Author(s): Andrew D. Foote 1 , * , Philip Francis Thomsen 1 , Signe Sveegaard 2 , Magnus Wahlberg 3 , 4 , Jos Kielgast 1 , Line A. Kyhn 2 , Andreas B. Salling 1 , Anders Galatius 2 , Ludovic Orlando 1 , M. Thomas P. Gilbert 1
Introduction
The use of molecular genetic markers for monitoring biodiversity and detecting and identifying species, individuals or measuring population genetic parameters can provide valuable information for the management and conservation of species and ecosystems [1]. Non-invasive sampling using hair or scat has been successfully used in genetic monitoring programs of wide-ranging terrestrial or semi-aquatic species, which often occur at low density [1] and can be a lower cost approach than direct sampling as the individual or species does not have to be directly encountered and greater number of samples can be collected. However, this is offset by what can be increased DNA extraction and sequencing costs and also a decrease in returns to the potentially large numbers of duplicate samples [2]. For fully aquatic species such as cetaceans, the collection of non-invasive samples is less straightforward and often (but not always; see ref [3]) requires the sampler to directly encounter the target species to collect non-invasive samples such as feces, sloughed skin or exhalation blow [3]-[6]. Current non-invasive sampling of marine species therefore has many of the same logistical and financial costs as biopsy sampling. However, biological excretory processes such as the sloughing of skin, urination and defecation can be sources of 'environmental' DNA (eDNA), and can provide a record of the species' presence over the period that the DNA persists in the environment [7]-[14].
In freshwater aquatic environments the use of eDNA for genetic monitoring has been tested by a number of recent studies (e.g. [9], [11]-[14]), which suggest that eDNA is homogenously distributed within freshwater systems and can be effectively used to detect and even quantify species presence [11]. Here, we investigate whether eDNA from the water column can be used to detect target species occurrence of mammals in the marine environment. The use of seawater samples for eDNA analysis is likely to be more challenging than freshwater due to the larger body of source water, strong tide and current action, which will rapidly dilute and disperse the eDNA. Further, the high salinity of the samples may also render amplification of eDNA by polymerase chain reactions (PCRs) more prone to inhibition [15]. Despite these potential drawbacks, quantification of DNA in the sea has been used to provide an indicator of biomass in marine ecosystems [16], and sampling and sequencing of intracellular DNA of microorganisms sampled from seawater has enabled the metagenomic investigation of their biodiversity and community structure [17], [18].
In this study, we test the potential for using eDNA to detect the presence of marine mammals, by using as a model a small cetacean species, the harbor porpoise Phocoena phocoena . The harbor porpoise is the only regularly occurring cetacean species in the western Baltic, the region where...