McCauley, D. J., Pinsky, M. L., Palumbi, S. R., Estes, J. A. & Warner, R. R. Marine defaunation: Animal loss in the global ocean. Science 347(6219), 1255641 (2015).
Google Scholar
Webb, T. J. & Mindel, B. L. Global patterns of extinction risk in marine and non-marine systems. Curr. Biol. 25(4), 506–511 (2015).
Google Scholar
Pinsky, M. L. & Fredston, A. A stark future for ocean life. Science 376(6592), 452–453 (2022).
Google Scholar
Bell, J. J., Bennett, H. M., Rovellini, A. & Webster, N. S. Sponges to be winners under near-future climate scenarios. Bioscience 68(12), 955–968 (2018).
Google Scholar
Dulvy, N. K. et al. Overfishing drives over one-third of all sharks and rays toward a global extinction crisis. Curr. Biol. 31(21), 4773-4787.e8 (2021).
Google Scholar
Penn, J. L. & Deutsch, C. Avoiding ocean mass extinction from climate warming. Science 376(6592), 524–526 (2022).
Google Scholar
Hubbard, D. M., Dugan, J. E., Schooler, N. K. & Viola, S. M. Local extirpations and regional declines of endemic upper beach invertebrates in southern California. Estuar. Coast. Shelf Sci. 150(Part A), 67–75 (2014).
Google Scholar
Poquita-Du, R. C. et al. Last species standing: loss of Pocilloporidae corals associated with coastal urbanization in a tropical city state. Mar. Biodivers. 49, 1727–1741 (2019).
Google Scholar
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).
Google Scholar
Bellwood, D. R. et al. Coral reef conservation in the Anthropocene: Confronting spatial mismatches and prioritizing functions. Biol. Conserv. 236, 604–615 (2019).
Google Scholar
Bell, et al. Global conservation status of sponges. Conserv. Biol. 29(1), 42–53 (2015).
Google Scholar
Kelmo, F., Bell, J. J. & Attrill, M. J. Tolerance of sponge assemblages to temperature anomalies: Resilience and proliferation of sponges following the 1997–8 El-Niño southern oscillation. PLoS ONE 8(10), e76441 (2013).
Google Scholar
Micaroni, V. et al. Adaptive strategies of sponges to deoxygenated oceans. Glob. Change Biol. 28(6), 1972–1989 (2022).
Google Scholar
Di Camillo, C. G., Bartolucci, I., Cerrano, C. & Bavestrello, G. Sponge disease in the Adriatic Sea. Mar. Ecol. 34(1), 62–71 (2013).
Google Scholar
Pérez, T. & Vacelet, J. Effect of climatic and anthropogenic disturbances on sponge fisheries. In The Mediterranean Sea (eds Goffredo, S. & Dubinsky, Z.) 577–587 (Springer, 2014).
Google Scholar
Ereskovsky, A., Ozerov, D. A., Pantyulin, A. N. & Tzetlin, A. B. Mass mortality event of White Sea sponges as the result of high temperature in summer 2018. Polar Biol. 42, 2313–2318 (2019).
Google Scholar
Lesser, M. P. & Slattery, M. Will coral reef sponges be winners in the Anthropocene?. Glob. Change Biol. 26(6), 3202–3211 (2020).
Google Scholar
Stevenson, A. et al. Warming and acidification threaten glass sponge Aphrocallistes vastus pumping and reef formation. Sci. Rep. 10, 8176 (2020).
Google Scholar
Beepat, S. S., Davy, S. K., Woods, L. & Bell, J. J. Short-term responses of tropical lagoon sponges to elevated temperature and nitrate. Mar. Environ. Res. 157, 104922 (2020).
Google Scholar
Shore, A. et al. On a reef far, far away: Anthropogenic impacts following extreme storms affect sponge health and bacterial communities. Front. Mar. Sci. 8, 608036 (2021).
Google Scholar
de Voogd et al. World Porifera Database https://www.marinespecies.org/porifera/ (2022).
Wulff, J. L. Assessing and monitoring coral reef sponges: Why and how?. Bull. Mar. Sci. 69(2), 831–846 (2001).
Google Scholar
Bell, J. J. The functional roles of marine sponges. Estuar. Coast. Shelf Sci. 79(3), 341–353 (2008).
Google Scholar
Folkers, M. & Rombouts, T. Sponges revealed: a synthesis of their overlooked ecological functions within aquatic ecosystems. In YOUMARES 9—The Oceans: Our Research, Our Future (eds Jungblut, S. et al.) 181–194 (Springer, 2019).
Pawlik, J. R. & McMurray, S. E. The emerging ecological and biogeochemical importance of sponges on coral reefs. Ann. Rev. Mar. Sci. 12, 315–337 (2020).
Google Scholar
Sawangwong, P. et al. Secondary metabolites from a marine sponge Cliona patera. Biochem. Syst. Ecol. 36(5), 493–496 (2008).
Google Scholar
Zhang, H. et al. Bioactive secondary metabolites from the marine sponge genus Agelas. Mar. Drugs 15(11), 351 (2017).
Google Scholar
He, Q., Miao, S., Ni, N., Man, Y. & Gong, K. A review of the secondary metabolites from the marine sponges of the genus Aaptos. Nat. Prod. Commun. 15(9), 1–12 (2020).
Google Scholar
Ho, et al. Assessing the diversity and biomedical potential of microbes associated with the Neptune’s Cup sponge, Cliona patera. Front. Microbiol. 12, 631445 (2021).
Google Scholar
Pronzato, R. Mediterranean sponge fauna: A biological, historical and cultural heritage. Biogeographia 24(1), 91–99 (2003).
DiBattista, J. D. et al. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci. Rep. 10, 8365 (2020).
Google Scholar
Halpern, B. S. et al. A global map of human impact on marine ecosystems. Science 319(5865), 948–952 (2008).
Google Scholar
Vosmaer, G. C. J. Poterion a boring sponge. K. Ned. Akad. Wet. Proc. 11, 37–41 (1908).
Lim, S. C., Tun, K. & Goh, E. Rediscovery of the Neptune’s Cup sponge in Singapore: Cliona or Poterion? Contributions to Marine Science 2012, 49–56 (2012).
Low, M. E. Y. The date of publication of Cliona patera (Hardwicke), the ‘sponge plant from the shores of Singapore’ (Porifera: Hadromerida: Clionaidae). Nat. Singap. 5, 223–227 (2012).
Knight, K. Super-rare giant sponge discovered in seahorse hotspot. Fauna & Floral International https://www.fauna-flora.org/news/super-rare-sponge-discovered-seahorse-hotspot/ (2018).
The State of Queensland (Queensland Museum). Cliona patera. Queensland Museum Network https://collections.qm.qld.gov.au/objects/73638/cliona-patera (2012–2022).
Heath, D. J. Simultaneous hermaphroditism; Cost and benefit. J. Theor. Biol. 64, 363–373 (1977).
Google Scholar
André, C. & Lindegarth, M. Fertilization efficiency and gamete viability of a sessile, free-spawning bivalve, Cerastoderma edule. Ophelia 43(3), 215–227 (1995).
Google Scholar
Bayer, S. R. et al. Fertilization success in scallop aggregations: Reconciling model predictions and field measurements of density effects. Ecosphere 9(8), e02359 (2018).
Google Scholar
Yund, P. O. How severe is sperm limitation in natural populations of marine free-spawners?. Trends Ecol. Evol. 15(1), 10–13 (2000).
Google Scholar
Frankham, R. Relationship of genetic variation to population size in wildlife. Conserv. Biol. 10(6), 1500–1508 (1996).
Google Scholar
Lim, S. C. Porifera. Singapore Red Data Book. https://www.nparks.gov.sg/biodiversity/wildlife-in-singapore/species-list/sponge (2022).
Quek, Z. B. R., Chang, J. J. M., Ip, Y. C. A., Chan, Y. K. S. & Huang, D. Mitogenomes reveal alternative initiation codons and lineage-specific gene order conservation in echinoderms. Mol. Biol. Evol. 38(3), 981–985 (2021).
Google Scholar
Wörheide, G., Nichols, S. A. & Goldberg, J. Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): Implications for phylogenetic studies. Mol. Phylogenet. Evol. 33(3), 816–830 (2004).
Google Scholar
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17), i884–i890 (2018).
Google Scholar
Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477 (2012).
Google Scholar
Hahn, C., Bachmann, L. & Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads: A baiting and iterative mapping approach. Nucleic Acids Res. 41(13), e129 (2013).
Google Scholar
Donath, A. et al. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res. 47(20), 10543–10552 (2019).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30(4), 772–780 (2013).
Google Scholar
Darriba, D. et al. ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37(1), 291–294 (2020).
Google Scholar
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35(21), 4453–4455 (2019).
Google Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35(6), 1547–1549 (2018).
Google Scholar
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9(7), 671–675 (2012).
Google Scholar
Xavier, J. R. et al. Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae). Mol. Phylogenet. Evol. 56(1), 13–20 (2010).
Google Scholar
de Paula, T. S., Zilberberg, C., Hajdu, E. & Lôbo-Hajdua, G. Morphology and molecules on opposite sides of the diversity gradient: Four cryptic species of the Cliona celata (Porifera, Demospongiae) complex in South America revealed by mitochondrial and nuclear markers. Mol. Phylogenet. Evol. 62(1), 529–541 (2012).
Google Scholar
Plese, B. et al. Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Mol Phylogenet Evol 155, 107011 (2021).
Google Scholar
Lavrov, D. V., Adamski, M., Chevaldonné, P. & Adamska, M. Extensive mitochondrial mRNA editing and unusual mitochondrial genome organization in calcaronean sponges. Curr. Biol. 26(1), 86–92 (2016).
Google Scholar
Lavrov, D. V. & Pett, W. Animal mitochondrial DNA as we do not know it: mt-genome organization and evolution in nonbilaterian lineages. Genome Biol. Evol. 8(9), 2896–2913 (2016).
Google Scholar
Haen, K. M., Pett, W. & Lavrov, D. V. Eight new mtDNA sequences of glass sponges reveal an extensive usage of + 1 frameshifting in mitochondrial translation. Gene 535(2), 336–344 (2014).
Google Scholar
Shearer, T. L., van Oppen, M. J. H., Romano, S. L. & Wörheide, G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11(12), 2475–2487 (2002).
Google Scholar
Lavrov, D. V., Forget, L., Kelly, M. & Lang, B. F. Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution. Mol. Biol. Evol. 22(5), 1231–1239 (2005).
Google Scholar
Huang, D., Meier, R., Todd, P. A. & Chou, L. M. Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J. Mol. Evol. 66(2), 167–174 (2008).
Google Scholar
Wörheide, G. Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific. Mar. Biol. 148, 907–912 (2006).
Google Scholar
León-Pech, M. G., Cruz-Barraza, J. A., Carballo, J. L., Calderon-Aguilera, L. E. & Rocha-Olivares, A. Pervasive genetic structure at different geographic scales in the coral-excavating sponge Cliona vermifera (Hancock, 1867) in the Mexican Pacific. Coral Reefs 34, 887–897 (2015).
Google Scholar
Yang, Q., Franco, C. M. M., Sorokin, S. J. & Zhang, W. Development of a multilocus-based approach for sponge (phylum Porifera) identification: Refinement and limitations. Sci. Rep. 7, 41422 (2017).
Google Scholar
Wörheide, G., Epp, L. S. & Macis, L. Deep genetic divergences among Indo-Pacific populations of the coral reef sponge Leucetta chagosensis (Leucettidae): Founder effects, vicariance, or both?. BMC Evol. Biol. 8, 24 (2008).
Google Scholar
Lai, S., Loke, L. H. L., Hilton, M. J., Bouma, T. J. & Todd, P. A. The effects of urbanisation on coastal habitats and the potential for ecological engineering: A Singapore case study. Ocean Coast. Manag. 103, 78–85 (2015).
Google Scholar
Kuempel, C. D. et al. Identifying management opportunities to combat climate, land, and marine threats across less climate exposed coral reefs. Conserv. Biol. 36(3), e13856 (2022).
Google Scholar
Neo, M. L. et al. Giant clams (Bivalvia: Cardiidae: Tridacninae): A comprehensive update of species and their distribution, current threats and conservation status. In Oceanography and Marine Biology: An Annual Review Vol. 55 (eds Hawkins, S. J. et al.) 87–388 (CRC Press, 2017).
Google Scholar
Orlando, L. et al. Ancient DNA analysis. Nat. Rev. Methods Prim. 1, 14 (2021).
Google Scholar
Cárdenas, P. & Moore, J. A. First records of Geodia demosponges from the New England seamounts, an opportunity to test the use of DNA mini-barcodes on museum specimens. Mar. Biodiv. 49, 163–174 (2019).
Google Scholar
Erpenbeck, D. et al. Minimalist barcodes for sponges: A case study classifying African freshwater Spongillida. Genome 62(1), 1–10 (2019).
Google Scholar
Chang, D. & Shapiro, B. Using ancient DNA and coalescent-based methods to infer extinction. Biol. Lett. 12(2), 20150822 (2016).
Google Scholar
Pacioni, C. et al. Genetic diversity loss in a biodiversity hotspot: Ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Mol. Ecol. 24(23), 5813–5828 (2015).
Google Scholar
Lombal, A. J. et al. Using ancient DNA to quantify losses of genetic and species diversity in seabirds: A case study of Pterodroma petrels from a Pacific island. Biodivers. Conserv. 29, 2361–2375 (2020).
Google Scholar
Ruzicka, R. & Gleason, D. F. Sponge community structure and anti-predator defenses on temperate reefs of the South Atlantic Bight. J. Exp. Mar. Biol. Ecol. 380(1–2), 36–46 (2009).
Google Scholar
Loh, T. L. & Pawlik, J. R. Chemical defenses and resource trade-offs structure sponge communities on Caribbean coral reefs. Proc. Natl. Acad. Sci. U.S.A. 111(11), 4151–4156 (2014).
Google Scholar
Wulff, J. L. Targeted predator defenses of sponges shape community organization and tropical marine ecosystem function. Ecol. Monogr. 91(2), e01438 (2021).
Google Scholar
Coppock, A. G., Kingsford, M. J., Battershill, C. N. & Jones, G. P. Significance of fish–sponge interactions in coral reef ecosystems. Coral Reefs 41, 1285–1308 (2022).
Google Scholar
Baumbach, D. S., Zhang, R., Hayes, C. T., Wright, M. K. & Dunbar, S. G. Strategic foraging: Understanding hawksbill (Eretmochelys imbricata) prey item energy values and distribution within a marine protected area. Mar. Ecol. 00, e12703 (2022).
Google Scholar
Guida, V. G. Sponge predation in the oyster reef community as demonstrated with Cliona celata Grant. J. Exp. Mar. Biol. Ecol. 25(2), 109–122 (1976).
Google Scholar
Verdín, P. C. J., Carballo, J. L. & Camacho, M. L. A qualitative assessment of sponge-feeding organisms from the Mexican Pacific coast. Open Mar. Biol. J. 4, 39–46 (2010).
Google Scholar
Márquez, J. C. & Zea, S. Parrotfish mediation in coral mortality and bioerosion by the encrusting, excavating sponge Cliona tenuis. Mar. Ecol. 33(4), 417–426 (2012).
Google Scholar
González-Rivero, M., Ferrari, R., Schönberg, C. H. L. & Mumby, P. J. Impacts of macroalgal competition and parrotfish predation on the growth of a common bioeroding sponge. Mar. Ecol. Prog. Ser. 444, 133–142 (2012).
Google Scholar
von Brandis, R. G., Mortimer, J. A., Reilly, B. K., van Soest, R. W. M. & Branch, G. M. Diet composition of hawksbill turtles (Eretmochelys imbricata) in the Republic of Seychelles. Western Indian Ocean J. Mar. Sci. 13(1), 81–91 (2014).
Mortimer, C., Dunn, M., Haris, A., Jompa, J. & Bell, J. Estimates of sponge consumption rates on an Indo-Pacific reef. Mar. Ecol. Prog. Ser. 672, 123–140 (2021).
Google Scholar
Hoppe, W. F. Growth, regeneration and predation in three species of large coral reef sponges. Mar. Ecol. Prog. Ser. 50(12), 117–125 (1988).
Google Scholar
Bell, J. J. Regeneration rates of a sublittoral demosponge. J. Mar. Biol. Assoc. U.K. 82(1), 169–170 (2002).
Google Scholar
Wu, Y.-C. et al. Opisthobranch grazing results in mobilisation of spherulous cells and re-allocation of secondary metabolites in the sponge Aplysina aerophoba. Sci. Rep. 10, 21934 (2020).
Google Scholar
Wu, Y.-C., Franzenburg, S., Ribes, M. & Pita, L. Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. Sci. Rep. 12, 1307 (2022).
Google Scholar
González-Rivero, M. et al. Life-history traits of a common Caribbean coral-excavating sponge, Cliona tenuis (Porifera: Hadromerida). J. Nat. Hist. 47(45–46), 1–20 (2013).
Chaves-Fonnegra, A., Maldonado, M., Blackwelder, P. & Lopez, J. V. Asynchronous reproduction and multi-spawning in the coral-excavating sponge Cliona delitrix. J. Mar. Biol. Assoc. U.K. 96(2), 515–528 (2015).
Google Scholar
Bautista-Guerrero, E., Carballo, J. L. & Maldonado, M. Abundance and reproductive patterns of the excavating sponge Cliona vermifera: A threat to Pacific coral reefs?. Coral Reefs 33, 259–266 (2014).
Google Scholar
Piscitelli, M., Corriero, G., Gaino, E. & Uriz, M.-J. Reproductive cycles of the sympatric excavating sponges Cliona celata and Cliona viridis in the Mediterranean Sea. Invertebr. Biol. 130(1), 1–10 (2011).
Google Scholar
Chaves-Fonnegra, A., Feldheim, K. A., Secord, J. & Lopez, J. V. Population structure and dispersal of the coral-excavating sponge Cliona delitrix. Mol. Ecol. 24(7), 1447–1466 (2015).
Google Scholar
Zilberberg, C., Maldonado, M. & Solé-Cava, A. Assessment of the relative contribution of asexual propagation in a population of the coral-excavating sponge Cliona delitrix from the Bahamas. Coral Reefs 25, 297–301 (2006).
Google Scholar
Wulff, J. L. Effects of a hurricane on survival and orientation of large erect coral reef sponges. Coral Reefs 14, 55–61 (1995).
Google Scholar
Wilkinson, C. R. & Thompson, J. E. Experimental sponge transplantation provides information on reproduction by fragmentation. Proc. 8th Int. Coral Reef Symp. 2, 1417–1420 (1997).
Google Scholar
da Silva, R. et al. Assessing the conservation potential of fish and corals in aquariums globally. J. Nat. Conserv. 48, 1–11 (2019).
Google Scholar
Neumann, A. C. Observations on coastal erosion in Bermuda and measurements of the boring rate of the sponge, Cliona lampa. Limnol. Oceanogr. 11(1), 92–108 (1966).
Google Scholar
Rosell, D. & Uriz, M. J. Do associated zooxanthellae and the nature of the substratum affect survival, attachment and growth of Cliona viridis (Porifera: Hadromerida)? An experimental approach. Mar. Biol. 114, 503–507 (1992).
Google Scholar
Ramsby, B. D., Hoogenboom, M. O., Smith, H. A., Whalan, S. & Webster, N. S. The bioeroding sponge Cliona orientalis will not tolerate future projected ocean warming. Sci. Rep. 8, 8302 (2018).
Google Scholar
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