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Unrooted maximum-likelihood bootstrap consensus tree based on the best fit substitution model (HKY_G4) determined by Bayesian information criteria. Known harbour porpoise haplotypes are indicated by CR01–CR58 (GenBank accession numbers available in electronic supplementary material, table S2). eDNA samples are denoted by blue text and samples with new haplotypes are labelled with red text. Sample names followed by ‘a' or ‘b' denote samples with multiple control region haplotypes.
