More stories

  • in

    Galápagos tortoise stable isotope ecology and the 1850s Floreana Island Chelonoidis niger niger extinction

    Sample procurement and data analysisTo establish a diachronic dataset of Galápagos tortoise dietary stable isotope ecology, we selected samples from five sources (see Supplemental Text): the American Museum of Natural History, New York, New York, (2) the California Academy of Sciences, San Francisco, California, (3) the Natural History Museum, London, England, (4) the National Museum of Natural History, Smithsonian Institution, Washington, D.C., and (5) the Thompson’s Cove (CA-SFR-186H) archaeological site in San Francisco, California. We provide details regarding sample provenience information and date-of-death as supplemental information. From these collections, we obtained single or multiple isotope samples from a total of 57 individual tortoises representing the following subspecies (n = 10) and islands: five C. n. abingdonii (Pinta Island), one C. n. becki (Volcán Wolf, Isabela Island), five C. n. chathamensis (San Cristóbal Island), four C. n. darwini (Santiago Island), thirteen C. n. duncanensis (Pinzón Island), four C. n. guentheri (Sierra Nega, Isabela Island), six C. n. hoodensis (Española Island), one C. n. microphyes (Volcán Darwin, Isabela Island), four C. n. niger (Floreana Island), nine C. n. porteri (Western Santa Cruz Island), one C. n. vicina (Cerro Azul, Isabela Island), one unknown Isabela Island tortoise, two C. n. vicina tortoises which were transported, lived and collected on Rabida Island, and one unknown tortoise (Chelonoidis niger ssp.; unknown Island—the San Francisco Gold Rush sample). The two earliest collected tortoises in our sample date to1833 and the latest tortoise is from 1967, representing a period of 134 years.To understand tissue-specific isotopic variation and fractionation for the purposes of reconstructing long-term dietary ecology, we sampled tortoise bone collagen (n = 57), bone apatite (n = 23), scute keratin (n = 8) and skin (n = 2) for carbon (δ13Ccollagen and δ13Capatite), nitrogen (δ15N), hydrogen (δD) and oxygen (δ18Oapatite) stable isotopes. All samples were drilled or cut using a Dremel rotary tool with either a blade or diamond spherical bit attachment and were transported to the University of New Mexico, Center for Stable Isotopes (UNM-CSI), Albuquerque, NM, for preparation and analysis. All statistical and metric data analysis and visualization occurred in R (4.0.4) and RStudio (2022.02.4). We provide reproducible source code supplemental to the text35.Bone collagen δ13C, δ15N and δDAnalysis of bone collagen, skin and scute keratin for carbon, nitrogen and hydrogen stable isotopes followed standardized protocols (e.g., see36). For bone collagen, we cut and demineralized a small portion of bulk bone in 0.5 N hydrochloric acid (HCl) at 5 °C for 24 h prior to rinsing all samples to neutrality using deionized water. For lipid extraction, we immersed the samples in a solution of 2:1 chloroform:methanol (C2H5Cl3) for 24 h (repeated three times) while also sonicating samples for 15 min to ensure complete chemical saturation. Preparation of skin and scute keratin samples was only included this during the later lipid extraction step (i.e., no demineralization required). After 72 h we rinsed all samples to neutrality and lyophilized the tortoise samples for another 24 h. We then measured approximately 0.5–0.6 mg of bone collagen/skin/scute tissue into tin capsules for carbon (δ13Ccollagen) and nitrogen (δ15N) stable isotope analysis. We also measured approximately 0.2–0.3 mg of bone collagen/skin/scute tissue into silver capsules for hydrogen (δD) isotope analysis. We report isotope values in delta (δ) notation, calculated as: ((Rsample/Rstandard) − 1) × 1000, where Rsample and Rstandard are the ratios (e.g., 13C/12C, 15N/14N) of the unknown and standard material, respectively. Delta values are reported as parts per thousand (‰).Carbon and nitrogen samples were measured on a Costech 4010 elemental analyzer (Valencia, California, USA) coupled to a Scientific Delta V Plus isotope ratio mass spectrometer by a Conflo IV, and hydrogen samples were measured on a Finnigan high-temperature conversion elemental analyzer (TC/EA) coupled to a Thermo Scientific Delta V Plus mass spectrometer by a Conflo IV at UNM-CSI (see37 for details on the high temperature conversion method for hydrogen analysis). All nitrogen and carbon isotope data are reported relative to atmospheric N2 and V-PDB, respectively. The data were corrected using lab standards with values of δ15 N = 6.4‰ and δ13C =  − 26.5‰ (casein protein), and of δ15N = 13.3‰ and δ13C =  − 16.7‰ (tuna muscle) that have been calibrated relative to the universally accepted standards: IAEA-N1, USGS 24, IAEA 600, USGS 63, and USGS 40.To ensure equilibrium between the exchangeable hydrogen in tissue samples and local atmosphere38, we weighed hydrogen standards and samples into silver capsules and allowed both to sit in the laboratory for at least 2 weeks before analysis. Hydrogen data were corrected using three UNM-CSI laboratory keratin standards (δDnon-ex =  − 174‰, − 93‰, and − 54‰) of which the δDnon-ex values were previously determined through a series of atmospheric exchange experiments. These standards were also calibrated to USGS standards CBS and KHS values of − 178.8‰ and − 47.5‰, respectively (see39,40 for details and updated values). To quantitate any error imparted to our collagen data through correction with keratin standards, a UNM-CSI cow (Bos taurus) bone collagen standard was analyzed in every run over a 6-month period (July 2017–January 2018) and gave an inter-run standard deviation of 3.9‰, suggesting the difference in percent exchangeable hydrogen between collagen and keratin tissues did not significantly impact our results. All hydrogen isotope data are reported relative to Vienna-Standard Mean Ocean Water (V-SMOW). The H3 factor was between 8 and 8.5 for all runs.Collagen precision (standard deviation; SD) for within-run analyses is  More

  • in

    Epibiotic fauna of the Antarctic minke whale as a reliable indicator of seasonal movements

    Rice, D. W. Marine mammals of the world: systematics and distribution. In The Society for Marine Mammalogy (ed. Rice, D. W.) 231 (Allen Press, 1998).
    Google Scholar 
    Best, P. B. External characters of southern minke whales and the existence of a diminutive form. Sci. Rep. Whales Res. Inst. 36, 1–33 (1985).
    Google Scholar 
    Acevedo, J. et al. Occurrence of dwarf minke whales (Balaenoptera acutorostrata subsp.) around the Antarctic Peninsula. Polar Biol. 34, 313–318 (2011).Article 

    Google Scholar 
    Risch, D., Norris, T., Curnock, M. & Friedlaender, A. Common and Antarctic minke whales: Conservation status and future research directions. Front. Mar. Sci. 6, 247. https://doi.org/10.3389/fmars.2019.00247 (2019).Article 

    Google Scholar 
    International Whaling Commission (IWC). Report of the scientific committee. J. Cetacean Res. Manag. 14, 102 (2013).
    Google Scholar 
    Matsuoka, K. et al. Overview of minke whale sightings surveys conducted on IWC/IDCR and SOWER Antarctic cruises from 1978/79 to 2000/01. J. Cetacean Res. Manag. 5, 173–201 (2003).
    Google Scholar 
    Glover, K. A. et al. Migration of Antarctic minke whales to the Arctic. PLoS One 5, e15197. https://doi.org/10.1371/journal.pone.0015197 (2010).Article 
    ADS 
    CAS 

    Google Scholar 
    Williams, R., Brierley, A., Friedlaender, A. & Scheidat, M. Densitiy of Antarctic minke whales in Weddell Sea from helicopter survey data. Ecology 63, IA14 (2011).
    Google Scholar 
    Williams, R. et al. Counting whales in a challenging, changing environment. Sci. Rep. 4, 4170. https://doi.org/10.1038/srep04170 (2014).Article 
    CAS 

    Google Scholar 
    Shabangu, F. W., Findlay, K. & Stafford, K. M. Seasonal acoustic occurrence, diel vocalizing patterns and bioduck call-type composition of Antarctic minke whales off the west coast of South Africa and the Maud Rise Antarctica. Mar. Mamm. Sci. 36, 658–675 (2019).Article 

    Google Scholar 
    Kasamatsu, F., Nishiwaki, S. & Ishikawa, H. Breeding areas and southbound migrations of southern minke whales Balaenoptera acutorostrata. Mar. Ecol. Prog. Ser. 119, 1–10 (1995).Article 
    ADS 

    Google Scholar 
    Tamura, T. & Konishi, K. Food habit and prey consumption of Antarctic minke whale Balaenoptera bonaerensis in the JARPA research area. J. Northwest Atl. Fish. Sci. 42, 13–25 (2009).Article 

    Google Scholar 
    Perrin, W. F., Mallette, S. D. & Brownell, R. L. Minke whales. In Encyclopedia of Marine Mammals (eds Perrin, W. F. et al.) 608–613 (Academic Press, 2018).Chapter 

    Google Scholar 
    Taylor, R. J. F. An unusual record of three species of whale being restricted to pools in Antarctic sea-ice. Proc. R. Soc. Lond. 129, 325–331 (1957).
    Google Scholar 
    Ensor, P. H. Minke whales in the pack ice zone, East Antarctica, during the period of maximum annual ice extent. Rep. Int. Whal. Commn 39, 219–225 (1989).
    Google Scholar 
    Scheidat, M. et al. Cetacean surveys in the Southern Ocean using icebreaker-supported helicopters. Polar Biol. 34, 1513–1522 (2011).Article 

    Google Scholar 
    Meirelles, A. C. O. & Furtado-Neto, M. A. A. Stranding of an Antarctic minke whale, Balaenoptera bonaerensis Burmeister, 1867, on the northern coast of South America. Lat. Am. J. Aquat. Mamm. 3, 81–82 (2004).Article 

    Google Scholar 
    Juri, E., Valdivia, M., Simoes-Lopes, P. C. & Le Bas, A. A note on minke whales (Cetacea: Balaenopteridae) in Uruguay: Strandings review. JCRM 21, 135–140 (2020).Article 

    Google Scholar 
    Williamson, G. R. Minke whales off Brazil. Sci. Rep. Whales Res. Inst. 27, 37–59 (1975).
    Google Scholar 
    Pastene, L. A. & Goto, M. Genetic characterization and population genetic structure of the Antarctic minke whale Balaenoptera bonaerensis in the Indo-Pacific region of the Southern Ocean. Fish Sci. 82, 873–886 (2016).Article 
    CAS 

    Google Scholar 
    Balbuena, J. A., Aznar, F. J., Fernández, M. & Raga, J. A. Parasites as indicators of social structure and stock identity of marine mammals. Dev. Mar. Biol. 4, 133–139 (1995).
    Google Scholar 
    Kuramochi, T., Araki, J., Uchida, Moriyama, N., Takeda, Y., Hayashi, N., Wakao, H., Machida, M. & Nagasawa, K. Summary of parasite and epizoit investigations during JARPN surveys 1994–1999, with reference to stock structure analysis for the western North Pacific minke whales. IWC Scientific Committee Workshop to Review the Japanese Whaling Programme under Special Permit for North Pacific Minke Whales (JARPN) SC/F2K/J19 (2000).Kaliszewska, Z. A. et al. Population histories of right whales (Cetacea: Eubalaena) inferred from mitochondrial sequence diversities and divergences of their whale lice (Amphipoda: Cyamus). Mol. Ecol. 14, 3439–3456 (2005).Article 
    CAS 

    Google Scholar 
    Ólafsdóttir, D. & Shinn, A. P. Epibiotic macrofauna on common minke whales, Balaenoptera acutorostrata Lacépède, 1804 Icelandic waters. Parasit. Vectors 6, 1–10 (2013).Article 

    Google Scholar 
    Matthews, C. J., Ghazal, M., Lefort, K. J. & Inuarak, E. Epizoic barnacles on Arctic killer whales indicate residency in warm waters. Mar. Mamm. Sci. 36, 1010–1014 (2020).Article 

    Google Scholar 
    Flach, L., Van Bressem, M. F., Pitombo, F. & Aznar, F. J. Emergence of the epibiotic barnacle Xenobalanus globicipitis in Guiana dolphins after a morbillivirus outbreak in Sepetiba Bay Brazil. Estuar. Coast. Shelf Sci. 263, 107632. https://doi.org/10.1016/j.ecss.2021.107632 (2021).Article 

    Google Scholar 
    Ten, S., Raga, J. A. & Aznar, F. J. Epibiotic fauna on cetaceans worldwide: A systematic review of records and indicator potential. Front. Mar. Sci. 9, 846558. https://doi.org/10.3389/fmars.2022.846558 (2022).Article 

    Google Scholar 
    Liouville, J. Cétacés de l’Antarctique. Paris: Deuxième Expédition Antarctique Française (1908–1910) (1913).Ohsumi, S., Masaki, Y. & Kawamura, A. Stock of the Antarctic minke whale. Sci. Rep. Whales Res. Inst. 22, 75–125 (1970).
    Google Scholar 
    Ohsumi, S. Find of marlin spear from the Antarctic minke whales. Sci. Rep. Whales Res. Inst. 25, 237–239 (1973).
    Google Scholar 
    Ivashin, M. V. External Parasites on Lesser Rorquals in the Antarctic 125–127 (Naukova Dumka, 1975).
    Google Scholar 
    Berzin, A. A. & Vlasova, L. P. Fauna of the Cetacea Cyamidae (Amphipoda) of the world ocean. Investig. Cet. 13, 149–164 (1982).
    Google Scholar 
    Best, P. B. Seasonal abundance, feeding, reproduction, age and growth in minke whales off Durban (with incidental observations from the Antarctic). Rep. Int. Whal. Commn 32, 759–786 (1982).
    Google Scholar 
    Avdeev, V. V. Parasitic amphipods of the family Cyamidae and the problem of Cetacea origin. Biol. Morja 4, 27–33 (1989).
    Google Scholar 
    Bushuev, S. G. A study of the population structure of the southern minke whale (Balaenoptera acutorostrata Lacepede) based on morphological and ecological variability. Rep. Int. Whal. Commn 40, 317–324 (1990).
    Google Scholar 
    Sedlak-Weinstein, E. Preliminary report of parasitic infestation of the minke whale Balaenoptera acutorostrata taken during the 1988/89 Antarctic expedition. Unpublished paper (1990).Dailey, M. D. & Vogelbein, W. Parasite fauna of 3 species of Antarctic whales with reference to their use as potential stock indicators. Fish. Bull. 89, 355–365 (1991).
    Google Scholar 
    Nemoto, T., Best, P. B., Ishimaru, K. & Takano, H. Diatom films on whales in South African waters. Sci. Rep. Whales Res. Inst. 32, 97–103 (1980).
    Google Scholar 
    Donovan, G. A review of IWC stock boundaries. Rep. Int. Whal. Commn 13, 39–68 (1991).
    Google Scholar 
    Lester, R. J. G. & MacKenzie, K. The use and abuse of parasites as stock markers for fish. Fish. Res. 97, 1–2 (2009).Article 

    Google Scholar 
    Ten, S. et al. Epibiotic barnacles of sea turtles as indicators of habitat use and fishery interactions: an analysis of juvenile loggerhead sea turtles, Caretta caretta, in the western Mediterranean. Ecol. Indic. 107, 105672. https://doi.org/10.1016/j.ecolind.2019.105672 (2019).Article 

    Google Scholar 
    Calman, W. T. A whale-barnacle of the genus Xenobalanus from Antarctic Seas. Ann. Mag. Nat. Hist. 6, 165–166 (1920).Article 

    Google Scholar 
    Kato, H., Hiroyama, H., Fujise, Y. & Ono, K. Preliminary report of the 1987/88 Japanese feasibility study of the special permit proposal for Southern Hemisphere Minke Whales. Rep. int. Whal. Commn 39, 235–248 (1989).
    Google Scholar 
    International Whaling Commission (IWC). Report of the Intersessional Workshop to review data and results from special permit research on minke whales in the Antarctic, Tokyo, 7–8 December 2006. J. Cetacean Res. Manag. 10, 411–445 (2008).
    Google Scholar 
    Bush, A. O., Lafferty, K. D., Lotz, J. M. & Shostak, A. W. Parasitology meets ecology on its own terms: Margolis et al. revisited. J. Parasitol. 83, 575–583 (1997).Article 
    CAS 

    Google Scholar 
    Kim, H., Chan, B., Kang, C., Kim, H. & Kim, W. How do whale barnacles live on their hosts? Functional morphology and mating-group sizes of Coronula diadema (Linnaeus, 1767) and Conchoderma auritum (Linnaeus, 1767) (Cirripedia: Thoracicalcarea). J. Crustac. Biol. 40, 808–824 (2020).Article 

    Google Scholar 
    Reiczigel, J. Confidence intervals for the binomial parameter: Some new considerations. Stat. Med. 22, 611–621 (2003).Article 

    Google Scholar 
    Kato, H. Migration strategy of southern minke whales to maintain high reproductive rate. Dev. Mar. Biol. 4, 465–480 (1995).
    Google Scholar 
    Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. M. Mixed effects models and extensions in ecology with R. In Statistics for Biology and Health (ed. Gail, M.) (Springer, 2009).MATH 

    Google Scholar 
    Fransen, C. H. J. M. & Smeenk, C. Whale-lice (Amphipoda: Cyamidae) recorded from The Netherlands. Zool. Meded. 65, 393–405 (1991).
    Google Scholar 
    Barton, N. A., Farewell, T. S. & Hallett, S. H. Using generalized additive models to investigate the environmental effects on pipe failure in clean water networks. NPJ Clean Water 3, 31. https://doi.org/10.1038/s41545-020-0077-3 (2020).Article 

    Google Scholar 
    Schindelin, J. et al. Fiji: An open-source platform for biological-image analysis. Nat. Methods 9, 676–682. https://doi.org/10.1038/nmeth.2019 (2012).Article 
    CAS 

    Google Scholar 
    Kane, E. A., Olson, P. A., Gerrodette, T. & Fiedler, P. Prevalence of the commensal barnacle Xenobalanus globicipitis on cetacean species in the eastern tropical Pacific Ocean, and a review of global occurrence. Fish. Bull. 106, 395–404 (2008).
    Google Scholar 
    Aznar, F. J., Balbuena, J. A. & Raga, J. A. Are epizoites biological indicators of a western Mediterranean striped dolphin die-off?. Dis. Aquat. Organ. 18, 159–163 (1994).Article 

    Google Scholar 
    Carrillo, J. M., Overstreet, R. M., Raga, J. A. & Aznar, F. J. Living on the edge: Settlement patterns by the symbiotic barnacle Xenobalanus globicipitis on small cetaceans. PLoS One 10, e0127367. https://doi.org/10.1371/journal.pone.0127367 (2015).Article 
    CAS 

    Google Scholar 
    Moreno-Colom, P., Ten, S., Raga, J. A. & Aznar, F. J. Spatial distribution and aggregation of Xenobalanus globicipitis on the flukes of striped dolphins, Stenella coeruleoalba: An indicator of host hydrodynamics?. Mar. Mamm. Sci. 36, 897–914 (2020).Article 

    Google Scholar 
    Aznar, F. J. et al. Changes in epizoic crustacean infestations during cetacean die-offs: The mass mortality of Mediterranean striped dolphins Stenella coeruleoalba revisited. Dis. Aquat. Org. 67, 239–247 (2005).Article 
    CAS 

    Google Scholar 
    Wood, S. N. & Augustin, N. H. GAMs with integrated model selection using penalized regression splines and applications to environmental modelling. Ecol. Modell. 157, 157–177 (2002).Article 

    Google Scholar 
    Wood, S. N. Generalized Additive Models: An Introduction with R (Chapman and Hall/CRC, 2017).Book 
    MATH 

    Google Scholar 
    Bloch, D. et al. Short-term movements of long-finned pilot whales Globicephala melas around the Faroe Islands. Wildl. Biol. 9, 47–58 (2003).Article 

    Google Scholar 
    Beasley, I. et al. Stomach contents of long-finned pilot whales, Globicephala melas mass-stranded in Tasmania. PLoS One 14, e0206747. https://doi.org/10.1371/journal.pone.0206747 (2019).Article 
    CAS 

    Google Scholar 
    Ohno, M. & Fujino, K. Biological investigation on the whales caught by the Japanese Antarctic whaling fleets, season 1950/51. Sci. Rep. Whales Res. Inst. 7, 125–188 (1952).
    Google Scholar 
    Clarke, R. The stalked barnacle Conchoderma, ectoparasitic on whales. Norsk Hvalfangst-Tidende 55, 153–168 (1966).
    Google Scholar 
    Christensen, I. First record of gooseneck barnacles (Conchoderma auritum) on a minke whale (Balaenoptera acutorostrata). ICES C. M. 1985/N:9 (1985).Bertulli, C. G., Cecchetti, A., Van Bressem, M. F. & Van Waerebeek, K. Skin disorders in common minke whales and white-beaked dolphins off Iceland, a photographic assessment. J. Mar. Anim. Ecol. 5, 29–40 (2012).
    Google Scholar 
    Knowlton, N. Sibling species in the sea. Annu. Rev. Ecol. Evol. Syst. 24, 189–216 (1993).Article 

    Google Scholar 
    Trontelj, P. & Fišer, C. Perspectives: Cryptic species diversity should not be trivialised. Syst. Biodivers. 7, 1–3 (2009).Article 

    Google Scholar 
    Norris, R. & Hull, P. The temporal dimension of marine speciation. Evol. Ecol. 26, 393–415 (2011).Article 

    Google Scholar 
    Rawson, P., Macnamee, R., Frick, M. & Williams, K. Phylogeography of the coronulid barnacle, Chelonibia testudinaria, from loggerhead sea turtles Caretta caretta. Mol. Ecol. 12, 2697–2706 (2003).Article 
    CAS 

    Google Scholar 
    Cabezas, M. P., Cabezas, P., Machordom, A. & Guerra-García, J. M. Hidden diversity and cryptic speciation refute cosmopolitan distribution in Caprella penantis (Crustacea: Amphipoda: Caprellidae). J. Zool. Syst. Evol. 51, 85–99 (2013).Article 

    Google Scholar 
    Boyd, L. L., Zardus, J. D., Knauer, C. M. & Wood, L. D. Evidence for host selectivity and specialization by epizoic Chelonibia barnacles between hawksbill and green sea turtles. Front. Ecol. Evol. 9, 807237. https://doi.org/10.3389/fevo.2021.807237 (2021).Article 

    Google Scholar 
    Schell, D., Rowntree, V. & Pfeiffer, C. Stable-isotope and electron-microscopic evidence that cyamids (Crustacea: Amphipoda) feed on whale skin. Can. J. Zool. 78, 721–727 (2000).Article 

    Google Scholar 
    Iwasa-Arai, T. & Serejo, C. S. Phylogenetic analysis of the family Cyamidae (Crustacea: Amphipoda): A review based on morphological characters. Zool. J. Linn. Soc. 184, 66–94 (2018).Article 

    Google Scholar 
    Fraija-Fernández, N. et al. Living in a harsh habitat: Epidemiology of the whale louse, Syncyamus aequus (Cyamidae), infecting striped dolphins in the Western Mediterranean. J. Zool. 303, 199–206 (2017).Article 

    Google Scholar 
    Angot, M. Rapport scientifique sur les expeditions baleinieres autour de Madagascar (saisons 1949 et 1950). Mem. Inst. Sci. Madag. Ser. A 6, 439–486 (1951).
    Google Scholar 
    Newman, W. A. & Abbott, D. P. Cirripedia: The barnacles. In Intertidal Invertebrates of California (eds Morris, R. H. et al.) 504–535 (Stanford University Press, 1980).
    Google Scholar 
    Nogata, Y. & Matsumura, K. Larval development and settlement of a whale barnacle. Biol Lett. 2, 92–93 (2006).Article 

    Google Scholar 
    Hiro, F. The fauna of Akkeshi Bay. II. Cirripedia. J. Fac. Sci. Hokkaido Univ. 4, 213–229 (1935).
    Google Scholar 
    Rice, D. W. Progress report on biological studies of the larger Cetacea in the waters off California. Norsk Hvalfangst-Tid 52, 181–187 (1963).
    Google Scholar 
    Klinkhart, E. G. The beluga whale in Alaska. State Alsk. Dep. Fish 7, 11 (1966).
    Google Scholar 
    Nilsson-Cantell, C. A. Cirripedia Thoracica and Acrothoracica. MIOS 5, 1–133 (1978).
    Google Scholar 
    Scarff, J. E. Occurrence of the barnacles Coronula diadema, C. reginae and Cetopirus complanatus (Cirripedia) on right whales. Sci. Rep. Whales Res. Inst. 37, 129–153 (1986).
    Google Scholar 
    Kakuwa, Z., Kawakami, T. & Iguchi, K. Biological investigation on the whales caught by the Japanese Antarctic whaling fleets in the 1951–52 season. Sci. Rep. Whales Res. Inst. 8, 147–213 (1953).
    Google Scholar 
    Nishiwaki, M. Humpback whales in Ryukyuan waters. Sci. Rep. Whales Res. Inst. 14, 49–87 (1959).
    Google Scholar 
    Best, P. B. The presence of coronuline barnacles on a southern right whale Eubalaena australis. S. Afr. J. Mar. Sci. 11, 585–587 (1991).Article 

    Google Scholar 
    Mackintosh, N. A. & Wheeler, J. F. G. Southern blue and fin whales. Disc. Rep. 1, 257–540 (1929).
    Google Scholar 
    Nilsson-Cantell, C. A. Thoracic cirripedes collected in 1925–1927. Disc. Rep. 2, 223–260 (1930).
    Google Scholar 
    Nishiwaki, M. & Hayashi, K. Biological survey of fin and blue whales taken in the Antarctic season 1947–48 by the Japanese fleet. Sci. Rep. Whales Res. Inst. 3, 132–190 (1950).
    Google Scholar 
    Mizue, K. & Murata, T. Biological investigation on the whales caught by the Japanese Antarctic whaling fleets season 1949–50. Sci. Rep. Whales Res. Inst. 6, 73–131 (1951).
    Google Scholar 
    Nishiwaki, M. & Oye, T. Biological investigation on blue whales (Balaenoptera musculus) and Fin Whales (Balaenoptera physalus) caught by the Japanese Antarctic Whaling Fleets. Sci. Rep. Whales Res. Inst. 5, 91–167 (1951).
    Google Scholar 
    Tomilin, A. G. Cetacea. In Mammals of the U.S.S.R. and Adjacent Countries Vol. 9 (ed. Tomilin, A. G.) 717 (Akademii Nauk SSSR, 1957).
    Google Scholar 
    Cockrill, W. R. Pathology of the cetacea. A veterinary study on whales. Br. Vet. J. 116, 1–28 (1960).
    Google Scholar 
    Kawamura, A. Some consideration on the stock unit of sei whales by the aspect of ectoparasitic organisms on the body. Bull. Jpn. Soc. Fish. Oceanogr. 14, 38–43 (1969).
    Google Scholar 
    Fraija-Fernández, N., Hernández-Hortelano, A., Ahuir-Baraja, A. E., Raga, J. A. & Aznar, F. J. Taxonomic status and epidemiology of the mesoparasitic copepod Pennella balaenoptera in cetaceans from the western Mediterranean. Dis. Aquat. Org. 128, 249–258 (2018).Article 

    Google Scholar 
    Foster, B. A. & Willan, R. C. Foreign barnacles transported to New Zealand on an oil platform. N. Z. J. Mar. Freshw. Res. 13, 143–149 (1979).Article 

    Google Scholar 
    González, J. et al. Cirripedia of the Canary islands: Distribution and ecological notes. J. Mar. Biol. Assoc. U.K. 92, 129–141 (2012).Article 

    Google Scholar 
    Zettler, M. L. An example for transatlantic hitchhiking by macrozoobenthic organisms with a research vessel. Helgol. Mar. Res. 75, 4. https://doi.org/10.1186/s10152-021-00549-w (2021).Article 

    Google Scholar 
    Matthews, L. H. The humpback whale Megaptera novaeangliae. Disc. Rep. 17, 7–92 (1937).
    Google Scholar 
    Scheffer, V. B. Organisms collected from whales in the Aleutian Islands. Murrelet 20, 67–69 (1939).Article 

    Google Scholar 
    Symons, H. W. & Weston, R. D. Studies on the humpback whale (Megaptera nodosa) in the Bellinghausen Sea. Norsk Hvalfangsttid 47, 53–81 (1958).
    Google Scholar 
    Van Waerebeek, K., Reyes, J. C. & Alfaro, J. Helminth parasites and phoronts of dusky dolphins Lagenorhynchus obscurus (Gray, 1828) from Peru. Aquat. Mamm. 19, 159–169 (1993).
    Google Scholar 
    Fertl, D. Barnacles. In Encyclopedia of Marine Mammals (eds Perrin, W. F. et al.) 75–78 (Academic Press, 2002).
    Google Scholar 
    Cornwall, I. E. The barnacles of british Columbia. Br. Col. Prov. Mus. Dept. 7, 5–69 (1955).
    Google Scholar 
    Abaunza, P., Arroyo, N. L. & Preciado, I. A contribution to the knowledge on the morphometry and the anatomical characters of Pennella balaenopterae (Copepoda, Ciphonostomatoida, Pennellidae), with special reference to the buccal complex. Crustaceana 74, 193–210 (2001).Article 

    Google Scholar 
    Marcer, F. et al. Parasitological and pathological findings in fin whales Balaenoptera physalus stranded along Italian coastlines. Dis. Aquat. Org. 133, 25–37 (2019).Article 
    CAS 

    Google Scholar 
    Turner, W. On Pennella balænopteræ: A crustacean, parasitic on a finner whale, Balaenoptera musculus. Earth. Environ. Sci. Trans. R. Soc. Edinb. 41, 409–434 (1905).Article 

    Google Scholar 
    Walker, W. A. & Hanson, M. B. Biological observations on Stejneger’s beaked whale, Mesoplodon stejnegeri, from strandings on Adak Alaska. Mar. Mamm. Sci. 15, 1314–1329 (1999).Article 

    Google Scholar 
    Delaney, M. A., Ford, J. K. B., Tang, K. & Gaydos, J. K. Mesoparasitic copepod (Pennella balaenopterae) infestation of a stranded offshore orca (Orcinus orca) in Southeast Alaska: Review of significance as a health indicator in cetaceans. In IAAAM 21–26 (2016).Suyama, S., Kakehi, S., Yanagimoto, T. & Chow, S. Infection of the pacific saury Cololabis saira (Brevoort, 1856) (Teleostei: Beloniformes: Scomberesocidae) by Pennella sp. (Copepoda: Siphonostomatoida: Pennellidae) south of the Subarctic Front. J. Crust. Biol. 40, 384–389 (2020).Article 

    Google Scholar 
    Rowntree, V. J. Feeding, distribution and reproductive behavior of cyamids (Crustacea: Amphipoda) living on humpback and right whales. Can. J. Zool. 74, 103–109 (1996).Article 

    Google Scholar 
    Leung, Y. M. Life cycle of Cyamus scammoni (Amphipoda: Cyamidae), ectoparasite of gray whale, with a remark on the associated species. Sci. Rep. Whales Res. Inst. 28, 153–160 (1976).
    Google Scholar 
    MacIntyre, R. J. Rapid growth in stalked barnacles. Nature 212, 637–638 (1966).Article 
    ADS 

    Google Scholar 
    Rasmussen, T. Notes on the biology of the shipfouling gooseneck barnacle Conchoderma auritum Linnaeus, 1776 (Cirripedia; Lepadomorpha). Biol. Mar. 2, 37–44 (1980).
    Google Scholar 
    Dalley, R. & Crisp, D. J. Conchoderma: A fouling hazard to ships underway. Mar. Biol. Lett. 2, 141–152 (1981).
    Google Scholar 
    Dalley, R. The larval stages of the oceanic, pedunculate barnacle Conchoderma auritum (L) (Cirripedia, Thoracica). Crustaceana 46, 39–54 (1984).Article 

    Google Scholar 
    Foskolos, I., Provata, M. T. & Frantzis, A. First record of Conchoderma auritum (Cirripedia: Lepadidae) on Ziphius cavirostris (Cetacea: Ziphiidae) in Greece. Ann. Ser. Hist. 27, 29–34 (2017).
    Google Scholar 
    Lee, J. F., Friedlaender, A. S., Oliver, M. J. & DeLiberty, T. L. Behavior of satellite-tracked Antarctic minke whales (Balaenoptera bonaerensis) in relation to environmental factors around the western Antarctic Peninsula. Anim. Biotelem. 5, 23. https://doi.org/10.1186/s40317-017-0138-7 (2017).Article 

    Google Scholar 
    Darwin, C. A Monograph on the Subclass Cirripedia Vol. 1 (The Ray Society, 1851).
    Google Scholar 
    Tsikhon-Lukanina, V. A., Soldatova, I. N., Kuznetsova, I. A. & Il’in, I. I. Macrofouling community in the Strait of Tunisia (Sicily). Oceanology 16, 519–522 (1977).
    Google Scholar 
    Nilsson-Cantell, C. A. Cirripedien von der Stewart Insel und von Südgeorgien. Senckenbergiana 12, 210–213 (1930).
    Google Scholar 
    Slijper, E. J. Whales (Hutchinson, 1962).
    Google Scholar 
    Kaufman, G. D. & Forestell, P. H. Hawaii’s humpback whales, a complete whalewatching guide (Pacific Whale Foundation Press, 1986).
    Google Scholar 
    Dawbin, W. H. Baleen whales. In Whales, Dolphins and Porpoises (eds Harrison, R. & Bryden, M.) 44–65 (Facts on File, 1988).
    Google Scholar 
    Félix, F., Bearson, B. & Falconí, J. Epizoic barnacles removed from the skin of a humpback whale after a period of intense surface activity. Mar. Mamm. Sci. 22, 979–984 (2006).Article 

    Google Scholar 
    Towers, J. R. et al. Seasonal movements and ecological markers as evidence for migration of common minke whales photo-identified in the eastern North Pacific. J. Cetacean Res. Manag. 13, 221–229 (2013).
    Google Scholar 
    Iwasa-Arai, T. et al. The host-specific whale louse (Cyamus boopis) as a potential tool for interpreting humpback whale (Megaptera novaeangliae) migratory routes. J. Exp. Mar. Biol. Ecol. 505, 45–51 (2018).Article 

    Google Scholar 
    Lehnert, K. et al. Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts – Morphological and molecular characterization and health implications. Int. J. Parasitol. 15, 22–30 (2021).
    Google Scholar 
    Dreyer, N. et al. How whale and dolphin barnacles attach to their hosts and the paradox of remarkably versatile attachment structures in cypris larvae. Org. Divers. Evol. 20, 233–249 (2020).Article 

    Google Scholar 
    Visser, I. N., Cooper, T. E. & Grimm, H. Duration of pseudo-stalked barnacles (Xenobalanus globicipitis) on a New Zealand Pelagic ecotype orca (Orcinus orca), with comments on cookie cutter shark bite marks (Isistius sp.); can they be used as biological tags?. Biol. Divers. 11, 1067–1086 (2020).
    Google Scholar 
    Van Waerebeek, K. & Reyes, J. C. A note on incidental fishery mortality of southern minke whales off western South America. Rep. Int. Whal. Commn 15, 521–523 (1994).
    Google Scholar 
    Félix, F. & Haase, B. A note on the northernmost record of the Antarctic minke whale (Balaenoptera bonaerensis) in the Eastern Pacific. J. Cetacean Res. Manag. 13, 191–194 (2013).
    Google Scholar 
    Esposito, C., Bichet, O. & Petit, M. First sightings of Antarctic minke whale (Balaenoptera bonaerensis) mother–calf pairs in French Polynesia. Aquat. Mamm. 47, 175–180 (2021).Article 

    Google Scholar 
    Karaa, S., Insacco, G., Bradai, M. N. & Scaravelli, D. Records of Xenobalanus globicipitis on Balaenoptera physalus and Stenella coeruleoalba in Tunisian and Sicilian waters. Nat. Rerum 1, 55–59 (2011).
    Google Scholar 
    Oliveira, J. B., Morales, J. A., González-Barrientos, R. C., Hernández-Gamboa, J. & Hernández-Mora, G. Parasites of cetaceans stranded on the Pacific Coast of Costa Rica. Vet. Parasitol. 182, 319–328. https://doi.org/10.1016/j.vetpar.2011.05.014 (2011).Article 
    CAS 

    Google Scholar 
    Dı́az-Gamboa, R. E. Varamiento de orcas pigmeas (Feresa attenuata Gray 1874) en Yucatán: Reporte de caso. Bioagrociencias 8, 36–43 (2015).
    Google Scholar 
    IJsseldijk, L. L. et al. Beached bachelors: An extensive study on the largest recorded sperm whale Physeter macrocephalus mortality event in the north sea. PloS One 13, e0201221. https://doi.org/10.1371/journal.pone.0201221 (2018).Article 
    CAS 

    Google Scholar 
    Guerrero-Ruiz, M. & Urbán, J. R. First report of remoras on two killer whales (Orcinus orca) in the Gulf of California Mexico. Aquat. Mamm. 26, 148–150 (2000).
    Google Scholar 
    Kautek, G., Van Bressem, M. F. & Ritter, F. External body conditions in cetaceans from La Gomera, Canary Islands Spain. J. Marine Anim. Ecol. 11, 4–17 (2008).
    Google Scholar 
    Bearzi, M. & Patonai, K. Occurrence of the barnacle (Xenobalanus globicipitis) on coastal and offshore common bottlenose dolphins (Tursiops truncatus) in Santa Monica Bay and adjacent areas California. Bull. S. Calif. Acad. Sci. 109, 37–44. https://doi.org/10.3160/0038-3872-109.2.37 (2010).Article 

    Google Scholar 
    Foote, A. D. et al. Genetic differentiation among North Atlantic killer whale populations. Mol. Ecol. 20, 629–641. https://doi.org/10.1111/j.1365-294X.2010.04957.x (2011).Article 

    Google Scholar 
    Toth, J. L., Hohn, A. A., Able, K. W. & Gorgone, A. M. Defining bottlenose dolphin (Tursiops truncatus) stocks based on environmental, physical and behavioral characteristics. Mar. Mamm. Sci. 28, 461–478. https://doi.org/10.1111/j.1748-7692.2011.00497.x (2012).Article 

    Google Scholar 
    Urian, K. W., Kaufmann, R., Waples, D. M. & Read, A. J. The prevalence of ectoparasitic barnacles discriminates stocks of Atlantic common bottlenose dolphins (Tursiops truncatus) at risk of entanglement in coastal gill net fisheries. Mar. Mamm. Sci. 35, 290–299. https://doi.org/10.1111/mms.12522 (2019).Article 

    Google Scholar 
    Siciliano, S. et al. Epizoic barnacle (Xenobalanus globicipitis) infestations in several cetacean species in South-Eastern Brazil. Mar. Biol. Res. 16, 1–13. https://doi.org/10.1080/17451000.2020.1783450 (2020).Article 

    Google Scholar 
    Whitehead, T. O., Rollinson, D. P. & Reisinger, R. R. Pseudostalked barnacles Xenobalanus globicipitis attached to killer whales Orcinus orca in South African waters. Mar. Biodivers. Rec. 45, 873–876. https://doi.org/10.1007/s12526-014-0296-2 (2014).Article 

    Google Scholar 
    Methion, S. & Dı́az López, B. First record of atypical pigmentation pattern in fin whale Balaenoptera physalus in the Atlantic ocean. Dis. Aquat. Org. 135, 121–125. https://doi.org/10.3354/dao03385 (2019).Article 

    Google Scholar 
    Herr, H., Burkhardt-Holm, P., Heyer, K., Siebert, U. & Selling, J. Injuries, malformations and epidermal conditions in cetaceans of the strait of Gibraltar. Aquat. Mamm. 46, 215–235. https://doi.org/10.1578/AM.46.2.2020.215 (2020).Article 

    Google Scholar 
    Herr, H. et al. Return of large fin whale feeding aggregations to historical whaling grounds in the southern ocean. Sci. Rep. 12, 9458. https://doi.org/10.1038/s41598-022-13798-7 (2022).Article 
    ADS 
    CAS 

    Google Scholar 
    Gruvel, J. A. Cirrhipèdes Provenant Des Campagnes Scientifiques De S.A.S. Le Prince De Monaco, (1885– 1913). In Résultas Des Campagnes Scientifiques Accomplies Sur Son Yacht Par Albert Ler (Monaco: Prince Souverain de Monaco) 1-88 (1920).Annandale, N. The rate of growth in Conchoderma and Lepas. Rec. Indian Mus. 3, 295 (1909).
    Google Scholar 
    Il’in, I. I., Kuznetsova, L. A. & Starostin, I. V. Oceanic fouling in the equatorial Atlantic. Oceanology 18, 597–599 (1978).
    Google Scholar 
    Eckert, K. L. & Eckert, S. A. Growth rate and reproductive condition of the barnacle Conchoderma virgatum on gravid leatherback sea turtles in Caribbean waters. J. Crust. Biol. 7, 682–690. https://doi.org/10.2307/1548651 (1987).Article 

    Google Scholar 
    Arroyo, N. L., Abaunza, P. & Preciado, I. The first naupliar stage of Pennella balaenopterae Koren and Danielssen 1877 (Copepoda: Siphonostomatoida, Pennellidae). Sarsia 87, 333–337. https://doi.org/10.1080/0036482021000155785 (2002).Article 

    Google Scholar  More

  • in

    Dung beetles prefer used land over natural greenspace in urban landscape

    Seto, K. C., Guneralp, B. & Hutyra, L. R. Global forecasts of urban expansion to 2030 and direct impacts on biodiversity and carbon pools. Proc. Natl Acad. Sci. USA 109, 16083–16088 (2012).Article 
    ADS 
    CAS 

    Google Scholar 
    McDonald, R. I., Marcotullio, P. J. & Güneralp, B. Urbanization and global trends in biodiversity and ecosystem services. in Urbanization, Biodiversity and Ecosystem Services: Challenges And Opportunities, 31–52 (Springer, 2013).McDonald, R. I., Kareiva, P. & Forman, R. T. T. The implications of current and future urbanization for global protected areas and biodiversity conservation. Biol. Conserv. 141, 1695–1703 (2008).Article 

    Google Scholar 
    Müller, N., Ignatieva, M., Nilon, C. H., Werner, P. & Zipperer, W. C. Patterns and trends in urban biodiversity and landscape design. In Urbanization, Biodiversity and Ecosystem Services: Challenges And Opportunities, 123–174 (Springer, 2013).Lahr, E. C., Dunn, R. R. & Frank, S. D. Getting ahead of the curve: Cities as surrogates for global change. Proc. R. Soc. B. 285, 20180643 (2018).Article 

    Google Scholar 
    Cadotte, M. W., Yasui, S. L. E., Livingstone, S. & MacIvor, J. S. Are urban systems beneficial, detrimental, or indifferent for biological invasion?. Biol. Invasions. 19, 3489–3503 (2017).Article 

    Google Scholar 
    Thompson, K. A., Rieseberg, L. H. & Schluter, D. Speciation and the city. Trends Ecol. Evol. 33, 815–826 (2018).Article 

    Google Scholar 
    Borden, J. B. & Flory, S. L. Urban evolution of invasive species. Front. Ecol. Environ. 19, 184–191 (2021).Article 

    Google Scholar 
    Melliger, R. L., Braschler, B., Rusterholz, H. P. & Baur, B. Diverse effects of degree of urbanisation and forest size on species richness and functional diversity of plants, and ground surface-active ants and spiders. PLoS ONE 13, e0199245 (2018).Article 

    Google Scholar 
    McKinney, M. L. Urbanization, biodiversity, and conservation: The impacts of urbanization on native species are poorly studied, but educating a highly urbanized human population about these impacts can greatly improve species conservation in all ecosystems. Bioscience 52, 883–890 (2002).Article 

    Google Scholar 
    Roshnath, R. & Sinu, P. A. Nesting tree characteristics of heronry birds of urban ecosystems in peninsular India: Implications for habitat management. Curr. Zool. 63, 599–605 (2017).Article 

    Google Scholar 
    Roshnath, R., Athira, K. & Sinu, P. A. Does predation pressure drive heronry birds to nest in the urban landscape?. J. Asia Pac. Biodivers. 12, 311–315 (2019).Article 

    Google Scholar 
    Fenoglio, M. S., Rossetti, M. R. & Videla, M. Negative effects of urbanization on terrestrial arthropod communities: A meta-analysis. Glob. Ecol. Biogeogr. 29, 1412–1429 (2020).Article 

    Google Scholar 
    Saari, S. et al. Urbanization is not associated with increased abundance or decreased richness of terrestrial animals-dissecting the literature through meta-analysis. Urban Ecosyst. 19, 1251–1264 (2016).Article 

    Google Scholar 
    Lessard, J. P. & Buddle, C. M. The effects of urbanization on ant assemblages (Hymenoptera: Formicidae) associated with the Molson Nature Reserve. Quebec. Can. Entomol. 137, 215–225 (2005).Article 

    Google Scholar 
    Uno, S., Cotton, J. & Philpott, S. M. Diversity, abundance, and species composition of ants in urban green spaces. Urban Ecosyst. 13, 425–441 (2010).Article 

    Google Scholar 
    Fortel, L. et al. Decreasing abundance, increasing diversity and changing structure of the wild bee community (Hymenoptera: Anthophila) along an urbanization gradient. PLoS ONE 9, e104679 (2014).Article 
    ADS 

    Google Scholar 
    Baldock, K. C. et al. Where is the UK’s pollinator biodiversity? The importance of urban areas for flower-visiting insects. Proc. R. Soc. B. 282, 20142849 (2015).Article 

    Google Scholar 
    Baldock, K. C. R. et al. A systems approach reveals urban pollinator hotspots and conservation opportunities. Nat. Ecol. Evol. 3, 363–373 (2019).Article 

    Google Scholar 
    Rocha, E. A. & Fellowes, M. D. Urbanisation alters ecological interactions: Ant mutualists increase and specialist insect predators decrease on an urban gradient. Sci. Rep. 10, 1–8 (2020).Article 
    ADS 

    Google Scholar 
    Theodorou, P. et al. Urban areas as hotspots for bees and pollination but not a panacea for all insects. Nat. Commun. 11, 1–13 (2020).Article 

    Google Scholar 
    Carvalho, R. L. et al. Understanding what bioindicators are actually indicating: Linking disturbance responses to ecological traits of dung beetles and ants. Ecol. Indic. 108, 105764 (2020).Article 

    Google Scholar 
    Asha, G., Manoj, K., Megha, P. P. & Sinu, P. A. Spatiotemporal effects on dung beetle activities in island forests-home garden matrix in a tropical village landscape. Sci. Rep. 11, 1–13 (2021).Article 

    Google Scholar 
    Correa, C. M. A., da Silva, P. G., Ferreira, K. R. & Puker, A. Residential sites increase species loss and cause high temporal changes in functional diversity of dung beetles in an urbanized Brazilian Cerrado landscape. J. Insect Conserv. 25, 417–428 (2021).Article 

    Google Scholar 
    Correa, C. M. A., Ferreira, K. R., Puker, A., Audino, L. D. & Korasaki, V. Greenspace sites conserve taxonomic and functional diversity of dung beetles in an urbanized landscape in the Brazilian Cerrado. Urban Ecosyst. 24, 1023–1034 (2021).Article 

    Google Scholar 
    Beiroz, W. et al. Spatial and temporal shifts in functional and taxonomic diversity of dung beetle in a human-modified tropical forest landscape. Ecol. Indic. 95, 418–526 (2018).Article 

    Google Scholar 
    Fuzessy, L. F. et al. Identifying the anthropogenic drivers of declines in tropical dung beetle communities and functions. Biol. Conserv. 256, 109063 (2021).Article 

    Google Scholar 
    Barragan, F., Moreno, C. E., Escobar, F., Halffter, G. & Navarrete, D. Negative impacts of human land use on dung beetle functional diversity. PLoS ONE 6, e17976 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Salomão, R. P. et al. Urbanization effects on dung beetle assemblages in a tropical city. Ecol. Indic. 103, 665–675 (2019).Article 

    Google Scholar 
    Filgueiras, B. K. C., Liberal, C. N., Aguiar, C. D. M., Hernández, M. I. M. & Iannuzzi, L. Attractivity of omnivore, carnivore and herbivore mammalian dung to Scarabaeinae (Coleoptera: Scarabaeidae) in a tropical Atlantic rainforest remnant. Rev. Bras. Entomol. 53, 422–427 (2009).Article 

    Google Scholar 
    Ramírez-Restrepo, L. & Halffter, G. Copro-necrophagous beetles (Coleoptera: Scarabaeinae) in urban areas: A global review. Urban Ecosyst. 19, 1179–1195 (2016).Article 

    Google Scholar 
    Krell, F. T. et al. Human influence on the dung fauna in Afrotropical grasslands (Insecta: Coleoptera). In African Biodiversity: Molecules Organisms Ecosystems (eds Huber, B. A. et al.) 133–139 (Springer, 2005).Chapter 

    Google Scholar 
    Jiménez-Ferbans, L., Mendieta-Otálora, W., García, H. & Amat-García, G. Notes on dung beetles (Coleoptera: Scarabaeinae) in dry environments of the Santa Marta region, Colombia. Acta Biol. Colomb. 13, 203–208 (2008).
    Google Scholar 
    Costa, F. C. et al. What is the importance of open habitat in a predominantly closed forest area to the dung beetle (Coleoptera, Scarabaeinae) assemblage?. Rev. Bras. Entomol. 57, 329–334 (2013).Article 

    Google Scholar 
    Korasaki, V., Lopes, J., Gardner, B. G. & Louzada, J. Using dung beetles to evaluate the effects of urbanization on Atlantic Forest biodiversity. Insect Sci. 20, 393–406 (2013).Article 

    Google Scholar 
    Audino, L., Louzada, J. & Comita, L. Dung beetles as indicators of tropical forest restoration success: Is it possible to recover species and functional diversity?. Biol. Conserv. 169, 248–257 (2014).Article 

    Google Scholar 
    Gómez-Cifuentez, A., Munevar, A., Gimenez, V. C., Gatti, M. G. & Zurita, G. A. Influence of land use on the taxonomic and functional diversity of dung beetles (Coleoptera: Scarabaeinae) in the southern Atlantic Forest of Argentina. J. Insect. Conserv. 21, 147–156 (2017).Article 

    Google Scholar 
    Gómez-Cifuentes, A., Gómez, V. C. G., Moreno, C. E. & Zurita, G. A. Tree retention in cattle ranching systems partially preserves dung beetle diversity and functional groups in the semideciduous Atlantic forest: The role of microclimate and soil conditions. Basic Appl. Ecol. 34, 64–74 (2019).Article 

    Google Scholar 
    Magnano, L. F. S. et al. Functional attributes change but functional richness is unchanged after fragmentation of Brazilian Atlantic forests. J. Ecol. 102, 475–485 (2014).Article 

    Google Scholar 
    GiménezGómez, V. C., Verdú, J. R., Casanoves, F. & Zurita, G. A. Functional responses to anthropogenic disturbance and the importance of selected traits: a study case using dung beetles. Ecol. Entomol. 1, 1–12 (2022).
    Google Scholar 
    Lobo, J. M. Decline of roller dung beetle (Scarabaeinae) populations in the Iberian Peninsula during the 20th century. Biol. Conserv. 97, 43–50 (2001).Article 

    Google Scholar 
    Ballullaya, U. P. et al. Stakeholder motivation for the conservation of sacred groves in south India: An analysis of environmentalperceptions of rural and urban neighbourhood communities. Land Use Policy 89, 104213 (2019).Article 

    Google Scholar 
    Lowman, M. D. & Sinu, P. A. Can the spiritual values of forests inspire effective conservation?. Bioscience 67, 688–690 (2017).Article 

    Google Scholar 
    Bhagwat, S. A., Kushalappa, C. G., Williams, P. H. & Brown, N. D. The role of informal protected areas in maintaining biodiversity in the Western Ghats of India. Ecol. Soc 10, 108 (2005).Article 

    Google Scholar 
    Rajesh, T. P., Prashanth Ballullaya, U., Unni, A. P., Parvathy, S. & Sinu, P. A. Interactive effects of urbanization and year on invasive and native ant diversity of sacred groves of South India. Urban Ecosyst. 23, 1335–1348 (2020).Article 

    Google Scholar 
    Asha, G., Navya, K. K., Rajesh, T. P. & Sinu, P. A. Roller dung beetles of dung piles suggest habitats are alike, but that of guarding pitfall traps suggest habitats are different. J. Trop. Ecol. 37, 209–213 (2021).Article 

    Google Scholar 
    Arrow, G. J. The Fauna Of British India Including Ceylon And Burma, Coleoptera: Lamellicornia (Coprinae) (Taylor and Francis, 1931).
    Google Scholar 
    Hsieh, T. C., Ma, K. H. & Chao, A. iNEXT: Interpolation and extrapolation for species diversity. R package version 2.0.20. http://chao.stat.nthu.edu.tw/wordpress/software-download/ (2020).Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    Fox, J. et al. Package ‘car’, Vol. 16, (R Foundation for Statistical Computing, 2012).Barton, K. MuMIn: Multi-Model Inference. R package version 1.43.17. https://CRAN.R-project.org/package=MuMIn (2020).Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-7. https://CRAN.R-project.org/package=vegan (2020).Hartig, F. & Hartig, M. F. Package ‘DHARMa’. R package (2017).Warnes, G. R. et al. gplots: Various R Programming Tools for Plotting Data. R package version 3.1.1. https://CRAN.R-project.org/package=gplots (2020).R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https://www.R-project.org/ (2021).Venugopal, K. S., Thomas, S. K. & Flemming, A. T. Diversity and community structure of dung beetles (Coleoptera: Scarabaeinae) associated with semi-urban fragmented agricultural land in the Malabar coast in southern India. J. Threat. Taxa. 4, 2685–2692 (2012).Article 

    Google Scholar 
    Sabu, T. K. & Nithya, S. Comparison of the arboreal dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) of the wet and dry forests of the western Ghats. India. Coleopt. Bull. 70, 144–148 (2016).Article 

    Google Scholar 
    Sabu, T. K., Vinod, K. V. & Vineesh, P. J. Guild structure, diversity and succession of dung beetles associated with Indian elephant dung in South Western Ghats forests. J. Insect Sci. 6, 6–17 (2006).Article 

    Google Scholar 
    Rodrigues, M. M., Uchôa, M. A. & Ide, S. Dung beetles (Coleoptera: Scarabaeoidea) in three landscapes in Mato Grosso do Sul, Brazil. Braz. J. Biol. 73, 211–220 (2013).Article 
    CAS 

    Google Scholar 
    Rios-Diaz, C. L. et al. Sheep herding in small grasslands promotes dung beetle diversity in a mountain forest landscape. J. Insect. Conserv. 25, 13–26 (2020).Article 

    Google Scholar 
    Carrión-Paladines, V. et al. Effects of land-use change on the community structure of the dung beetle (Scarabaeinae) in an altered ecosystem in Southern Ecuador. Insects. 12, 306 (2021).Article 

    Google Scholar 
    Gómez, V. C. G., Verdú, J. R. & Zurita, G. A. Thermal niche helps to explain the ability of dung beetles to exploit disturbed habitats. Sci. Rep. 10, 1–14 (2020).ADS 

    Google Scholar 
    Slade, E. M., Mann, D. J., Villanueva, J. F. & Lewis, O. T. Experimental evidence for the effects of dung beetle functional group richness and composition on ecosystem function in a tropical forest. J. Anim. Ecol. 76, 1094–1104 (2007).Article 

    Google Scholar 
    Vinod, K. V. & Sabu, T. K. Species composition and community structure of dung beetles attracted to dung of gaur and elephant in the moist forests of South Western Ghats. J. Insect. Sci. 7, 1–14 (2007).Article 
    CAS 

    Google Scholar 
    Milotić, T. et al. Functionally richer communities improve ecosystem functioning: Dung removal and secondary seed dispersal by dung beetles in the Western Palaearctic. J. Biogeogr. 46, 70–82 (2019).Article 

    Google Scholar 
    Braga, R. F., Korasaki, V., Andresen, E. & Louzada, J. Dung beetle community and functions along a habitat-disturbance gradient in the amazon: A rapid assessment of ecological functions associated to biodiversity. PLoS ONE 8, e57786 (2013).Article 
    ADS 
    CAS 

    Google Scholar 
    Nichols, E. et al. Trait-dependent response of dung beetle populations to tropical forest conversion at local and regional scales. Ecology 94, 180–189 (2013).Article 

    Google Scholar 
    Gardner, T. A. et al. The cost-effectiveness of biodiversity surveys in tropical forests. Ecol. Lett. 11, 139–150 (2008).Article 

    Google Scholar  More

  • in

    Artificial intelligence convolutional neural networks map giant kelp forests from satellite imagery

    Poloczanska, E. S. et al. Global imprint of climate change on marine life. Nat. Clim. Change 3, 919–925 (2013).Article 
    ADS 

    Google Scholar 
    Wiens, J. J. Climate-related local extinctions are already widespread among plant and animal species. PLoS Biol. 14, e2001104 (2016).Article 

    Google Scholar 
    Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W. & Courchamp, F. Impacts of climate change on the future of biodiversity. Ecol. Lett. 15, 365–377 (2012).Article 

    Google Scholar 
    Assis, J., Serrão, E. A., Duarte, C. M., Fragkopoulou, E. & Krause-Jensen, D. Major expansion of marine forests in a warmer Arctic. Front. Mar. Sci. 9, 850368 (2022).Article 

    Google Scholar 
    Assis, J. et al. Major shifts at the range edge of marine forests: The combined effects of climate changes and limited dispersal. Sci. Rep. 7(44348), 1–10 (2017).CAS 

    Google Scholar 
    O’Leary, J. K. et al. The resilience of marine ecosystems to climatic disturbances. BioScience. https://doi.org/10.1093/biosci/biw161 (2017).Article 

    Google Scholar 
    Steneck, R. S. et al. Kelp forest ecosystems: Biodiversity, stability, resilience and future. Environ. Conserv. 29, 436–459 (2002).Article 

    Google Scholar 
    Filbee-Dexter, K. & Scheibling, R. E. Detrital kelp subsidy supports high reproductive condition of deep-living sea urchins in a sedimentary basin. Aquat. Biol. 23, 71–86 (2014).Article 

    Google Scholar 
    Filbee-Dexter, K. Ocean forests hold unique solutions to our current environmental crisis. One Earth https://doi.org/10.1016/j.oneear.2020.05.004 (2020).Article 

    Google Scholar 
    Krumhansl, K. A. & Scheibling, R. E. Production and fate of kelp detritus. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps09940 (2012).Article 

    Google Scholar 
    Edwards, M. S. & Hernández-Carmona, G. Delayed recovery of giant kelp near its southern range limit in the North Pacific following El Niño. Mar. Biol. 147, 273–279 (2005).Article 

    Google Scholar 
    Cavanaugh, K. C., Reed, D. C., Bell, T. W., Castorani, M. C. N. & Beas-Luna, R. Spatial variability in the resistance and resilience of giant kelp in southern and Baja California to a multiyear heatwave. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00413 (2019).Article 

    Google Scholar 
    Butler, C. L., Lucieer, V. L., Wotherspoon, S. J. & Johnson, C. R. Multi-decadal decline in cover of giant kelp Macrocystis pyrifera at the southern limit of its Australian range. Mar. Ecol. Prog. Ser. 653, 1–18 (2020).Article 
    ADS 

    Google Scholar 
    Martínez, B. et al. Distribution models predict large contractions of habitat-forming seaweeds in response to ocean warming. Divers. Distrib. 24, 1350–1366 (2018).Article 

    Google Scholar 
    Bell, T. W., Allen, J. G., Cavanaugh, K. C. & Siegel, D. A. Three decades of variability in California’s giant kelp forests from the Landsat satellites. Remote Sens. Environ. 238, 110811 (2020).Article 
    ADS 

    Google Scholar 
    Mann, M. E. & Emanuel, K. A. Atlantic Hurricane trends linked to climate change. Eos 87, 233–241 (2006).Article 
    ADS 

    Google Scholar 
    Jensen, J. R., Estes, J. E. & Tinney, L. Remote sensing techniques for kelp surveys. Photogramm. Eng Remote Sens. 46, 743–755 (1980).
    Google Scholar 
    Cavanaugh, K. C. et al. A review of the opportunities and challenges for using remote sensing for management of surface-canopy forming kelps. Front. Mar. Sci. https://doi.org/10.3389/fmars.2021.753531 (2021).Article 

    Google Scholar 
    Cavanaugh, K. C., Siegel, D. A., Reed, D. C. & Dennison, P. E. Environmental controls of giant-kelp biomass in the Santa Barbara Channel, California. Mar. Ecol. Prog. Ser. 429, 1–17 (2011).Article 
    ADS 

    Google Scholar 
    Kadhim, M. A. & Abed, M. H. Convolutional neural network for satellite image classification. Stud. Comput. Intell. 830, 165–178 (2020).Article 

    Google Scholar 
    Segal-Rozenhaimer, M., Li, A., Das, K. & Chirayath, V. Cloud detection algorithm for multi-modal satellite imagery using convolutional neural-networks (CNN). Remote Sens. Environ. 237, 111446 (2020).Article 
    ADS 

    Google Scholar 
    Canonico, G. et al. Global observational needs and resources for marine biodiversity. Front. Mar. Sci. 6, 367 (2019).Article 

    Google Scholar 
    LeCun, Y., Bengio, Y. & Hinton, G. Deep learning. Nature 521, 436–444 (2015).Article 
    ADS 
    CAS 

    Google Scholar 
    Yu, L. & Gong, P. Google Earth as a virtual globe tool for Earth science applications at the global scale: Progress and perspectives. Int. J. Remote Sens. 33, 3966–3986 (2012).Article 

    Google Scholar 
    Guirado, E., Tabik, S., Rivas, M. L., Alcaraz-Segura, D. & Herrera, F. Whale counting in satellite and aerial images with deep learning. Sci. Rep. 9, 14259 (2019).Article 
    ADS 

    Google Scholar 
    Borowicz, A. et al. Aerial-trained deep learning networks for surveying cetaceans from satellite imagery. PLoS ONE 14, 1–15 (2019).Article 

    Google Scholar 
    Lorencin, I., Anđelić, N., Mrzljak, V. & Car, Z. Marine objects recognition using convolutional neural networks. Nase More 66, 112–119 (2019).Article 

    Google Scholar 
    Ridge, J. T., Gray, P. C., Windle, A. E. & Johnston, D. W. Deep learning for coastal resource conservation: Automating detection of shellfish reefs. Remote Sens. Ecol. Conserv. 6, 431–440 (2020).Article 

    Google Scholar 
    Wang, Y. et al. Machine learning-based ship detection and tracking using satellite images for maritime surveillance. J. Ambient Intell. Smart Environ. 13, 361–371 (2021).Article 

    Google Scholar 
    Han, Q., Yin, Q., Zheng, X. & Chen, Z. Remote sensing image building detection method based on Mask R-CNN. Complex Intell. Syst. https://doi.org/10.1007/s40747-021-00322-z (2021).Article 

    Google Scholar 
    Girshick, R. Fast R-CNN. In 2015 IEEE International Conference on Computer Vision (ICCV) 1440–1448. https://doi.org/10.1109/ICCV.2015.169 (2015).Ren, S., He, K., Girshick, R. & Sun, J. Faster R-CNN: Towards real-time object detection with region proposal networks. IEEE Trans Pattern Anal. Mach. Intell. 39, 28 (2017).Article 

    Google Scholar 
    Shelhamer, E., Long, J. & Darrell, T. Fully convolutional networks for semantic segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 39, 3431–3440 (2017).Article 

    Google Scholar 
    He, K., Gkioxari, G., Dollár, P. & Girshick, R. Mask R-CNN. In Proceedings of the IEEE international Conference on Computer Vision (2017).Arafeh-Dalmau, N. et al. Extreme Marine Heatwaves alter kelp forest community near its equatorward distribution limit. Front. Mar. Sci. 6, 1–18 (2019).Article 
    ADS 

    Google Scholar 
    Nie, X., Duan, M., Ding, H., Hu, B. & Wong, E. K. Attention Mask R-CNN for ship detection and segmentation from remote sensing images. IEEE Access 8, 9325–9334 (2020).Article 

    Google Scholar 
    Abdulla, W. Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow. GitHub Repository (2017).Fragkopoulou, E. et al. Global biodiversity patterns of marine forests of brown macroalgae. Glob. Ecol. Biogeogr. https://doi.org/10.1111/geb.13450 (2022).Article 

    Google Scholar 
    Markham, B. L., Storey, J. C., Williams, D. L. & Irons, J. R. Landsat sensor performance: History and current status. IEEE Trans. Geosci. Remote Sens. https://doi.org/10.1109/TGRS.2004.840720 (2004).Article 

    Google Scholar 
    Gorelick, N. et al. Google Earth Engine: Planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27 (2017).Article 
    ADS 

    Google Scholar 
    Aghamohamadnia, M. & Abedini, A. A morphology-stitching method to improve Landsat SLC-off images with stripes. Geodesy Geodyn. 5, 27–33 (2014).Article 

    Google Scholar 
    Houskeeper, H. F. et al. Automated satellite remote sensing of giant kelp at the Falkland Islands (Islas Malvinas). PLoS ONE 17, e0257933 (2022).Article 
    CAS 

    Google Scholar 
    Mantha, K. B. et al. From Fat Droplets to Floating Forests: Cross-Domain Transfer Learning Using a PatchGAN-Based Segmentation Model (2022).Finger, D. J. I., McPherson, M. L., Houskeeper, H. F. & Kudela, R. M. Mapping bull kelp canopy in northern California using Landsat to enable long-term monitoring. Remote Sens. Environ. 254, 112243 (2021).Article 
    ADS 

    Google Scholar 
    Siegel, D. A., Wang, M., Maritorena, S. & Robinson, W. Atmospheric correction of satellite ocean color imagery: The black pixel assumption. Appl. Opt. 39, 3582–3591 (2000).Article 
    ADS 
    CAS 

    Google Scholar 
    Loisel, H., Nicolas, J. M., Sciandra, A., Stramski, D. & Poteau, A. Spectral dependency of optical backscattering by marine particles from satellite remote sensing of the global ocean. J. Geophys. Res. Oceans https://doi.org/10.1029/2005JC003367 (2006).Article 

    Google Scholar 
    Hansen, M. C. et al. High-resolution global maps of 21st-century forest cover change. Science 342, 850–853 (2013).Article 
    ADS 
    CAS 

    Google Scholar 
    Dutta, A. & Zisserman, A. The VIA annotation software for images, audio and video. In MM 2019: Proceedings of the 27th ACM International Conference on Multimedia. https://doi.org/10.1145/3343031.3350535 (2019).Pfister, C. A., Berry, H. D. & Mumford, T. The dynamics of Kelp Forests in the Northeast Pacific Ocean and the relationship with environmental drivers. J. Ecol. 106, 1520–1533 (2018).Article 

    Google Scholar 
    Cavanaugh, K. C., Cavanaugh, K. C., Bell, T. W. & Hockridge, E. G. An automated method for mapping giant kelp canopy dynamics from UAV. Front. Environ. Sci. 8, 587354 (2021).Article 

    Google Scholar 
    Castorani, M. C. N. et al. Connectivity structures local population dynamics: A long-term empirical test in a large metapopulation system. Ecology 96, 3141–3152 (2015).Article 

    Google Scholar 
    Irmak, E. Implementation of convolutional neural network approach for COVID-19 disease detection. Physiol. Genom. 52, 590–601 (2020).Article 
    CAS 

    Google Scholar 
    Assis, J., Araújo, M. B. & Serrão, E. A. Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic. Glob. Change Biol. 24, 1365–2486 (2017).
    Google Scholar 
    Cao, C. et al. An improved faster R-CNN for small object detection. IEEE Access 7, 106838–106846 (2019).Article 

    Google Scholar 
    Konar, J., Khandelwal, P. & Tripathi, R. Comparison of various learning rate scheduling techniques on convolutional neural network. In 2020 IEEE International Students’ Conference on Electrical, Electronics and Computer Science, SCEECS 2020. https://doi.org/10.1109/SCEECS48394.2020.94 (2020).LeCun, Y., Bottou, L., Bengio, Y. & Haffner, P. Gradient-based learning applied to document recognition. Proc. IEEE 86, 2278–2324 (1998).Article 

    Google Scholar 
    Johnson, J. W. Automatic nucleus segmentation with mask-RCNN. Adv. Intell. Syst. Comput. 944, 399–407 (2020).
    Google Scholar 
    Lin, T. Y. et al. Microsoft COCO: Common objects in context. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 8693 LNCS (2014).McKnight, P. E. & Najab, J. Mann-Whitney U Test. Corsini Encycl. Psychol. https://doi.org/10.1002/9780470479216.corpsy0524 (2010).Article 

    Google Scholar 
    R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2021).
    Google Scholar 
    Haklay, M. & Weber, P. OpenStreet map: User-generated street maps. IEEE Pervasive Comput. 7, 12–18 (2008).Article 

    Google Scholar 
    Wäldchen, J. & Mäder, P. Machine learning for image based species identification. Methods Ecol. Evol. https://doi.org/10.1111/2041-210X.13075 (2018).Article 
    MATH 

    Google Scholar 
    Weinstein, B. G. A computer vision for animal ecology. J. Anim. Ecol. https://doi.org/10.1111/1365-2656.12780 (2018).Article 

    Google Scholar 
    Chilson, C. et al. Automated detection of bird roosts using NEXRAD radar data and Convolutional Neural Networks. Remote Sens. Ecol. Conserv. 5, 20–32 (2019).Article 

    Google Scholar 
    O’Gara, S. & McGuinness, K. Comparing data augmentation strategies for deep image classification. Ir. Mach. Vis. Image Process. Conf. https://doi.org/10.21427/148b-ar75 (2019).Article 

    Google Scholar 
    Li, W., Chen, C., Zhang, M., Li, H. & Du, Q. Data augmentation for hyperspectral image classification with deep CNN. IEEE Geosci. Remote Sens. Lett. 16, 593–597 (2019).Article 
    ADS 

    Google Scholar 
    Bharati, P. & Pramanik, A. Deep learning techniques—R-CNN to Mask R-CNN: A survey. In Computational Intelligence in Pattern Recognition (eds Das, A. K. et al.) 657–668 (Springer, 2020).Chapter 

    Google Scholar 
    Li, A. S., Chirayath, V., Segal-Rozenhaimer, M., Torres-Perez, J. L. & van den Bergh, J. NASA NeMO-Net’s convolutional neural network: Mapping marine habitats with spectrally heterogeneous remote sensing imagery. IEEE J. Sel. Top. Appl. Earth Obs. Remote Sens. 13, 5115–5133 (2020).Article 
    ADS 

    Google Scholar 
    Hamilton, S. L., Bell, T. W., Watson, J. R., Grorud-Colvert, K. A. & Menge, B. A. Remote sensing: generation of long-term kelp bed data sets for evaluation of impacts of climatic variation. Ecology 101, e03031 (2020).Article 

    Google Scholar 
    Bell, T. W., Cavanaugh, K. C. & Siegel, D. A. Remote monitoring of giant kelp biomass and physiological condition: An evaluation of the potential for the Hyperspectral Infrared Imager (HyspIRI) mission. Remote Sens. Environ. 167, 218–228 (2015).Article 
    ADS 

    Google Scholar 
    Schroeder, S. B., Dupont, C., Boyer, L., Juanes, F. & Costa, M. Passive remote sensing technology for mapping bull kelp (Nereocystis luetkeana): A review of techniques and regional case study. Glob. Ecol. Conserv. https://doi.org/10.1016/j.gecco.2019.e00683 (2019).Article 

    Google Scholar 
    Kristollari, V. & Karathanassi, V. Convolutional neural networks for detecting challenging cases in cloud masking using Sentinel-2 imagery. Remote Sens. Geoinf. Environ. https://doi.org/10.1117/12.2571111 (2020).Article 

    Google Scholar 
    Wilson, M. J. & Oreopoulos, L. Enhancing a simple MODIS cloud mask algorithm for the landsat data continuity mission. IEEE Trans. Geosci. Remote Sens. 51, 723–731 (2013).Article 
    ADS 

    Google Scholar 
    Zhuge, X. Y., Zou, X. & Wang, Y. A fast cloud detection algorithm applicable to monitoring and nowcasting of daytime cloud systems. IEEE Trans. Geosci. Remote Sens. 55, 6111–6119 (2017).Article 
    ADS 

    Google Scholar 
    Lin, T. Y. et al. Feature pyramid networks for object detection. In Proceedings: 30th IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2017 (2017).Jacox, M. G. et al. Impacts of the 2015–2016 El Niño on the California Current System: Early assessment and comparison to past events. Geophys. Res. Lett. https://doi.org/10.1002/2016GL069716 (2016).Article 

    Google Scholar 
    Chavez, F. P. et al. Biological and chemical consequences of the 1997–1998 El Niño in central California waters. Prog. Oceanogr. https://doi.org/10.1016/S0079-6611(02)00050-2 (2002).Article 

    Google Scholar 
    Tegner, M. J. & El Dayton, P. K. Niño effects on Southern California kelp forest communities. Adv. Ecol. Res. 17, 243–279 (1987).Article 

    Google Scholar 
    Bartsch, I. et al. Changes in kelp forest biomass and depth distribution in Kongsfjorden, Svalbard, between 1996–1998 and 2012–2014 reflect Arctic warming. Polar Biol. 39, 2021–2036 (2016).Article 

    Google Scholar 
    Simonson, E. J., Scheibling, R. E. & Metaxas, A. Kelp in hot water: I. Warming seawater temperature induces weakening and loss of kelp tissue. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps11438 (2015).Article 

    Google Scholar 
    Oliver, E. C. J. et al. Projected marine heatwaves in the 21st century and the potential for ecological impact. Front. Mar. Sci. https://doi.org/10.3389/fmars.2019.00734 (2019).Article 

    Google Scholar  More

  • in

    Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison

    Schilling, A.-M. & Rössner, G. E. The (sleeping) beauty in the beast—a review on the water deer, Hydropotes inermis. Hystrix Ital. J. Mammal. 28, 121–133 (2017).
    Google Scholar 
    Geist, V. Deer of the World: Their Evolution, Behaviour and Ecology (Stackpole Books, Pennsylvania, 1998).
    Google Scholar 
    Cooke, A. Muntjac and Water Deer: Natural History, Environmental Impact and Management (Pelagic Publishing Ltd, UK, 2019).Book 

    Google Scholar 
    Kim, B. J., Lee, B. K. & Kim, Y. J. Korean water deer (National Institute of Ecology, South Korea, 2016).
    Google Scholar 
    Belyaev, D. A. & Jo, Y.-S. Northernmost finding and further information on water deer Hydropotes inermis in Primorskiy Krai, Russia. Mammalia 85, 71–73 (2021).Article 

    Google Scholar 
    Harris, R. B. & Duckworth, J. W. Hydropotes inermis. The IUCN Red List of Threatened Species, e.T10329A22163569 (2015).National Institute of Biological Resources. Harmful wildlife. https://species.nibr.go.kr/home/mainHome.do?cont_link=011&subMenu=011016&contCd=011016001 (2015).Hofmann, R. R. Evolutionary steps of ecophysiological adaptation and diversification of ruminants: a comparative view of their digestive system. Oecologia 78, 443–457 (1989).Article 
    ADS 
    CAS 

    Google Scholar 
    Guo, G. & Zhang, E. Diet of the Chinese water deer (Hydropotes inermis) in Zhoushan Archipelago, China. Acta Theriol. Sin. 25, 122–130 (2005).
    Google Scholar 
    Kim, B. J., Lee, N. S. & Lee, S. D. Feeding diets of the Korean water deer (Hydropotes inermis argyropus) based on a 202 bp rbcL sequence analysis. Conserv. Genet. 12, 851–856 (2011).Article 

    Google Scholar 
    Park, J.-E., Kim, B.-J., Oh, D.-H., Lee, H. & Lee, S.-D. Feeding habit analysis of the Korean water deer. Korean J. Environ. Ecol. 25, 836–845 (2011).
    Google Scholar 
    Kim, J., Joo, S. & Park, S. Diet composition of Korean water deer (Hydropotes inermis argyropus) from the Han River Estuary Wetland in Korea using fecal DNA. Mammalia 85, 487–493 (2021).Article 

    Google Scholar 
    Hofmann, R., Kock, R. A., Ludwig, J. & Axmacher, H. Seasonal changes in rumen papillary development and body condition in free ranging Chinese water deer (Hydropotes inermis). J. Zool. 216, 103–117 (1988).Article 

    Google Scholar 
    Nielsen, J. M., Clare, E. L., Hayden, B., Brett, M. T. & Kratina, P. Diet tracing in ecology: Method comparison and selection. Methods Ecol. Evol. 9, 278–291 (2018).Article 

    Google Scholar 
    Birnie-Gauvin, K., Peiman, K. S., Raubenheimer, D. & Cooke, S. J. Nutritional physiology and ecology of wildlife in a changing world. Conserv. Physiol. 5, cox030 (2017).Article 

    Google Scholar 
    Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21, 2045–2050 (2012).Article 
    CAS 

    Google Scholar 
    Glenn, T. C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11, 759–769 (2011).Article 
    CAS 

    Google Scholar 
    Nichols, R. V., Åkesson, M. & Kjellander, P. Diet assessment based on rumen contents: A comparison between DNA metabarcoding and macroscopy. PLoS ONE 11, e0157977 (2016).Article 

    Google Scholar 
    Pompanon, F. et al. Who is eating what: diet assessment using next generation sequencing. Mol. Ecol. 21, 1931–1950 (2012).Article 
    CAS 

    Google Scholar 
    Kumari, P. et al. DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates. PLoS ONE 14, e0226253 (2019).Article 
    CAS 

    Google Scholar 
    Iwanowicz, D. D. et al. Metabarcoding of fecal samples to determine herbivore diets: A case study of the endangered Pacific pocket mouse. PLoS ONE 11, e0165366 (2016).Article 

    Google Scholar 
    Berry, T. E. et al. DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea). Ecol. Evol. 7, 5435–5453 (2017).Article 

    Google Scholar 
    Ford, M. J. et al. Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces. PLoS ONE 11, e0144956 (2016).Article 

    Google Scholar 
    Ando, H. et al. Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon (Columba janthina nitens) in oceanic island habitats. Ecol. Evol. 3, 4057–4069 (2013).Article 

    Google Scholar 
    Kim, E.-K. Behavioral ecology, habitat evaluation and genetic characteristics of water deer (Hydropotes inermis) in Korea. Ph.D. thesis. Kangwon National University (2011).Park, J.-E., Kim, B.-J. & Lee, S.-D. A study of potential of diet analysis in the Korean water deer (Hydropotes inermis argyropus) using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Korean J. Environ. Ecol. 24, 318–324 (2010).
    Google Scholar 
    Hollingsworth, P. M. Refining the DNA barcode for land plants. Proc. Natl. Acad. Sci. USA 108, 19451–19452 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Li, D.-Z. et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. USA 108, 19641–19646 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Park, E. & Nam, M. Changes in land cover and the cultivation area of ginseng in the Civilian Control Zone -Paju City and Yeoncheon County-. Korean J. Environ. Ecol. 27, 507–515 (2013).
    Google Scholar 
    Cheng, T. et al. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Mol. Ecol. Resour. 16, 138–149 (2016).Article 
    CAS 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).Article 
    CAS 

    Google Scholar 
    Ankenbrand, M. J., Keller, A., Wolf, M., Schultz, J. & Förster, F. ITS2 database V: Twice as much. Mol. Biol. Evol. 32, 3030–3032 (2015).Article 
    CAS 

    Google Scholar 
    Sickel, W. et al. Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach. BMC Ecol. 15, 20 (2015).Article 

    Google Scholar 
    Edgar, R. C. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ 6, e4652 (2018).Article 

    Google Scholar 
    Oksanen, J. et al. vegan: Community ecology package v 2.5–7 (R Foundation, Vienna, Austria, 2020).
    Google Scholar 
    Hsieh, T., Ma, K. & Chao, A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol. Evol. 7, 1451–1456 (2016).Article 

    Google Scholar 
    Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26, 32–46 (2001).
    Google Scholar 
    De Cáceres, M. & Legendre, P. Associations between species and groups of sites: indices and statistical inference. Ecology 90, 3566–3574 (2009).Article 

    Google Scholar 
    Yan, L. ggvenn: Draw venn diagram by ‘ggplot2’ v. 0.1.8 (R Foundation, Vienna, Austria, 2021).Choi, D.-Y. et al. Flora of province Gyonggi-do. Bull. Seoul Nat’l Univ. Arbor. 21, 25–76 (2001).
    Google Scholar 
    Ko, S. & Shin, Y. Flora of middle part in Gyeonggi Province. Korean J. Plant Res. 22, 49–70 (2009).
    Google Scholar 
    Lee, S.-K., Ryu, Y. & Lee, E. J. Endozoochorous seed dispersal by Korean water deer (Hydropotes inermis argyropus) in Taehwa Research Forest, South Korea. Glob. Ecol. Conserv. 40, e02325 (2022).Article 

    Google Scholar 
    Kim, K.-H. & Kang, S.-H. Flora of western civilian control zone (CCZ) in Korea. Korean J. Plant Res. 32, 565–588 (2019).
    Google Scholar 
    Gyeonggi Tourism Organization. Pyeonghwa-Nuri Trail ecological resource survey. (Paju City, Gyeonggi Province, Korea, 2018).Wickham, H. ggplot2: Elegant Graphics for Data Analysis 2nd edn. (Springer, New York, 2016).Book 
    MATH 

    Google Scholar 
    R Core Team. R: A language and environment for statistical computing (R Foundation, Vienna, Austria, 2020).Pertoldi, C. et al. Comparing DNA metabarcoding with faecal analysis for diet determination of the Eurasian otter (Lutra lutra) in Vejlerne. Denmark. Mammal. Res. 66, 115–122 (2021).Article 

    Google Scholar 
    Lee, B. Morphological, ecological and DNA taxonomic characteristics of Chinese water deer (Hydropotes inermis Swinhoe). Ph.D. thesis. Chungbuk National University (2003).Wilmshurst, J. F., Fryxell, J. M. & Hudsonb, R. J. Forage quality and patch choice by wapiti (Cervus elaphus). Behav. Ecol. 6, 209–217 (1995).Article 

    Google Scholar 
    Langvatn, R. & Hanley, T. A. Feeding-patch choice by red deer in relation to foraging efficiency. Oecologia 95, 164–170 (1993).Article 
    ADS 

    Google Scholar 
    Gray, P. B. & Servello, F. A. Energy intake relationships for white-tailed deer on winter browse diets. J. Wildl. Manag. 59, 147–152 (1995).Article 

    Google Scholar 
    Brown, D. T. & Doucet, G. J. Temporal changes in winter diet selection by white-tailed deer in a northern deer yard. J. Wildl. Manag. 55, 361–376 (1991).Article 

    Google Scholar 
    Takahashi, H. & Kaji, K. Fallen leaves and unpalatable plants as alternative foods for sika deer under food limitation. Ecol. Res. 16, 257–262 (2001).Article 

    Google Scholar 
    Bee, J. N. et al. Spatio-temporal feeding selection of red deer in a mountainous landscape. Austral Ecol. 35, 752–764 (2010).Article 

    Google Scholar 
    Gebert, C. & Verheyden-Tixier, H. Variations of diet composition of red deer (Cervus elaphus L.) in Europe. Mammal. Rev. 31, 189–201 (2001).Article 

    Google Scholar 
    Cornelis, J., Casaer, J. & Hermy, M. Impact of season, habitat and research techniques on diet composition of roe deer (Capreolus capreolus): a review. J. Zool. 248, 195–207 (1999).Article 

    Google Scholar 
    Kim, B. J. & Lee, S.-D. Home range study of the Korean water deer (Hydropotes inermis agyropus) using radio and GPS tracking in South Korea: Comparison of daily and seasonal habitat use pattern. J. Ecol. Field Biol. 34, 365–370 (2011).
    Google Scholar 
    Beier, P. Sex differences in quality of white-tailed deer diets. J. Mammal. 68, 323–329 (1987).Article 

    Google Scholar 
    Staines, B. W., Crisp, J. M. & Parish, T. Differences in the quality of food eaten by red deer (Cervus elaphus) stags and hinds in winter. J. Appl. Ecol. 19, 65–77 (1982).Article 

    Google Scholar 
    Koga, T. & Ono, Y. Sexual differences in foraging behavior of sika deer, Cervus nippon. J. Mammal. 75, 129–135 (1994).Article 

    Google Scholar 
    Han, S.-H., Lee, S.-S., Cho, I.-C., Oh, M.-Y. & Oh, H.-S. Species identification and sex determination of Korean water deer (Hydropotes inermis argyropus) by duplex PCR. J. Appl. Anim. Res. 35, 61–66 (2009).Article 
    CAS 

    Google Scholar 
    You, Z. et al. Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris). PeerJ 10, e13753 (2022).Article 

    Google Scholar 
    Zhao, W. et al. Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer. Gene Genom. 43, 43–53 (2021).Article 
    CAS 

    Google Scholar 
    Amato, K. R. et al. Gut microbiome, diet, and conservation of endangered langurs in Sri Lanka. Biotropica 52, 981–990 (2020).Article 

    Google Scholar 
    Stumpf, R. M. et al. Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biol. Conserv. 199, 56–66 (2016).Article 

    Google Scholar 
    Redford, K. H., Segre, J. A., Salafsky, N., del Rio, C. M. & McAloose, D. Conservation and the microbiome. Conserv. Biol. 26, 195–197 (2012).Article 

    Google Scholar 
    Deagle, B. E. et al. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?. Mol. Ecol. 28, 391–406 (2019).Article 

    Google Scholar 
    Corse, E. et al. A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies. Mol. Ecol. Resour. 17, e146–e159 (2017).Article 
    CAS 

    Google Scholar 
    Alberdi, A. et al. Promises and pitfalls of using high-throughput sequencing for diet analysis. Mol. Ecol. Resour. 19, 327–348 (2019).Article 

    Google Scholar 
    Nakahara, F. et al. The applicability of DNA barcoding for dietary analysis of sika deer. DNA Barcodes 3, 200–206 (2015).Article 

    Google Scholar 
    Thomas, A. C., Jarman, S. N., Haman, K. H., Trites, A. W. & Deagle, B. E. Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias. Mol. Ecol. 23, 3706–3718 (2014).Article 
    CAS 

    Google Scholar 
    Deagle, B. E., Eveson, J. P. & Jarman, S. N. Quantification of damage in DNA recovered from highly degraded samples–a case study on DNA in faeces. Front. Zool. 3, 11 (2006).Article 

    Google Scholar 
    Coissac, E., Riaz, T. & Puillandre, N. Bioinformatic challenges for DNA metabarcoding of plants and animals. Mol. Ecol. 21, 1834–1847 (2012).Article 
    CAS 

    Google Scholar 
    Estes, J. A. et al. Trophic downgrading of planet Earth. Science 333, 301–306 (2011).Article 
    ADS 
    CAS 

    Google Scholar 
    Clare, E. L. Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications. Evol. Appl. 7, 1144–1157 (2014).Article 

    Google Scholar 
    Ramirez, R., Quintanilla, J. & Aranda, J. White-tailed deer food habits in northeastern Mexico. Small Rumin. Res. 25, 141–146 (1997).Article 

    Google Scholar 
    Anouk Simard, M., Côté, S. D., Weladji, R. B. & Huot, J. Feedback effects of chronic browsing on life-history traits of a large herbivore. J. Anim. Ecol. 77, 678–686 (2008).Article 
    CAS 

    Google Scholar 
    Putman, R. J. & Staines, B. W. Supplementary winter feeding of wild red deer Cervus elaphus in Europe and North America: justifications, feeding practice and effectiveness. Mammal Rev. 34, 285–306 (2004).Article 

    Google Scholar 
    Milner, J. M., Van Beest, F. M., Schmidt, K. T., Brook, R. K. & Storaas, T. To feed or not to feed? Evidence of the intended and unintended effects of feeding wild ungulates. J. Wildl. Manag. 78, 1322–1334 (2014).Article 

    Google Scholar 
    Carpio, A. J., Apollonio, M. & Acevedo, P. Wild ungulate overabundance in Europe: contexts, causes, monitoring and management recommendations. Mammal Rev. 51, 95–108 (2021).Article 

    Google Scholar 
    Cappa, F., Lombardini, M. & Meriggi, A. Influence of seasonality, environmental and anthropic factors on crop damage by wild boar Sus scrofa. Folia Zool. 68, 261–268 (2019).Article 

    Google Scholar  More

  • in

    Incorporating dead material in ecosystem assessments and projections

    Stokland, J. N., Siitonen, J. & Jonsson, B. G. Biodiversity in Dead Wood (Cambridge Univ. Press, 2012).Turetsky, M. R. et al. Nat. Geosci. 8, 11–14 (2014).Article 

    Google Scholar 
    Wenger, S. J., Subalusky, A. L. & Freeman, M. C. Food Webs 18, e00106 (2019).Article 

    Google Scholar 
    Tomatsuri, M. & Kon, K. Hydrobiologia 790, 225–232 (2017).Article 

    Google Scholar 
    Henry, L. A. & Roberts, J. M. in Marine Animal Forests (eds Rossi, S. et al.) 235–256 (Springer, 2017).Walton, M. E. M. et al. Sci. Total Environ. 820, 153191 (2022).Article 
    CAS 

    Google Scholar 
    Wolfe, K., Kenyon, T. M. & Mumby, P. J. Coral Reefs 40, 1769–1806 (2021).Article 

    Google Scholar 
    Kim, H. et al. Glob. Change Biol. 28, 6180–6193 (2022).Jackson, R. B. et al. Annu. Rev. Ecol. Evol. Syst. 48, 419–445 (2017).Article 

    Google Scholar 
    Pan, Y. et al. Science 333, 988–993 (2011).Article 
    CAS 

    Google Scholar 
    Hedges, J. I., Keil, R. G. & Benner, R. Org. Geochem. 27, 195–212 (1997).Article 
    CAS 

    Google Scholar 
    Lønborg, C. et al. Front. Mar. Sci. 7, 466 (2020).Article 

    Google Scholar 
    Harden, J. W. et al. Glob. Change Biol. 6, 174–184 (2000).Davidson, E. A. & Janssens, I. A. Nature 440, 165–173 (2006).Article 
    CAS 

    Google Scholar 
    Hugelius, G. et al. Proc. Natl Acad. Sci. USA 117, 20438–20446 (2020).Article 
    CAS 

    Google Scholar 
    Hennige, S. J. et al. Front. Mar. Sci. https://doi.org/10.3389/fmars.2020.00668 (2020).Article 

    Google Scholar 
    Wolfram, U. et al. Sci. Rep. 12, 8052 (2022).Article 
    CAS 

    Google Scholar 
    Roberts, J. M., Wheeler, A. J. & Freiwald, A. Science 312, 543–547 (2006).Article 
    CAS 

    Google Scholar 
    Mortensen, P. B. & Fosså, J. H. Species diversity and spatial distribution of invertebrates on deep-water Lophelia reefs in Norway. In Proc. 10th Int. Coral Reef Symp. 1849–1868 (ICRS, 2006).Maier, S. R. et al. Deep Sea Res. I 175, 103574 (2021).. More

  • in

    A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands

    MAG binning and general featuresFrom the four hot springs, we assembled four associated metagenomes and then binned a total of 42 MAGs. We recovered 12 MAGs from RB10 hot spring, 13 from RB13, 14 from RB32 and 3 from RB108. Out of these 42 MAGs, 7 were of high-quality, 25 of nearly-high quality, 9 of medium quality and 1 of low quality (Table 1) based on metagenomic standards26. The GC% was quite variable, ranging from 25.76 to 70.35% among all MAGs and between 32.15 and 69.21% only among the high- and near high-quality MAGs. With the exception of RB108 from which we only recovered bacterial MAGs, we retrieved both bacterial and archaeal MAGs in the other hot springs. Two thirds of the MAGs (26/42) were assigned to the domain Bacteria and the rest to the domain Archaea (16/42) (Table 2).Table 1 General characteristics of the 42 MAGs obtained from RB10, RB13, RB32 and RB108 samples.Full size tableTable 2 Classification of the MAGs based on the taxonomic classification of GTDB-Tk software (v2.1.0) and the Genome Taxonomy Database (07-RS207 release).Full size tableTaxonomic and phylogenomic analyses of MAGsThe taxonomic affiliation of the MAGs was investigated in detail through the workflow classify of GTDB-Tk (v 2.1.0; GTDB reference tree 07-RS207) (Table 2) and through de novo phylogenomic analyses (Fig. S1a–i). We also tried to classify MAGs on the basis of overall genome relatedness indices (OGRI), which is detailed in supplementary material (Text S1, Table S2, Fig. S2).De novo phylogenomic analyses globally confirmed the positioning of MAGs provided by GTDB-Tk, with high branching support. For Bacteria, GTDB-Tk analyses allowed us to place the MAGs in the following clades: six in the phylum Aquificota from the four different springs, comprising four MAGs belonging to the genus Hydrogenivirga (family Aquificaceae) (RB10-MAG07, RB13-MAG10, RB32-MAG07, RB108-MAG02), and two belonging to the family ‘Hydrogenobaculaceae’ (RB10-MAG12, RB32-MAG11) (Table 2, Fig. S1a). Their closest cultured relatives originated either from hot springs or from deep-sea hydrothermal vents27. Three MAGs from three geothermal springs belonged to the phylum Armatimonadota (RB10-MAG03, RB13-MAG04, RB32-MAG03) and had no close cultured relatives. Seven MAGs have been classified into the phylum Chloroflexota: three MAGs belonging to the genus Thermoflexus from three different springs (RB10-MAG04, RB13-MAG05, RB32-MAG02), one affiliating with the genus Thermomicrobium (RB32-MAG08), one falling into the family Ktedonobacteraceae (RB108-MAG03), one belonging to the class Dehalococcoidia (RB32-MAG04) and another one whose phylogenetic position is more difficult to assert because it is a MAG of medium quality (RB32-MAG14). Six MAGs from four various hot springs belonged to the phylum Deinococcota, and to the genera Thermus (RB10-MAG08, RB10-MAG11, RB13-MAG09, RB32-MAG10, RB108-MAG01) and Meiothermus (RB13-MAG13). One MAG belonged to the family ‘Sulfurifustaceae’ (RB13-MAG01), in the phylum Proteobacteria (Gamma-class). The MAG referenced as RB32-MAG13 was classified into the phylum ‘Patescibacteria’, in the class ‘Paceibacteria’, and was distantly related to MAGs originating from groundwater and from hot springs. Finally, two MAGs from two different springs belonged to the phylum WOR-3, in the Candidatus genus ‘Caldipriscus’ (RB32-MAG12, RB10-MAG09).For Archaea, almost all the MAGs reconstructed in this study, e.g. 15 of the 16 archaeal MAGs, belonged to the phylum Thermoproteota. Among them, four belonged to the genus Ignisphaera (RB10-MAG05, RB13-MAG08, RB13-MAG11, RB32-MAG05), three to the genus Infirmifilum (RB10-MAG06, RB13-MAG03, RB32-MAG09), two to the genus Zestosphaera (RB10-MAG02, RB13-MAG06), three to the family Acidilobaceae (RB10-MAG01, RB13-MAG02, RB32-MAG01) and two to the order Geoarchaeales (RB10-MAG10, RB32-MAG06). Additionally, one belonged to the family Thermocladiaceae (RB13-MAG07). Lastly, the MAG belonging to another phylum (RB13-MAG12) was affiliated with the ‘Aenigmatarchaeota’, class ‘Aenigmatarchaeia’, and was distantly related to MAGs from hot springs and from deep-sea hydrothermal vent sediments28,29.Out of these 42 MAGs, at least 19 MAGs corresponded to different taxa at the taxonomic rank of species or higher according to GTDB (Table 2). Eighteen of them belonged to lineages with several cultivated representatives including the species Thermus thermophilus. 13 new genomic species within the GTDB genera Hydrogenivirga, HRBIN17, Thermoflexus, SpSt-223, CADDYT01, Zestosphaera, Ignisphaera, Infirmifilum, Thermus, Thermus_A, Meiothermus_B, JAHLMO01 and Caldipriscus, and 6 putative new genomic genera belonging to the GTDB families Hydrogenobaculaceae, Acidilobaceae, WAQG01, Thermocladiaceae, Sulfurifustaceae and HR35 could be identified (Table 2). In addition, 9 MAGs belonged to lineages that are predominantly or exclusively known through environmental DNA sequences. Thus, these 42 MAGs comprised a broad phylogenetic range of Bacteria and Archaea at different levels of taxonomic organization, of which a large majority were not reported before.The approaches implemented here were not intended to describe the microbial diversity present in these sources in an exhaustive way or to compare them in a fine way, and cannot allow it because of a 2-year storage at 4 °C. This long storage has probably led to changes in the microbial communities and to the selective loss or enrichment of some taxa. As a result, no analysis of abundance or absence of taxa can be conducted from these metagenomes and the results are discussed taking this bias into account. However, they do provide an overview of the microbial diversity effectively present. If we compare the phylogenetic diversity of the MAGs found in the four hot springs, we can observe that 3 shared phyla (Deinococcota, Aquificota and Chloroflexota: phyla names according to GTDB), 2 shared families (Thermaceae and Aquificaceae), and one shared genus (Hydrogenivirga) were found among the four sources (Fig. 2). In addition, hot springs RB10, RB13 and RB32, that are geographically close ( More

  • in

    Economic and biophysical limits to seaweed farming for climate change mitigation

    Monte Carlo analysisSeaweed production costs and net costs of climate benefits were estimated on the basis of outputs of the biophysical and technoeconomic models described below. The associated uncertainties and sensitivities were quantified by repeatedly sampling from uniform distributions of plausible values for each cost and economic parameter (n = 5,000 for each nutrient scenario from the biophysical model, for a total of n = 10,000 simulations; see Supplementary Figs. 14 and 15)47,48,49,50,51,52. Parameter importance across Monte Carlo simulations (Fig. 3 and Supplementary Fig. 9) was determined using decision trees in LightGBM, a gradient-boosting machine learning framework.Biophysical modelG-MACMODS is a nutrient-constrained, biophysical macroalgal growth model with inputs of temperature, nitrogen, light, flow, wave conditions and amount of seeded biomass30,53, that we used to estimate annual seaweed yield per area (either in tons of carbon or tons of dry weight biomass per km2 per year)33,34. In the model, seaweed takes up nitrogen from seawater, and that nitrogen is held in a stored pool before being converted to structural biomass via growth54. Seaweed biomass is then lost via mortality, which includes breakage from variable ocean wave intensity. The conversion from stored nitrogen to biomass is based on the minimum internal nitrogen requirements of macroalgae, and the conversion from biomass to units of carbon is based on an average carbon content of macroalgal dry weight (~30%)55. The model accounts for farming intensity (sub-grid-scale crowding) and employs a conditional harvest scheme, where harvest is optimized on the basis of growth rate and standing biomass33.The G-MACMODS model is parameterized for four types of macroalgae: temperate brown, temperate red, tropical brown and tropical red. These types employed biophysical parameters from genera that represent over 99.5% of present-day farmed macroalgae (Eucheuma, Gracilaria, Kappahycus, Sargassum, Porphyra, Saccharina, Laminaria, Macrocystis)39. Environmental inputs were derived from satellite-based and climatological model output mapped to 1/12-degree global resolution, which resolves continental shelf regions. Nutrient distributions were derived from a 1/10-degree resolution biogeochemical simulation led by the National Center for Atmospheric Research (NCAR) and run in the Community Earth System Model (CESM) framework35.Two nutrient scenarios were simulated with G-MACMODS and evaluated using the technoeconomic model analyses described below: the ‘ambient nutrient’ scenario where seaweed growth was computed using surface nutrient concentrations without depletion or competition, and ‘limited nutrient’ simulations where seaweed growth was limited by an estimation of the nutrient supply to surface waters (computed as the flux of deep-water nitrate through a 100 m depth horizon). For each Monte Carlo simulation in the economic analysis, the technoeconomic model randomly selects either the 5th, 25th, 50th, 75th or 95th percentile G-MACMODS seaweed yield map from a normal distribution to use as the yield map for that simulation. Figures and numbers reported in the main text are based on the ambient-nutrient scenario; results based on the limited-nutrient scenario are shown in Supplementary Figures.Technoeconomic modelAn interactive web tool of the technoeconomic model is available at https://carbonplan.org/research/seaweed-farming.We estimated the net cost of seaweed-related climate benefits by first estimating all costs and emissions related to seaweed farming, up to and including the point of harvest at the farm location, then estimating costs and emissions related to the transportation and processing of harvested seaweed, and finally estimating the market value of seaweed products and either carbon sequestered or GHG emissions avoided.Production costs and emissionsSpatially explicit costs of seaweed production ($ tDW−1) and production-related emissions (tCO2 tDW−1) were calculated on the basis of ranges of capital costs ($ km−2), operating costs (including labour, $ km−2), harvest costs ($ km−2) and transport emissions per distance travelled (tCO2 km−1) in the literature (Table 1, Supplementary Tables 1 and 2); annual seaweed biomass (tDW km−2, for the preferred seaweed type in each grid cell), line spacing and number of harvests (species-dependent) from the biophysical model; as well as datasets of distances to the nearest port (km), ocean depth (m) and significant wave height (m).Capital costs were calculated as:$$c_{cap} = c_{capbase} + left( {c_{capbase} times left( {k_d + k_w} right)} right) + c_{sl}$$
    (1)
    where ccap is the total annualized capital costs per km2, ccapbase is the annualized capital cost per km2 (for example, cost of buoys, anchors, boats, structural rope) before applying depth and wave impacts, kd and kw are the impacts of depth and waviness on capital cost, respectively, each expressed as a multiplier between 0 and 1 modelled using our Monte Carlo method and applied only to grid cells with depth >500 m and/or significant wave height >3 m, respectively, and csl is the total annual cost of seeded line calculated as:$$c_{sl} = c_{slbase} times p_{sline}$$
    (2)
    where cslbase is the cost per metre of seeded line, and psline is the total length of line per km2, based on the optimal seaweed type grown in each grid cell.Operating and maintenance costs were calculated as:$$c_{op} = c_{ins} + c_{lic} + c_{lab} + c_{opbase}$$
    (3)
    where cop is the total annualized operating and maintenance costs per km2, cins is the annual insurance cost per km2, clic is the annual cost of a seaweed aquaculture license per km2, clab is the annual cost of labour excluding harvest labour, and copbase is all other operating and maintenance costs.Harvest costs were calculated as:$$c_{harv} = c_{harvbase} times n_{harv}$$
    (4)
    where charv is the total annual costs associated with harvesting seaweed per km2, charvbase is the cost per harvest per km2 (including harvest labour but excluding harvest transport), and nharv is the total number of harvests per year.Costs associated with transporting equipment to the farming location were calculated as:$$c_{eqtrans} = c_{transbase} times m_{eq} times d_{port}$$
    (5)
    where ceqtrans is total annualized cost of transporting equipment, ctransbase is the cost to transport 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons and dport is the ocean distance to the nearest port in km.The total production cost of growing and harvesting seaweed was therefore calculated as:$$c_{prod} = frac{{left( {c_{cap}} right) + left( {c_{op}} right) + left( {c_{harv}} right) + (c_{eqtrans})}}{{s_{dw}}}$$
    (6)
    where cprod is total annual cost of seaweed production (growth + harvesting), ccap is as calculated in equation (1), cop is as calculated in equation (3), charv is as calculated in equation (4), ceqtrans is as calculated in equation (5) and sdw is the DW of seaweed harvested annually per km2.Emissions associated with transporting equipment to the farming location were calculated as:$$e_{eqtrans} = e_{transbase} times m_{eq} times d_{port}$$
    (7)
    where eeqtrans is the total annualized CO2 emissions in tons from transporting equipment, etransbase is the CO2 emissions from transporting 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons and dport is the ocean distance to the nearest port in km.Emissions from maintenance trips to/from the seaweed farm were calculated as:$$e_{mnt} = left( {left( {2 times d_{port}} right) times e_{mntbase} times left( {frac{{n_{mnt}}}{{a_{mnt}}}} right)} right) + (e_{mntbase} times d_{mnt})$$
    (8)
    where emnt is total annual CO2 emissions from farm maintenance, dport is the ocean distance to the nearest port in km, nmnt is the number of maintenance trips per km2 per year, amnt is the area tended to per trip, dmnt is the distance travelled around each km2 for maintenance and emntbase is the CO2 emissions from travelling 1 km on a typical fishing maintenance vessel (for example, a 14 m Marinnor vessel with 2 × 310 hp engines) at an average speed of 9 knots (16.67 km h−1), resulting in maintenance vessel fuel consumption of 0.88 l km−1 (refs. 28,56).Total emissions from growing and harvesting seaweed were therefore calculated as:$$e_{prod} = frac{{(e_{eqtrans}) + (e_{mnt})}}{{s_{dw}}}$$
    (9)
    where eprod is total annual emissions from seaweed production (growth + harvesting), eeqtrans is as calculated in equation (7), emnt is as calculated in equation (8) and sdw is the DW of seaweed harvested annually per km2.Market value and climate benefits of seaweedFurther transportation and processing costs, economic value and net emissions of either sinking seaweed in the deep ocean for carbon sequestration or converting seaweed into usable products (biofuel, animal feed, pulses, vegetables, fruits, oil crops and cereals) were calculated on the basis of ranges of transport costs ($ tDW−1 km−1), transport emissions (tCO2-eq t−1 km−1), conversion cost ($ tDW−1), conversion emissions (tCO2-eq tDW−1), market value of product ($ tDW−1) and the emissions avoided by product (tCO2-eq tDW−1) in the literature (Table 1). Market value was treated as globally homogeneous and does not vary by region. Emissions avoided by products were determined by comparing estimated emissions related to seaweed production to emissions from non-seaweed products that could potentially be replaced by seaweed (including non-CO2 greenhouse gas emissions from land use)24. Other parameters used are distance to nearest port (km), water depth (m), spatially explicit sequestration fraction (%)57 and distance to optimal sinking location (km; cost-optimized for maximum emissions benefit considering transport emissions combined with spatially explicit sequestration fraction; see ‘Distance to sinking point calculation’ below). Each Monte Carlo simulation calculated the cost of both CDR via sinking seaweed and GHG emissions mitigation via seaweed products.For seaweed CDR, after the seaweed is harvested, it can either be sunk in the same location that it was grown, or be transported to a more economically favourable sinking location where more of the seaweed carbon would remain sequestered for 100 yr (see ‘Distance to optimal sinking point’ below). Immediately post-harvest, the seaweed still contains a large amount of water, requiring a conversion from dry mass to wet mass for subsequent calculations33:$$s_{ww} = frac{{s_{dw}}}{{0.1}}$$
    (10)
    where sww is the annual wet weight of seaweed harvested per km2 and sdw is the annual DW of seaweed harvested per km2.The cost to transport harvested seaweed to the optimal sinking location was calculated as:$$c_{swtsink} = c_{transbase} times d_{sink} times s_{ww}$$
    (11)
    where cswtsink is the total annual cost to transport harvested seaweed to the optimal sinking location, ctransbase is the cost to transport 1 ton of material 1 km on a barge, dsink is the distance in km to the economically optimized sinking location and sww is the annually harvested seaweed wet weight in t km−2 as in equation (10).The costs associated with transporting replacement equipment (for example, lines, buoys,anchors) to the farming location and hauling back used equipment at the end of its assumed lifetime (1 yr for seeded line, 5–20 yr for capital equipment by equipment type) in the sinking CDR pathway were calculated as:$$c_{eqtsink} = left( {c_{transbase} times left( {2 times d_{sink}} right) times m_{eq}} right) + (c_{transbase} times d_{port} times m_{eq})$$
    (12)
    where ceqtsink is the total annualized cost to transport both used and replacement equipment, ctransbase is the cost to transport 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons, dsink is the distance in km to the economically optimized sinking location and dport is the ocean distance to the nearest port in km. We assumed that the harvesting barge travels from the farming location directly to the optimal sinking location with harvested seaweed and replaced (used) equipment in tow (including used seeded line and annualized mass of used capital equipment), sinks the harvested seaweed, returns to the farm location and then returns to the nearest port (see Supplementary Fig. 16). These calculations assumed the shortest sea-route distance (see Distance to optimal sinking point).The total value of seaweed that is sunk for CDR was therefore calculated as:$$v_{sink} = frac{{left( {v_{cprice} – left( {c_{swtsink} + c_{eqtsink}} right)} right)}}{{s_{dw}}}$$
    (13)
    where vsink is the total value (cost, if negative) of seaweed farmed for CDR in $ tDW−1, vcprice is a theoretical carbon price, cswtsink is as calculated in equation (11), ceqtsink is as calculated in equation (12) and sdw is the annually harvested seaweed DW in t km−2. We did not assume any carbon price in our Monte Carlo simulations (vcprice is equal to zero), making vsink negative and thus representing a net cost.To calculate net carbon impacts, our model included uncertainty in the efficiency of using the growth and subsequent deep-sea deposition of seaweed as a CDR method. The uncertainty is expected to include the effects of reduced phytoplankton growth from nutrient competition, the relationship between air–sea gas exchange and overturning circulation (hereafter collectively referred to as the ‘atmospheric removal fraction’) and the fraction of deposited seaweed carbon that remains sequestered for at least 100 yr. The total amount of atmospheric CO2 removed by sinking seaweed was calculated as:$$e_{seqsink} = k_{atm} times k_{fseq} times frac{{tC}}{{tDW}} times frac{{tCO_2}}{{tC}}$$
    (14)
    where eseqsink is net atmospheric CO2 sequestered annually in t km−2, katm is the atmospheric removal fraction and kfseq is the spatially explicit fraction of sunk seaweed carbon that remains sequestered for at least 100 yr (see ref. 57).The emissions from transporting harvested seaweed to the optimal sinking location were calculated as:$$e_{swtsink} = e_{transbase} times d_{sink} times s_{ww}$$
    (15)
    where eswtsink is the total annual CO2 emissions from transporting harvested seaweed to the optimal sinking location in tCO2 km−2, etransbase is the CO2 emissions (tons) from transporting 1 ton of material 1 km on a barge (tCO2 per t-km), dsink is the distance in km to the economically optimized sinking location and sww is the annually harvested seaweed wet weight in t km−2 as in equation (10). Since the unit for etransbase is tCO2 per t-km, the emissions from transporting seaweed to the optimal sinking location are equal to (e_{mathrm{transbase}} times d_{mathrm{sink}} times s_{mathrm{ww}}), and the emissions from transporting seaweed from the optimal sinking location back to the farm are equal to 0 (since the seaweed has already been deposited, the seaweed mass to transport is now 0). Note that this does not yet include transport emissions from transport of equipment post-seaweed-deposition (see equation 16 below and Supplementary Fig. 16).The emissions associated with transporting replacement equipment (for example, lines, buoys, anchors) to the farming location and hauling back used equipment at the end of its assumed lifetime (1 yr for seeded line, 5–20 yr for capital equipment by equipment type)28,41 in the sinking CDR pathway were calculated as:$$e_{eqtsink} = left( {e_{transbase} times left( {2 times d_{sink}} right) times m_{eq}} right) + (e_{transbase} times d_{port} times m_{eq})$$
    (16)
    where eeqtsink is the total annualized CO2 emissions in tons from transporting both used and replacement equipment, etransbase is the CO2 emissions from transporting 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons, dsink is the distance in km to the economically optimized sinking location and dport is the ocean distance to the nearest port in km. We assumed that the harvesting barge travels from the farming location directly to the optimal sinking location with harvested seaweed and replaced (used) equipment in tow (including used seeded line and annualized mass of used capital equipment), sinks the harvested seaweed, returns to the farm location and then returns to the nearest port. These calculations assumed the shortest sea-route distance (see Distance to optimal sinking point).Net CO2 emissions removed from the atmosphere by sinking seaweed were thus calculated as:$$e_{remsink} = frac{{left( {e_{seqsink} – left( {e_{swtsink} + e_{eqtsink}} right)} right)}}{{s_{dw}}}$$
    (17)
    where eremsink is the net atmospheric CO2 removed per ton of seaweed DW, eseqsink is as calculated in equation (14), eswtsink is as calculated in equation (15), eeqtsink is as calculated in equation (16) and sdw is the annually harvested seaweed DW in t km−2.Net cost of climate benefitsSinkingTo calculate the total net cost and emissions from the production, harvesting and transport of seaweed for CDR, we combined the cost and emissions from the sinking-pathway cost and value modules. The total net cost of seaweed CDR per DW ton of seaweed was calculated as:$$c_{sinknet} = c_{prod} – v_{sink}$$
    (18)
    where csinknet is the total net cost of seaweed for CDR per DW ton harvested, cprod is the net production cost per DW ton as calculated in equation (6) and vsink is the net value (or cost, if negative) per ton seaweed DW as calculated in equation (13).The total net CO2 emissions removed per DW ton of seaweed were calculated as:$$e_{sinknet} = e_{remsink} – e_{prod}$$
    (19)
    where esinknet is the total net atmospheric CO2 removed per DW ton of seaweed harvested annually (tCO2 tDW−1 yr−1), eremsink is the net atmospheric CO2 removed via seaweed sinking annually as calculated in equation (17) and eprod is the net CO2 emitted from production and harvesting of seaweed annually as calculated in equation (9). For each Monte Carlo simulation, locations where esinknet is negative (that is, net emissions rather than net removal) were not included in subsequent calculations since they would not be contributing to CDR in that location under the given scenario. Note that these net emissions cases only occur in areas far from port in specific high-emissions scenarios. Even in such cases, most areas still contribute to CO2 removal (negative emissions), hence costs from locations with net removal were included.Total net cost was then divided by total net emissions to get a final value for cost per ton of atmospheric CO2 removed:$$c_{pertonsink} = frac{{c_{sinknet}}}{{e_{sinknet}}}$$
    (20)
    where cpertonsink is the total net cost per ton of atmospheric CO2 removed via seaweed sinking ($ per tCO2 removed), csinknet is total net cost per ton seaweed DW harvested as calculated in equation (18) ($ tDW−1) and esinknet is the total net atmospheric CO2 removed per ton seaweed DW harvested as calculated in equation (19) (tCO2 tDW−1).GHG emissions mitigationInstead of sinking seaweed for CDR, seaweed can be used to make products (including but not limited to food, animal feed and biofuels). Replacing convention products with seaweed-based products can result in ‘avoided emissions’ if the emissions from growing, harvesting, transporting and converting seaweed into products are less than the total greenhouse gas emissions (including non-CO2 GHGs) embodied in conventional products that seaweed-based products replace.When seaweed is used to make products, we assumed it is transported back to the nearest port immediately after being harvested. The annualized cost to transport the harvested seaweed and replacement equipment (for example, lines, buoys, anchors) was calculated as:$$c_{transprod} = frac{{left( {c_{transbase} times d_{port} times left( {s_{ww} + m_{eq}} right)} right)}}{{s_{dw}}}$$
    (21)
    where ctransprod is the annualized cost per ton seaweed DW to transport seaweed and equipment back to port from the farm location, ctransbase is the cost to transport 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons, dport is the ocean distance to the nearest port in km, sww is the annual wet weight of seaweed harvested per km2 as calculated in equation (10) and sdw is the annual DW of seaweed harvested per km2.The total value of seaweed that is used for seaweed-based products was calculated as:$$v_{product} = v_{mkt} – left( {c_{transprod} + c_{conv}} right)$$
    (22)
    where vproduct is the total value (cost, if negative) of seaweed used for products ($ tDW−1), vmkt is how much each ton of seaweed would sell for, given the current market price of conventional products that seaweed-based products replace ($ tDW−1), ctransprod is as calculated in equation (21) and cconv is the cost to convert each ton of seaweed to a usable product ($ tDW−1).The annualized CO2 emissions from transporting harvested seaweed and equipment back to port were calculated as:$$e_{transprod} = frac{{left( {e_{transbase} times d_{port} times left( {s_{ww} + m_{eq}} right)} right)}}{{s_{dw}}}$$
    (23)
    where etransprod is the annualized CO2 emissions per ton seaweed DW to transport seaweed and equipment back to port from the farm location, etransbase is the CO2 emissions from transporting 1 ton of material 1 km on a barge, meq is the annualized equipment mass in tons, dport is the ocean distance to the nearest port in km, sww is the annual wet weight of seaweed harvested per km2 as calculated in equation (10) and sdw is the annual DW of seaweed harvested per km2.Total emissions avoided by each ton of harvested seaweed DW were calculated as:$$e_{avprod} = e_{subprod} – left( {e_{transprod} + e_{conv}} right)$$
    (24)
    where eavprod is total CO2-eq emissions avoided per ton of seaweed DW per year (including non-CO2 GHGs using a GWP time period of 100 yr), esubprod is the annual CO2-eq emissions avoided per ton seaweed DW by replacing a conventional product with a seaweed-based product, etransprod is as calculated in equation (23) and econv is the annual CO2 emissions per ton seaweed DW from converting seaweed into usable products. esubprod was calculated by converting seaweed DW to caloric content58 for food/feed and comparing emissions intensity per kcal to agricultural products24, or by converting seaweed DW into equivalent biofuel content with a yield of 0.25 tons biofuel per ton DW59 and dividing the CO2 emissions per ton fossil fuel by the seaweed biofuel yield.To calculate the total net cost and emissions from the production, harvesting, transport and conversion of seaweed for products, we combined the cost and emissions from the product-pathway cost and value modules. The total net cost of seaweed for products per ton DW was calculated as:$$c_{prodnet} = c_{prod} – v_{product}$$
    (25)
    where cprodnet is the total net cost per ton DW of seaweed harvested for use in products, cprod is the net production cost per ton DW as calculated in equation (6) and vproduct is the net value (or cost, if negative) per ton DW as calculated in equation (22).The total net CO2-eq emissions avoided per ton DW of seaweed used in products were calculated as:$$e_{prodnet} = e_{avprod} – e_{prod}$$
    (26)
    where eprodnet is the total net CO2-eq emissions avoided per ton DW of seaweed harvested annually (tCO2 tDW−1 yr−1), eavprod is the net CO2-eq emissions avoided by seaweed products annually as calculated in equation (24) and eprod is the net CO2 emitted from production and harvesting of seaweed annually as calculated in equation (9). For each Monte Carlo simulation, locations where eprodnet is negative (that is, net emissions rather than net emissions avoided) were not included in subsequent calculations since they would not be avoiding any emissions in that scenario.Total net cost was then divided by total net emissions avoided to get a final value for cost per ton of CO2-eq emissions avoided:$$c_{pertonprod} = frac{{c_{prodnet}}}{{e_{prodnet}}}$$
    (27)
    where cpertonprod is the total net cost per ton of CO2-eq emissions avoided by seaweed products ($ per tCO2-eq avoided), cprodnet is total net cost per ton seaweed DW harvested for products as calculated in equation (25) ($ tDW−1) and eprodnet is total net CO2-eq emissions avoided per ton seaweed DW harvested for products as calculated in equation (26) (tCO2 tDW−1).Parameter ranges for Monte Carlo simulationsFor technoeconomic parameters with two or more literature values (see Supplementary Table 1), we assumed that the maximum literature value reflected the 95th percentile and the minimum literature value represented the 5th percentile of potential costs or emissions. For parameters with only one literature value, we added ±50% to the literature value to represent greater uncertainty within the modelled parameter range. Values at each end of parameter ranges were then rounded before Monte Carlo simulations as follows: capital costs, operating costs and harvest costs to the nearest $10,000 km−2, labour costs and insurance costs to the nearest $1,000 km−2, line costs to the nearest $0.05 m−1, transport costs to the nearest $0.05 t−1 km−1, transport emissions to the nearest 0.000005 tCO2 t−1 km−1, maintenance transport emissions to the nearest 0.0005 tCO2 km−1, product-avoided emissions to the nearest 0.1 tCO2-eq tDW−1, conversion cost down to the nearest $10 tDW−1 on the low end of the range and up to the nearest $10 tDW−1 on the high end of the range, and conversion emissions to the nearest 0.01 tCO2 tDW−1.We extended the minimum range values of capital costs to $10,000 km−2 and transport emissions to 0 to reflect potential future innovations, such as autonomous floating farm setups that would lower capital costs and net-zero emissions boats that would result in 0 transport emissions. To calculate the minimum value of $10,000 km−2 for a potential autonomous floating farm, we assumed that the bulk of capital costs for such a system would be from structural lines and flotation devices, and we therefore used the annualized structural line (system rope) and buoy costs from ref. 41 rounded down to the nearest $5,000 km−2. The full ranges used for our Monte Carlo simulations and associated literature values are shown in Supplementary Table 1.Distance to optimal sinking pointDistance to the optimal sinking point was calculated using a weighted distance transform (path-finding algorithm, modified from code in ref. 60) that finds the shortest ocean distance from each seaweed growth pixel to the location at which the net CO2 removed is maximized (including impacts of both increased sequestration fraction and transport emissions for different potential sinking locations) and the net cost is minimized. This is not necessarily the location in which the seaweed was grown, since the fraction of sunk carbon that remains sequestered for 100 yr is spatially heterogeneous (see ref. 57). For each ocean grid cell, we determined the cost-optimal sinking point by iteratively calculating equations (11–20) and assigning dsink as the distance calculated by weighted distance transform to each potential sequestration fraction (0.01–1.00) in increments of 0.01. Except for transport emissions, the economic parameter values used for these calculations were the averages of unrounded literature value ranges; we assumed that the maximum literature value reflected the 95th percentile and the minimum literature value represented the 5th percentile of potential costs or emissions, or for parameters with only one literature value, we added ±50% to the literature value to represent greater uncertainty within the modelled parameter range. For transport and maintenance transport emissions, we extended the minimum values of the literature ranges to zero to reflect potential net-zero emissions transport options and used the mean values of the resulting ranges. The dsink that resulted in minimum net cost per ton CO2 for each ocean grid cell was saved as the final dsink map, and the associated sequestration fraction value that the seaweed is transported to via dsink was assigned to the original cell where the seaweed was farmed and harvested (Supplementary Fig. 19). If the cost-optimal location to sink using this method was the same cell where the seaweed was harvested, then dsink was 0 km and the sequestration fraction was not modified from its original value (Supplementary Fig. 18).Comparison of gigaton-scale sequestration area to previous estimatesPrevious related work estimating the ocean area suitable for macroalgae cultivation13 and/or the area that might be required to reach gigaton-scale carbon removal via macroalgae cultivation13,19,36 has yielded a wide range of results, primarily due to differences in modelling methods. For example, Gao et al. (2022)36 estimate that 1.15 million km2 would be required to sequester 1 GtCO2 annually when considering carbon lost from seaweed biomass/sequestered as particulate organic carbon (POC) and refractory dissolved organic carbon (rDOC), and assume that the harvested seaweed is sold as food such that the carbon in the harvested seaweed is not sequestered. The area (0.31 million km2) required to sequester 1 GtCO2 in our study assumes that all harvested seaweed is sunk to the deep ocean to sequester carbon.Additionally, Wu et al.19 estimates that roughly 12 GtCO2 could be sequestered annually via macroalgae cultivation in approximately 20% of the world ocean area (that is, 1.67% ocean area per GtCO2), which is a much larger area per GtCO2 than our estimate of 0.085% ocean area. This notable difference arises for several reasons (including differences in yields, which in Wu et al. are around 500 tDW yr−1 in the highest-yield areas, whereas yields in our cheapest sequestration areas from G-MACMODS average 3,400 tDW km−2 yr−1) that arise from differences in model methodology. First, Wu et al. model temperate brown seaweeds, while our study considers different seaweed types, many of which have higher growth rates, and uses the most productive seaweed type for each ocean grid cell. The G-MACMODS seaweed growth model we use also has a highly optimized harvest schedule, includes luxury nutrient uptake (a key feature of macroalgal nutrient physiology) and does not directly model competition with phytoplankton during seaweed growth. Finally, tropical red seaweeds (the seaweed type in our cheapest sequestration areas) grow year-round, while others, such as the temperate brown seaweeds modelled by Wu et al., only grow seasonally. These differences all contribute to higher productivity in our model, leading to a smaller area required for gigaton-scale CO2 sequestration compared with Wu et al.Conversely, the ocean areas we model for seaweed-based CO2 sequestration or GHG emissions avoided are much larger than the 48 million km2 that Froehlich et al.13 estimate to be suitable for macroalgae farming globally. Although our maps show productivity and costs everywhere, the purpose of our modelling was to evaluate where different types of seaweed grow best and how production costs and product values vary over space, to highlight the lowest-cost areas (which are often the highest-producing areas) under various technoeconomic assumptions.Comparison of seaweed production costs to previous estimatesAlthough there are not many estimates of seaweed production costs in the scientific literature, our estimates for the lowest-cost 1% area of the ocean ($190–$2,790 tDW−1) are broadly consistent with previously published results: seaweed production costs reported in the literature range from $120 to $1,710 tDW−1 (refs. 40,41,61,62), but are highly dependent on assumed seaweed yields. For example, Camus et al.41 calculate a cost of $870 tDW−1 assuming a minimum yield of 12.4 kgDW m−1 of cultivation line (equivalent to 8.3 kgDW m−2 using 1.5 m spacing between lines). Using the economic values from Camus et al. but with our estimates of average yield for the cheapest 1% production cost areas (2.6 kgDW m−2) gives a much higher average cost of $2,730 tDW−1. Contrarily, van den Burg et al.40 calculate a cost of $1,710 tDW−1 using a yield of 20 tDW ha−1 (that is, 2.0 kg m−2). Instead assuming the average yield to be that from our lowest-cost areas (that is, 2.6 kgDW m−2 or 26 tDW ha−1) would decrease the cost estimated by van den Burg et al. (2016) to $1,290 tDW−1. Most recently, Capron et al.62 calculate an optimistic scenario cost of $120 tDW−1 on the basis of an estimated yield of 120 tDW ha−1 (12 kg m−2; over 4.5 times higher than the average yield in our lowest-cost areas). Again, instead assuming the average yield to be that in our lowest-cost areas would raise Capron et al.’s production cost to $540 tDW−1 (between the $190–$880 tDW−1 minimum to median production costs in the cheapest 1% areas from our model; Fig. 1a,b).Data sourcesSeaweed biomass harvestedWe used spatially explicit data for seaweed harvested globally under both ambient and limited-nutrient scenarios from the G-MACMODS seaweed growth model33.Fraction of deposited carbon sequestered for 100 yrWe used data from ref. 57 interpolated to our 1/12-degree grid resolution.Distance to the nearest portWe used the Distance from Port V1 dataset from Global Fishing Watch (https://globalfishingwatch.org/data-download/datasets/public-distance-from-port-v1) interpolated to our 1/12-degree grid resolution.Significant wave heightWe used data for annually averaged significant wave height from the European Center for Medium-range Weather Forecasts (ECMWF) interpolated to our 1/12-degree grid resolution.Ocean depthWe used data from the General Bathymetric Chart of the Oceans (GEBCO).Shipping lanesWe used data of Automatic Identification System (AIS) signal count per ocean grid cell, interpolated to our 1/12-degree grid resolution. We defined a major shipping lane grid cell as any cell with >2.25 × 108 AIS signals, a threshold that encompasses most major trans-Pacific and trans-Atlantic shipping lanes as well as major shipping lanes in the Indian Ocean, the North Sea, and coastal routes worldwide.Marine protected areas (MPAs)We used data from the World Database on Protected Areas (WDPA) and defined an MPA as any ocean MPA >20 km2.Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article. More