Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters.

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here, we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at eight localities across the North Atlantic and adjacent waters, which we used for population structure, demographic and genotype-environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena and P.p. meridionalis), and three distinct populations within P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima's D suggest population contraction in Black Sea and Iberian porpoises, but expansion in the P.p. phocoena populations. Phylogenetic trees indicate post-glacial colonization from a southern refugium. Genotype-environment association analysis identified salinity as major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation, and how neutral and adaptive markers can give different perspectives on population subdivision. The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

Estimating the abundance of the critically endangered Baltic Proper harbour porpoise (Phocoena phocoena) population using passive acoustic monitoring.

Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid-20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers' spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71-1105 individuals (95% CI, point estimate 491) during May-October within the population's proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighboring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.

No need to shout? Harbor porpoises (Phocoena phocoena) echolocate quietly in confined murky waters of the Wadden Sea.

Porpoise echolocation parameters may vary depending on their acoustic habitat and predominant behavior. Research was conducted in the Wadden Sea, an acoustically complex, tidally driven habitat with high particle resuspension. Source levels and echolocation parameters of wild harbor porpoises were estimated from time-of-arrival-differences of a six-element hydrophone array. The back-calculated peak-to-peak apparent source level of 169 ± 5 dB re 1 µPa was significantly lower than reported from Inner Danish Waters (-20 dB) and British Columbia (-9 dB) with narrower bandwidth. Porpoises therefore reduce their source level in the Wadden Sea under acoustically complex conditions suggesting an avoidance of cluttering.

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.

Determining the detection thresholds for harbor porpoise clicks of autonomous data loggers, the Timing Porpoise Detectors.

Timing Porpoise Detectors (T-PODs, Chelonia Ltd.) are autonomous passive acoustic devices for monitoring odontocetes. They register the time of occurrence and duration of high frequency pulsed sounds as possible odontocetes echolocation clicks. Because of evolution, five T-POD versions exist. Although the manufacturer replaced those by a digital successor, the C-POD, T-PODs are still used, and data from many field studies exist. Characterizing the acoustic properties of T-PODs enables the interpretation of data obtained with different devices. Here, the detection thresholds of different T-POD versions for harbor porpoise clicks were determined. While thresholds among devices were quite variable in the first T-POD generations, they became more standardized in newer versions. Furthermore, the influence of user-controlled settings on the threshold was investigated. From version 3 on, the detection threshold was found to be easily adjustable with version-dependent setting options "minimum intensity" and "sensitivity," enabling the presetting of standard thresholds. In version 4, the setting "click bandwidth" had a strong influence on the detection threshold, while "selectivity" in version 3 and "noise adaptation = ON" or "OFF" in version 4 hardly influenced thresholds obtained in the tank tests. Nevertheless, the latter setting may influence thresholds in a complex acoustic environment like the sea.

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

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.