Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterize long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector’s and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector’s dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilizing chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores >96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector’s and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.

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.