Pim is the McCosker Chair of Aquatic Biology and Curator of Invertebrate Zoology at the California Academy of Sciences in San Francisco. He is also an Associate Editor for the journal "Molecular Ecology". He studies the biodiversity and evolution of tropical reef corals, from close to the surface to well into the twilight zone. As a molecular ecologist, he combines genomics and field ecology to understand how corals diversify and adapt to different and changing environmental conditions. Prior to his appointment at the Academy, he was an ARC DECRA Research Fellow at the Global Change Institute (The University of Queensland), and lead scientist for the Deep Reef component of the "XL Catlin Seaview Survey".

  Please note that only publications relevant to mesophotic reefs are indexed.

	Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea | article Englebert N, Bongaerts P, Muir P, Hay KB, Hoegh-Guldberg O (2014) Marine Biodiversity 45:1-2
	The first record of Hippocampus denise (Syngnathidae) from Australia | article Foster R, Bridge TCL, Bongaerts P (2012) Aqua Int J Ichthyol 18:55-57
	Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbea... | article Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJA, Bak RPM, Visser PM, Hoegh-Guldberg O (2013) BMC Evol Biol
	Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats | article Bongaerts P, Riginos C, Hay KB, van Oppen MJH, Hoegh-Guldberg O, Dove S (2011) BMC Evol Biol
	Cyclone damage at mesophotic depths on Myrmidon Reef (GBR) | article Bongaerts P, Muir P, Englebert N, Bridge TCL, Hoegh-Guldberg O (2013) Coral Reefs 32:935
	Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia | article Bridge TCL, Fabricius KE, Bongaerts P, Wallace CC, Muir PR, Done TJ, Webster JM (2012) Coral Reefs 31:179-189
	Assessing the 'deep reef refugia' hypothesis: focus on Caribbean reefs | review Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010) Coral Reefs 29:309-327
	Mesophotic coral ecosystems on the walls of Coral Sea atolls | article Bongaerts P, Bridge TCL, Kline DI, Muir PR, Wallace CC, Beaman RJ, Hoegh-Guldberg O (2011) Coral Reefs 30:335
	In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, and algal symbiont | article Frade PR, Bongaerts P, Winkelhagen AJS, Tonk L, Bak RPM (2008) Limnol Oceanogr 53:2711-2723
	Symbiodinium diversity in mesophotic coral communities on the Great Barrier Reef: a first assessment | article Bongaerts P, Sampayo EM, Bridge TCL, Ridgway T, Vermeulen F, Englebert N, Webster JM, Hoegh-Guldberg O (2011) Mar Ecol Prog Ser 439:117-126
	The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia | article van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF (2011) Mol Ecol 20:1647-1660
	Call to protect all coral reefs | article Bridge TC, Hughes TP, Guinotte JM, Bongaerts P (2013) Nat Clim Chang 3:528-530
	Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium | article Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O (2010) PLoS ONE 5:e10871
	The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts | article Ainsworth TD, Krause L, Bridge T, Torda G, Raina J-B, Zakrzewski M, Gates RD, Padilla-Gamiño JL, Spalding HL, Smith C, Woolsey ES, Bourne DG, Bongaerts P, Hoegh-Guldberg O, Leggat W (2015) ISME J 9:2261-2274
	Diverse Staghorn Coral Fauna on the Mesophotic Reefs of North-East Australia | article Muir P, Wallace C, Bridge TCL, Bongaerts P (2015) PLoS ONE 10:e0117933
	Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix | article Pantos O, Bongaerts P, Dennis PG, Tyson GW, Hoegh-Guldberg O (2015) ISME J 9:1916-1927
	Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species | article Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015) R Soc Open Sci 2:140297
	Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community | article Bongaerts P, Frade PR, Hay KB, Englebert N, Latijnhouwers KRW, Bak RPM, Vermeij MJA, Hoegh-Guldberg O (2015) Sci Rep 5:7652
	The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats | article Hernandez-Agreda A, Leggat W, Bongaerts P, Ainsworth TD (2016) mBio 7:e00560-16
	To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? | review Laverick JH, Andradi-Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slattery M, Wagner D, Rogers AD (2016) Environ Evid 5:1-8
	Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) | article Glasl B, Bongaerts P, Elisabeth NH, Hoegh-Guldberg O, Herndl GJ, Frade PR (2017) Coral Reefs 36:447–452
	Lower mesophotic coral communities (60-125 m depth) of the Northern Great Barrier Reef and Coral Sea | article Englebert N, Bongaerts P, Muir PR, Hay KB, Pichon M, Hoegh-Guldberg O (2017) PLoS ONE 12:e0170336
	Deep reefs are not universal refuges: Reseeding potential varies among coral species | article Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2017) Science Advances 3:e1602373
	Seriatopora diversity preserved in upper Mesophotic Coral Ecosystems in Southern Japan | article Sinniger F, Prasetia R, Yorifuji M, Bongaerts P, Harii S (2017) Front Mar Sci 4:155
	High coral cover at lower mesophotic depths: a dense Agaricia community at the leeward side of Curaçao, Dutch Caribbean | article Hoeksema BW, Bongaerts P, Baldwin CC (2017) Marine Biodiversity 47:67-70
	Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone | article Gonzalez-Zapata FL, Gonzalez-Zapata FL, Bongaerts P, Ramírez-Portilla C, Adu-Oppong B, Walljasper G, Reyes A, Sanchez JA (2018) Front Mar Sci
	Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs | article Rocha LA, Pinheiro HT, Shepherd B, Papastamatiou YP, Luiz OJ, Pyle RL, Bongaerts P (2018) Science
	To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic review | review Laverick JH, Piango S, Andradi‑Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slattery M, Wagner D, Rogers AD (2018) Environ Evid
	Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere | article Hernandez-Agreda A, Leggat W, Bongaerts P, Herrera C, Ainsworth TD (2018) mBio 9:e00812-18
	High species richness and lineage diversity of reef corals in the mesophotic zone | article Muir PR, Wallace CC, Pichon, Bongaerts P (2018) Proc R Soc B
	Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching | article Frade PR, Bongaerts P, Englebert N, Rogers A, Gonzalez-Rivero M, Hoegh-Guldberg O (2018) Nature communications 9:3447
	Bonaire and Curaçao | chapter Frade PR, Bongaerts P, Baldwin CC, Trembanis AC, Bak RPM, Vermeij MJA (2019) in: Mesophotic Coral Ecosystems () by Loya Y, Puglise KA, Bridge TCL
	The Great Barrier Reef and Coral Sea | chapter Bridge TCL, Beaman RJ, Bongaerts P, Muir PR, Ekins M, Sih T (2019) in: Mesophotic Coral Ecosystems, Coral Reefs of the World () by Loya Y, Puglise KA, Bridge TCL
	Beyond the “Deep Reef Refuge” Hypothesis: A Conceptual Framework to Characterize Persistence at Depth | chapter Bongaerts P, Smith TB (2019) in: Mesophotic Coral Ecosystems (Springer Nature Switzerland AG 2019) by Yossi L, Puglise KA, Bridge T
	Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) | article Rouzé H, Galand PE, Medina M, Bongaerts P, Pichon M, Pérez-Rosales G, Torda G, Moya A, Under The Pole Consortium, Raina J-B, Hédouin L (2021) ISME J
	Mesophotic coral communities escape thermal coral bleaching in French Polynesia | article Pérez-Rosales G, Rouzé H, Torda G, Bongaerts P, Pichon M, Under The Pole Consortium, Parravicini V, Hédouin L (2021) R Soc Open Sci 8:210139
	Mesophotic depths hide high coral cover communities in French Polynesia | article Pérez-Rosales G, Hernández-Agreda A, Bongaerts P, Rouzé H, Pichon M, Carlot J, Torda G, Under The Pole Consortium, Parravicini V, Hédouin L (2022) Science of The Total Environment
	Key questions for research and conservation of mesophotic coral ecosystems and temperate mesophotic ecosystems | chapter Turner JA, Andradi-Brown DA, Gori A, Bongaerts P, Burdett HL, Ferrier-Pagès C, Voolstra CR, Weinstein DK, Bridge TCL, Costantini F, Gress E, Laverick J, Loya Y, Goodbody-Gringley G, Rossi S, Taylor ML, Viladrich N, Voss JD, Williams J, Woodall LC, Eyal G (2019) in: Mesophotic Coral Ecosystems () by Loya Y, Puglise KA, Bridge TCL
	Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages | article Pérez-Rosales G, Pichon M, Rouzé H, Villéger S, Torda G, Bongaerts P, Carlot J, Under The Pole Consortium, Parravicini V, Hédouin L (2022) Diversity and Distributions 28: 1391–1403
	Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs | article Bongaerts P, Dubé C, Prata KE, Gijsbers JC, Achlatis M, Hernandez-Agreda A (2021) Front Mar Sci
	In the shadow of a giant reef: Palaeoecology of mesophotic coral communities from the Givetian of Anti-Atlas (Morocco) | article Majchrzyk A, Jakubowicz M, Berkowski B, Bongaerts P, Zapalski MK (2022) Palaeogeogr Palaeoclimatol Palaeoecol 602:111177
	Deep connections: Divergence histories with gene flow in mesophotic Agaricia corals | article Prata KE, Riginos C, Gutenkunst RN, Latijnhouwers KR, Sánchez JA, Englebert N, Hay KB, Bongaerts P (2022) Mol Ecol 31:2511-27
	Mesophotic Coral Ecosystems | review Bongaerts P (2022)
	Morphological stasis masks ecologically divergent coral species on tropical reefs | article Bongaerts P, Cooke IR, Ying H, Wels D, den Haan S, Hernandez-Agreda A, Brunner CA, Dove S, Englebert N, Eyal G, Forêt S, Grinblat M, Hay KB, Harii S, Hayward DC, Lin Y, Mihaljević M, Moya A, Muir P, Sinniger F, Smallhorn-West P, Torda G, Ragan MA, Van Oppen MJH, Hoegh-Guldberg O (2021) Curr Biol 31:2286-2298.e8
	Mesophotic.org: a repository for scientific information on mesophotic ecosystems | article Bongaerts P, Perez-Rosales G, Radice VZ, Eyal G, Gori A, Gress E, Hammerman NM, Hernandez-Agreda A, Laverick J, Muir P, Pinheiro H, Pyle RL, Rocha L, Turner JA, Booker R (2019) Database (Oxford)
	The Great Barrier Reef outer-shelf | chapter Bridge TCL, Webster JM, Sih TL, Bongaerts P (2019) in: The Great Barrier Reef () by Hutchings P, Kingsford M, Hoegh-Guldberg O
	Mesophotic coral ecosystems of the Great Barrier Reef are understudied and underexplored | article Eyal G, Laverick JH, Bongaerts P, Levy O, Pandolfi JM (2021) Front Mar Sci 8:622856
	Different times, similar mechanism? Convergent patterns in light-induced phenotypic plasticity in Devonian and modern corals | article Majchrzyk A, Jakubowicz M, Bongaerts P, Zapalski MK (2023) Coral Reefs 41:893-903
	Hidden in the deep: Distinct benthic trajectories call for monitoring of mesophotic reefs | article Hernandez‐Agreda A, Sahit FM, Englebert N, Hoegh‐Guldberg O, Bongaerts P (2022) Conserv. Lett. 15:e12875
	Differential strategies developed by two light-dependent scleractinian corals to extend their vertical range to mesophotic depths | article Pérez-Rosales G, Rouzé H, Pichon M, Bongaerts P, Bregere N, Carlot J, Parravicini V, Hedouin L, Under The Pole Consortium (2024) Coral Reefs

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