Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology

6. Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One. 2012; 7(8). https://doi. org/10.1371/journal.pone.0041732 PMID: 22952584 7. Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine spe- cies. R Soc Open Sci. 2015; 2(7):150088. https://doi.org/10.1098/rsos.150088 PMID: 26587265 8. Valsecchi E, Bylemans J, Goodman SJ, Lombardi R, Carr I, Castellano L, et al. Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Envi- ronmental DNA. 2020; 2(4):460–476. https://doi.org/10.1002/edn3.72 9. Ballance LT. Cetacean ecology. Encyclopedia of marine mammals (Third Edition). Academic Press. 2018:172–180. 10. Parsons ECM, Baulch S, Bechshoft T, Bellazzi G, Bouchet P, Cosentino AM, et al. Key research ques- tions of global importance for cetacean conservation. Endangered Species Research. 2015; 27(2):113– 118. https://doi.org/10.3354/esr00655 11. Evans PG. Habitat pressures. Encyclopedia of marine mammals (Third Edition). Academic Press. 2018:441–446. https://doi.org/10.1016/B978-0-12-804327-1.00111–4 12. Suarez-Bregua P, A´ lvarez-Gonza´lez M, Parsons KM, Rotllant J, Pierce GJ, Saavedra C. Environmental DNA (eDNA) for monitoring marine mammals: Challenges and opportunities. Frontiers in Marine Sci- ence. 2022; 9:1886. https://doi.org/10.3389/fmars.2022.987774

13. Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, et al. Investigating the Poten- tial Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals. PLoS One. 2012; 7 (8). https://doi.org/10.1371/journal.pone.0041781 PMID: 22952587 14. Ma H, Stewart K, Lougheed S, Zheng J, Wang Y, Zhao J. Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal. Conservation Genet- ics Resources. 2016; 8:561–568. https://doi.org/10.1007/s12686-016-0597-9 15. Baker CS, Steel D, Nieukirk S, Klinck H. Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science. 2018; 5:133. https://doi.org/10.3389/fmars.2018.00133 16. Sze´ kely D, Corfixen NL, Mørch LL, Knudsen SW, McCarthy ML, Teilmann J, et al. Environmental DNA captures the genetic diversity of bowhead whales (Balaena mysticetus) in West Greenland. Environ- mental DNA. 2021; 3(1):248–260. https://doi.org/10.1002/edn3.176 17. Port JA, O’Donnell JL, Romero-Maraccini OC, Leary PR, Litvin SY, Nickols KJ, et al. Assessing verte- brate biodiversity in a kelp forest ecosystem using environmental DNA. Molecular Ecology. 2016; 25 (2):527–541. https://doi.org/10.1111/mec.13481 PMID: 26586544 18. Closek CJ, Santora JA, Starks HA, Schroeder ID, Andruszkiewicz EA, Sakuma KM, et al. Marine Verte- brate Biodiversity and Distribution Within the Central California Current Using Environmental DNA

(eDNA) Metabarcoding and Ecosystem Surveys. Frontiers in Marine Science. 2019; 6. https://doi.org/ 10.3389/fmars.2019.00732 19. Sigsgaard EE, Torquato F, Frøslev TG, Moore ABM, Sørensen JM, Range P, et al. Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats. Conservation Biology. 2020; 34:697–710. https://doi.org/10.1111/cobi.13437 PMID: 31729081 20. Gold Z, Sprague J, Kushner DJ, Zerecero Marin E, Barber PH. eDNA metabarcoding as a biomonitoring tool for marine protected areas. PLoS One. 2021; 16(2). https://doi.org/10.1371/journal.pone.0238557 PMID: 33626067 21. Juhel JB, Marques V, Polanco Ferna´ ndez A, Borrero-Pe´ rez GH, Mutis Martinezguerra M, Valentini A, et al. Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia). Ecology and Evolution. 2021; 11(7):2956–2962. https://doi.org/10. 1002/ece3.7057 PMID: 33841757 22. Valsecchi E, Arcangeli A, Lombardi R, Boyse E, Carr IM, Galli P, et al. Ferries and environmental DNA: Underway sampling from commercial vessels provides new opportunities for systematic genetic sur- veys of marine biodiversity. Frontiers in Marine Science. 2021; 8:704786. https://doi.org/10.3389/fmars. 2021.704786 23. Alter SE, King CD, Chou E, Chin SC, Rekdahl M, Rosenbaum HC. Using Environmental DNA to Detect Whales and Dolphins in the New York Bight. Frontiers in Conservation Science. 2022; 3. https://doi.org/ 10.3389/fcosc.2022.820377 24. Zhang S, Cao Y, Chen B, Jiang P, Fang L, Li H, et al. Assessing the potential use of environmental DNA

for multifaceted genetic monitoring of cetaceans: Example of a wandering whale in a highly disturbed bay area. Ecological Indicators. 2023; 148:110125. https://doi.org/10.1016/j.ecolind.2023.110125 PLOS ONE Environmental DNA as a complementary tool for biodiversity monitoring PLOS ONE | https://doi.org/10.1371/journal.pone.0300992 October 16, 2024 17 / 20