Harald Benke

Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters

The population status of the harbour porpoise (Phocoena phocoena) in the Baltic area has been a continuous matter of debate. Here we present the by far most comprehensive genetic population structure assessment to date for this region, both with regard to geographic coverage and sample size: 497 porpoise samples from North Sea, Skagerrak, Kattegat, Belt Sea, and Inner Baltic Sea were sequenced at the mitochondrial Control Region and 305 of these specimens were typed at 15 polymorphic microsatellite loci. Samples were stratified according to sample type (stranding vs. by-caught), sex, and season (breeding vs. non-breeding season). Our data provide ample evidence for a population split between the Skagerrak and the Belt Sea, with a transition zone in the Kattegat area. Among other measures, this was particularly visible in significant frequency shifts of the most abundant mitochondrial haplotypes. A particular haplotype almost absent in the North Sea was the most abundant in Belt Sea and Inner Baltic Sea. Microsatellites yielded a similar pattern (i.e., turnover in occurrence of clusters identified by STRUCTURE). Moreover, a highly significant association between microsatellite assignment and unlinked mitochondrial haplotypes further indicates a split between North Sea and Baltic porpoises. For the Inner Baltic Sea, we consistently recovered a small, but significant separation from the Belt Sea population. Despite recent arguments that separation should exceed a predefined threshold before populations shall be managed separately, we argue in favour of precautionary acknowledging the Inner Baltic porpoises as a separate management unit, which should receive particular attention, as it is threatened by various factors, in particular local fishery measures.

Methodology and results of calibration of tonal click detectors for small odontocetes (C-PODs)a)

Static acoustic monitoring (SAM) is one major technology for observing small cetacean species. Automatic click loggers deployed for long time periods (>2 months) with a single hydrophone are a standard solution. Acoustic properties, like detection thresholds of these instruments, are essential for interpretation of results, but have nevertheless received little attention. A methodology for calibrating tonal click detectors in small tanks consisting of the determination of the horizontal directivity pattern and detection thresholds including a transfer function is presented. Two approaches were tested to determine detection thresholds by (a) determining the 50% detection threshold and (b) fitting a linear regression model to the recorded relative amplitudes. The tests were carried out on C-PODs (Cetacean PODs, tonal click detectors), the most commonly used instrument for SAM in Europe. Directivity and threshold were tested between 60 and 150 kHz. Directivity showed a maximum variation of 8.5 dB in the horizontal plane. Sensitivity is highest between 80 and 130 kHz and linear (± 3 dB) in this frequency range for most of the instruments tested. C-PODs have a detection threshold (calculated with the linear model) of 114.5 ± 1.2 (standard deviation) dB re 1 μPa peak-peak at 130 kHz.

Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise.

The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

Marine debris in harbour porpoises and seals from German waters

Records of marine debris in and attached to stranded harbour porpoises (Phocoena phocoena), harbour seals (Phoca vitulina) and grey seals (Halichoerus grypus) were studied comprising information on 6587 carcasses collected along the German coast between 1990 and 2014, the decomposition state allowed for necropsy in 1622 cases. Marine debris items were recorded in 31 carcasses including 14 entanglements (5 harbour porpoises, 6 harbour seals, 3 grey seals) and 17 cases of ingestion (4 harbour porpoises, 10 harbour seals, 3 grey seals). Objects comprised general debris (35.1%) and fishing related debris (64.9%). Injuries associated with marine debris included lesions, suppurative ulcerative dermatitis, perforation of the digestive tract, abscessation, suppurative peritonitis and septicaemia. This study is the first investigation of marine debris findings in all three marine mammal species from German waters. It demonstrates the health impacts marine debris can have, including severe suffering and death. The results provide needed information on debris burdens in the North and Baltic Seas for implementing management directives, such as the Marine Strategy Framework Directive (MSFD).

Seasonal and geographical variation of harbour porpoise ( Phocoena phocoena ) habitat use in the German Baltic Sea monitored by passive acoustic methods (PODs)

Harbour porpoises (Phocoena phocoena) were known to be common in the Baltic Sea. In the past several decades, the abundance and distribution has decreased, leading to national and international agreements on the protection of this species. Plans for offshore windmill constructions and proposals for Marine Protected Areas (MPAs) to implement NATURA 2000, led to an increased research effort on the harbour porpoise in the German Exclusive Economic Zones (EEZs) of the North and Baltic Sea. Within this scope, the harbour porpoise habitat use of the German Baltic Sea from Fehmarn to the Pommeranian Bay (Pommersche Bucht) was investigated with the help of self-contained submersible data logger (Porpoise detectors, T-PODs), which register harbour porpoise echolocation click trains.

Arrayvolution—An overview of array systems to study bats and toothed whales

Some echolocation signal parameters can be studied using a single receiver. However, studying parameters such as source level, directionality, and direction of signal emission require the use of multi-receiver arrays. Acoustic localization allows for determination of the position of echolocators at the time of signal emission, and when multiple animals are present, calls can be assigned to individuals based on their location. This combination makes large multi-receiver arrays a powerful tool. Here we present an overview of different array configurations used to study both toothed whales and bats, using a suite of systems ranging from semi-3D-minimum receiver number-number-arrays (3D-MINNAs), linear-2-D-over determined arrays (2D-ODAs), to 3-D-over-determined-arrays (3D-ODAs). We discuss approaches to process and summarize the usually large amounts of data. In some studies, the absolute position of an echolocator and not only relative to the array is crucial. Combining acoustic localizations from a source ...

Large-scale static acoustic survey of a low-density population—Estimating the abundance of the Baltic Sea harbor porpoise

SAMBAH (Static Acoustic Monitoring of the Baltic Sea Harbor Porpoise) is an EU LIFE + -funded project with the primary goal of estimating the abundance and distribution of the critically endangered Baltic Sea harbor porpoise. From May 2011 to April 2013, project members in all EU countries around the Baltic Sea undertook a static acoustic survey using 304 porpoise detectors distributed in a randomly positioned systematic grid in waters 5–80 m deep. In the recorded data, click trains originating from porpoises have been identified automatically using an algorithm developed specifically for Baltic conditions. To determine the click train C-POD detection function, a series of experiments have been carried out, including acoustic tracking of wild free ranging porpoises using hydrophone arrays in an area with moored C-PODs and playbacks of porpoise-like signals at SAMBAH C-PODs during various hydrological conditions. Porpoise abundance has been estimated by counting the number of individuals detected in short time interval windows (snapshots), and then accounting for false positive detections, probability of animals being silent, and probability of detection of non-silent animals within a specified maximum range. We describe the method in detail, and how the auxiliary experiments have enabled us to estimate the required quantities.

Determining the detection function of passive acoustic data loggers for porpoises using a large hydrophone array

Click loggers such as C-PODs are an important tool to monitor the spatial distribution and seasonal occurrence of small odontocetes. To determine absolute density, information on the detection function, the detection probability as a function of distance, and derived from this, the effective detection radius (EDR), is needed. In this study a 15 channel hydrophone array, deployed next to 12 C-PODs, was used to localize porpoises and determine their geo-referenced swim paths using the ship’s GPS and motion sensors. The detection function of C-PODs was then computed using the distance between the animals and each C-POD. In addition to this, the acoustic detection function of C-PODs has been measured by playing back porpoise-like clicks using an omni-directional transducer. The EDR for these porpoise-like clicks with a source level of 168 dB re 1 μPa pp varied from 41 to 243 m. This variation seemed to be related to the sensitivity of the devices; however, season and water depth also seemed to have an influen...