Towards population genetic assessments and species abundance from environmental DNA: A case study with zebrafish in controlled aquaria

Developing robust methods for amplifying and analysing highly-polymorphic nuclear genetic markers from environmental samples could assist in the reliable and scalable long-term monitoring of elusive, threatened or invasive species that are otherwise challenging to observe. In this study, we used zebrafish in controlled aquaria to apply forensic science approaches and demonstrate that microhaplotypes, which are short segments of nuclear DNA (100–300bp) containing two or more single nucleotide polymorphisms (SNPs), can be amplified from trace DNA in water samples to accurately estimate population genetic diversity and species abundance. We successfully amplified a panel of 17 microhaplotypes that comprised 69 SNPs which could reliably estimate population-level allele frequencies and genetic diversity estimates from water DNA. The panel of microhaplotypes amplified from water samples from replicate tanks strongly matched allele frequency estimates from corresponding tissue samples, and could also be used for estimating number of contributors from multi-individual samples. Our research demonstrates the effectiveness and potential of amplifying microhaplotype panels from eDNA as a non-invasive and scalable tool for population genetic studies of aquatic species.