Detecting the pest fish, <i>Gambusia affinis</i> from environmental DNA in New Zealand: a comparison of methods

We assessed the usefulness of environmental DNA (eDNA) for monitoring the introduced pest fish <i>Gambusia affinis</i> by filtering water samples from streams in the Nelson and Tasman regions, South Island, New Zealand, known to contain <i>G. affinis,</i> and from streams where <i>G. affinis</i> were absent. We used the Smith Root DNA sampler backpack with two types of filters (1.2 and 5 µm pores), to filter water and capture eDNA, and used quantitative polymerase chain reactions (qPCR), and digital droplet PCR (ddPCR) to measure the amount of <i>G. affinis</i> DNA collected by the two filter sizes. We also used high throughput (Illumina MiSeq) sequencing (HTS) to detect <i>G. affinis.</i> Results from the two PCR methods and the high throughput sequencing were compared to hand net counts of <i>G. affinis</i>. We found that all three methods were equally successful at detecting <i>G. affinis</i> when four replicates were taken from each site, but that sensitivity over all replicates was ddPCR &gt; qPCR &gt; HTS. We conclude that the use of environmental DNA to detect the presence of <i>G. affinis</i> is a useful tool to assist in mapping the distribution of <i>G. affinis</i> and will aid in the control of this invasive species.