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Table S1. List of tissue samples used in the analyses. Samples that were removed because they were identified as duplicates are not included. Samples listed are contained in the SWFSC Marine Mammal and Turtle Molecular Research Sample Collection. For the CA-offshore samples, designation of strata is recorded in the location column.

Table S2. PCR cycling profiles used for microsatellite amplification.

Table S3. Polymorphic sites for 40 mtDNA haplotypes detected in the eastern North Pacific Ocean (CA_Ttru_##) and an additional 15 mtDNA haplotypes from the Gulf of California (TTGC##), as reported by Segura et al. 2006.

Table S4. Mean log-likelihood of populations tested in structure for CA-coastal and CA-offshore dolphins. Highest value is highlighted in bold.

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