.

Table S5. Tests of significant difference in spotted owl ancestry. We here provide the t-values from multiple Welch’s t-tests conducted for comparisons of spotted owl ancestry among populations. The “All Western Barred Owls” population was a superset of the Siskiyou and Western Barred Owl populations. An asterisk (*) and bold font indicate those tests with p<0.0125, which is the significance cut-off after applying the Bonferroni correction. The “All Barred Owls” population is a combination of all of the Strix varia samples and the “All Spotted Owls” population is a combination of all of the S. occidentalis samples.