Population genetic data is often essential to inform conservation management. Understanding the distribution of genetic variants within and between populations can reveal novel insights into genetic connectivity and evolutionary processes. However, obtaining such data using invasive approaches such as tissue sampling may negatively affect the very species we are seeking to protect. Thus, interest in using non-invasive environmental DNA (eDNA) techniques for identifying genetic variation within target species populations has grown. Along with this interest comes the desire to expand the amount of population genetic information that can be obtained from eDNA to increasingly large fragments of the genome, such as entire mitogenomes. Here, we introduce an eDNA hybridisation capture approach to sequencing complete mitochondrial genomes of New Zealand fur seals (Arctocephalus forsteri) (Māori: kekeno) from marine water samples. We show that our approach can recover up to 99% of the fur seal mitogenome. Furthermore, we present a pipeline to extract haplotype diversity from such eDNA population genetic data. Haplotypic variation identified using this approach matches previously identified patterns of intraspecific genetic variation from fur seal tissue samples, suggesting that eDNA methods can accurately identify mitochondrial variation. Our study demonstrates that whole mitogenomes can be recovered using hybridisation capture enrichment of eDNA and indicates that eDNA may be a promising tool for population genetics. Within this context, we discuss some of the key challenges that must be overcome before the promise of eDNA can be fully realized.

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

Aquatic environmental DNA (eDNA) surveys have emerged as an alternative method for monitoring complex and vast marine ecosystems. One-to-one comparisons between existing survey techniques and eDNA approaches are essential to determine biases associated with this novel methodology. To date, such direct comparative studies have been scarce in the context of marine eDNA surveys. In this study, we conducted simultaneous baited remote underwater video (BRUV) and eDNA surveys to describe the fish community in Paterson Inlet, Stewart Island/Rakiura, New Zealand. BRUV detected three distinct families of bony fish (Actinopterygii) and four families of cartilaginous fish (Chondrichthyes). Three different eDNA assays, detected 32 (MiFish-U), 42 (MiFish-E), and 23 (16S-Fish) families, spanning the classes of Actinopterygii, Chondrichthyes, Hyperoartia, Mammalia, and Aves. Our direct comparison identified the need for (i) increased sampling, (ii) spatial pooling, and (iii) multiple targeted eDNA assays, to achieve similar detection rates of a given species in eDNA and BRUV monitoring. Diversity, ordination, and indicator species analyses identified distinct eDNA signals between different habitats in our relatively small sampling area, showcasing the high spatial resolution of eDNA approaches in marine habitats. Our results provide valuable insights into the potential biases associated with eDNA monitoring, as well as highlight the power of eDNA for detecting a broad range of taxa beyond traditional observational approaches, including terrestrial, invasive and migratory organisms.