Environmental changes are prominent in Arctic ecosystems, where the distribution, abundance, life history, and health of marine organisms such as the bowhead whale (Balaena mysticetus) are tightly connected to sea ice and sea temperature. However, due to logistical and other challenges of data collection in the Arctic, appropriate assessments of past, present and future effects of climate change and human activities are lacking for many Arctic species. Environmental DNA (eDNA) is emerging as a noninvasive and cost‐effective way of obtaining genetic material from the environment and has the potential to complement traditional methods for biodiversity and genetic monitoring. In this study, we investigate whether eDNA isolated from seawater samples has the capacity to capture the genetic diversity of bowhead whales in Disko Bay, West Greenland, for the implementation of long‐term genetic monitoring programs of key Arctic marine species. A total of 41 eDNA “footprint” samples were obtained from the water surface after a whale had dived and an additional 54 eDNA samples were collected along transect lines. Samples were screened for bowhead DNA using a species‐specific qPCR primer and probe assay, and a subset of 30 samples were successfully Sanger‐sequenced to generate individual mitochondrial control region haplotypes. Moreover, by shotgun sequencing ten footprint samples on an Illumina NovaSeq platform we show that footprints generally contain less than 1% endogenous DNA, resulting in partial mitochondrial genomes in four samples out of ten samples. Our findings suggest that sampling in the footprint or wake of traveling animals is a promising method for capturing the genetic diversity of bowhead whales and other marine megafauna. With optimization of sampling and target DNA sequencing for higher endogenous DNA yield, seawater eDNA samples have a large potential for implementation in the long‐term population genetic monitoring of marine megafauna in the Arctic and elsewhere.

Copepods are considered high quality live feed for fish larvae due to their large within species size span, swimming pattern triggering hunting behaviour, and complete biochemical profile. In a continuous cultivation system aiming at the planktonic calanoid Acartia tonsa an intruding harpacticoid frequently appears. We experimentally evaluate how the interaction from the semi-benthic Tisbe holothuriae is affecting our cultures and ask whether the two copepod-species are expected to pose competitive exclusion or co-exist long-term. This is pursued by establishing 40 days mono-and mixed copepod cultures reared in a stationary setup (S) theoretically advantageous for T. holothuriae and a rotating setup (R) with organisms kept in suspension by use of a plankton wheel, theoretically advantageous for A. tonsa. The carrying capacities of A. tonsa in either mono-or mixed cultures are not affected whether the copepods are subject to S or R treatment. Only exception is the S-setup containing mixed culture were A. tonsa obtains a significantly lower carrying capacity compared with A. tonsa alone in R-setup. The mono-and mixed cultures of T. holothuriae are, however, highly negatively affected by the R setup compared with S setup. A long-term solution to limit the presence of T. holothuriae is to apply turbulence level in a classical stagnant tank setup to an extend that suppress T. holothuriae and simultaneously allow algae in suspension as food for A. tonsa, make their eggs sediment as well as minimize risk of benthic-predation on eggs. K E Y W O R D Sco-existence, culture contamination, logistic population development, niche differentiation, polyculture