Summary of the five haplotypes (317bp in length) identified in 9 of the 12 samples judged to be likely positives from ddPCR quantification for eDNA from Blainville’s beaked whales.

Sample codes correspond to Fig 2 and S1 Table. ddPCR concentrations are in copies/μl. Haplotypes identified by conventional amplification and Sanger sequencing are indicated by a ‘+’. Haplotypes identified by next-generation sequencing are represented by the number of assembled reads from triplicate libraries and runs of the MiSeq (250 bp, paired-end). Three of the candidate samples, indicated by an ‘*’, failed to provide an identifiable sequence by either method. See Table 1 for sequence variation defining each haplotype.