Exploring the historical presence of kākahi (freshwater mussel) in lakes using sedimentary ancient DNA

The freshwater mussel <i>Echyridella</i> spp. (also known as kākahi) is endemic to Aotearoa New Zealand, with 3 different species recorded. Kākahi are critical for maintaining aquatic ecosystem health and have high cultural significance. All 3 species are classified as at risk, and thus the need to better understand their current and historical distribution and abundance across lakes of Aotearoa New Zealand. In this study, we applied a species-specific droplet digital polymerase chain reaction (ddPCR) assay to investigate the historical presence of kākahi DNA preserved along sedimentary sequences retrieved by gravity coring from 9 lakes. Kākahi sedimentary ancient DNA (sedaDNA) from a single species (<i>Echyridella menziesii</i>) was detected within specific layers in 7 of the 9 sediment cores, but it was only consistently identified in 3 lakes, and only in sediment less than ∼500 years old. The kākahi sedaDNA was patchy or absent in the other 6 study lakes, despite the presence of contemporary kākahi populations in at least 2 of them. We assume that no to poor detection resulted from increased distance between coring sites and source populations as well as biotic (e.g., degradation) and abiotic (e.g., sorption) factors specific to each lake affecting sedaDNA preservation in their sediments. Our findings highlight the importance of exercising caution when interpreting results from sedaDNA studies, especially those exploring macroorganisms with low and spatially heterogeneous environmental DNA concentrations.