See readme.txt file. Funding provided by: European CommissionCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000780Award Number: LIFE08 NAT/S/000261Funding provided by: Bundesamt für NaturschutzCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100010415Award Number: SAMBAH II 5 Vw/52602/2011-Mar 36032/66Funding provided by: Bundesministerium für Umwelt, Naturschutz, Bau und ReaktorsicherheitCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100005910Award Number: COSAMM FKZ 0325238Funding provided by: CarlsbergfondetCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100002808Award Number: CF16-0861Funding provided by: European Association of Zoos and AquariaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100009167Award Number: Funding provided by: Havs- och VattenmyndighetenCrossref Funder Registry ID: http://dx.doi.org/10.13039/100009486Award Number: Funding provided by: Instytut Meteorologii i Gospodarki Wodnej – Państwowy Instytut BadawczyCrossref Funder Registry ID: http://dx.doi.org/10.13039/100012960Award Number: Funding provided by: Japanese Science and Technology Agency-CREST*Crossref Funder Registry ID: Award Number: 7620-7Funding provided by: Kolmårdens Djurpark*Crossref Funder Registry ID: Award Number: Funding provided by: Maailmann Luonnon Säätiö (WWF) Suomen Rahasto*Crossref Funder Registry ID: Award Number: Funding provided by: MiljøministerietCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100002981Award Number: Funding provided by: Miljø- og FødevareministerietCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100011055Award Number: SN 343/SN-0008Funding provided by: Narodowy Fundusz Ochrony Środowiska i Gospodarki WodnejCrossref Funder Registry ID: http://dx.doi.org/10.13039/100012962Award Number: 561/2009/Wn-50/OP/RE-LF/DFunding provided by: NaturvårdsverketCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100004357Award Number: Funding provided by: SNAK Ph.D. School, Aarhus University*Crossref Funder Registry ID: Award Number: 91147/365Funding provided by: Tampereen Särkänniemi Ltd., Finland*Crossref Funder Registry ID: Award Number: Funding provided by: Turun ammattikorkeakoulu, Finland*Crossref Funder Registry ID: Award Number: Funding provided by: Gdański Uniwersytet MedycznyCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100010609Award Number: Funding provided by: Wojewódzki Fundusz Ochrony Środowiska i Gospodarki Wodnej w GdańskuCrossref Funder Registry ID: http://dx.doi.org/10.13039/100012961Award Number: Funding provided by: YmpäristöministeriöCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100013872Award Number:

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 71-1,105 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 neighbouring 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.

Four main datasets are provided, together with meta-data and processing code files. 1. SAMBAH main survey: passive acoustic monitoring data collected by CPOD click loggers in the Baltic Sea May 2011-April 2013. 2. Great Belt tracking experiment: detection/nondetection of acoustically tracked harbour porpoises May-June 2013 in Great Belt, Denmark. 3. Playback experiment: detection/nondetection of artificial clicks produced to estimate click detectability during the SAMBAH main survey and Great Belt tracking experiment. 4. Tagging study: click production and depth data from 6 tagged porpoises in Danish waters between May 2010 and April 2011.