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".

Only publications relevant to mesophotic reefs are indexed.

Differential strategies developed by two light-dependent scleractinian corals to extend their vertical range to mesop...

Pérez-Rosales G, Rouzé H, Pichon M, Bongaerts P, Bregere N, Carlot J, Parravicini V, Hedouin L, Under The Pole Consortium (2024)

Coral Reefs

Article DOI

Different times, similar mechanism? Convergent patterns in light-induced phenotypic plasticity in Devonian and modern...

Majchrzyk A, Jakubowicz M, Bongaerts P, Zapalski MK (2023)

Coral Reefs

Article DOI

Hidden in the deep: Distinct benthic trajectories call for monitoring of mesophotic reefs

Hernandez‐Agreda A, Sahit FM, Englebert N, Hoegh‐Guldberg O, Bongaerts P (2022)

Conserv. Lett.

Article DOI

Mesophotic Coral Ecosystems

Bongaerts P (2022)

Review DOI

Deep connections: Divergence histories with gene flow in mesophotic Agaricia corals

Prata KE, Riginos C, Gutenkunst RN, Latijnhouwers KR, Sánchez JA, Englebert N, Hay KB, Bongaerts P (2022)

Mol Ecol

Article DOI

In the shadow of a giant reef: Palaeoecology of mesophotic coral communities from the Givetian of Anti-Atlas (Morocco)

Majchrzyk A, Jakubowicz M, Berkowski B, Bongaerts P, Zapalski MK (2022)

Palaeogeogr Palaeoclimatol Palaeoecol

Article DOI

Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian as...

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

Article DOI

Mesophotic depths hide high coral cover communities in French Polynesia

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

Article DOI

Mesophotic coral ecosystems of the Great Barrier Reef are understudied and underexplored

Eyal G, Laverick JH, Bongaerts P, Levy O, Pandolfi JM (2021)

Front Mar Sci

Article Open Access DOI

Morphological stasis masks ecologically divergent coral species on tropical reefs

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

Article DOI

Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs

Bongaerts P, Dubé C, Prata KE, Gijsbers JC, Achlatis M, Hernandez-Agreda A (2021)

Front Mar Sci

Article Open Access DOI

Mesophotic coral communities escape thermal coral bleaching in French Polynesia

Pérez-Rosales G, Rouzé H, Torda G, Bongaerts P, Pichon M, Under The Pole Consortium, Parravicini V, Hédouin L (2021)

R Soc Open Sci

Article Open Access DOI

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)

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

Article DOI

The Great Barrier Reef outer-shelf

Bridge TCL, Webster JM, Sih TL, Bongaerts P (2019)

Chapter

Mesophotic.org: a repository for scientific information on mesophotic ecosystems

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)

Article DOI

Key questions for research and conservation of mesophotic coral ecosystems and temperate mesophotic ecosystems

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)

Chapter

Beyond the “Deep Reef Refuge” Hypothesis: A Conceptual Framework to Characterize Persistence at Depth

Bongaerts P, Smith TB (2019)

Chapter

The Great Barrier Reef and Coral Sea

Bridge TCL, Beaman RJ, Bongaerts P, Muir PR, Ekins M, Sih T (2019)

Chapter

Bonaire and Curaçao

Frade PR, Bongaerts P, Baldwin CC, Trembanis AC, Bak RPM, Vermeij MJA (2019)

Chapter

Deep reefs of the Great Barrier Reef offer limited thermal refuge during mass coral bleaching

Frade PR, Bongaerts P, Englebert N, Rogers A, Gonzalez-Rivero M, Hoegh-Guldberg O (2018)

Nature communications

Article DOI

High species richness and lineage diversity of reef corals in the mesophotic zone

Muir PR, Wallace CC, Pichon, Bongaerts P (2018)

Proc R Soc B

Article DOI

Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere

Hernandez-Agreda A, Leggat W, Bongaerts P, Herrera C, Ainsworth TD (2018)

mBio

Article Open Access DOI

To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic ...

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

Review Open Access DOI

Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs

Rocha LA, Pinheiro HT, Shepherd B, Papastamatiou YP, Luiz OJ, Pyle RL, Bongaerts P (2018)

Science

Article DOI

Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone

Gonzalez-Zapata FL, Gonzalez-Zapata FL, Bongaerts P, Ramírez-Portilla C, Adu-Oppong B, Walljasper G, Reyes A, Sanchez JA (2018)

Front Mar Sci

Article Open Access DOI

High coral cover at lower mesophotic depths: a dense Agaricia community at the leeward side of Curaçao, Dutch Caribbean

Hoeksema BW, Bongaerts P, Baldwin CC (2017)

Marine Biodiversity

Article DOI

Seriatopora diversity preserved in upper Mesophotic Coral Ecosystems in Southern Japan

Sinniger F, Prasetia R, Yorifuji M, Bongaerts P, Harii S (2017)

Front Mar Sci

Article Open Access DOI

Deep reefs are not universal refuges: Reseeding potential varies among coral species

Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2017)

Science Advances

Article Open Access DOI

Lower mesophotic coral communities (60-125 m depth) of the Northern Great Barrier Reef and Coral Sea

Englebert N, Bongaerts P, Muir PR, Hay KB, Pichon M, Hoegh-Guldberg O (2017)

PLoS ONE

Article Open Access DOI

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m)

Glasl B, Bongaerts P, Elisabeth NH, Hoegh-Guldberg O, Herndl GJ, Frade PR (2017)

Coral Reefs

Article DOI

To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest?

Laverick JH, Andradi-Brown DA, Exton DA, Bongaerts P, Bridge TCL, Lesser MP, Pyle RL, Slattery M, Wagner D, Rogers AD (2016)

Environ Evid

Review Open Access DOI

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats

Hernandez-Agreda A, Leggat W, Bongaerts P, Ainsworth TD (2016)

mBio

Article Open Access DOI

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community

Bongaerts P, Frade PR, Hay KB, Englebert N, Latijnhouwers KRW, Bak RPM, Vermeij MJA, Hoegh-Guldberg O (2015)

Sci Rep

Article Open Access DOI

Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species

Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015)

R Soc Open Sci

Article Open Access DOI

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

Pantos O, Bongaerts P, Dennis PG, Tyson GW, Hoegh-Guldberg O (2015)

ISME J

Article DOI

Diverse Staghorn Coral Fauna on the Mesophotic Reefs of North-East Australia

Muir P, Wallace C, Bridge TCL, Bongaerts P (2015)

PLoS ONE

Article Open Access DOI

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

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

Article DOI

Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea

Englebert N, Bongaerts P, Muir P, Hay KB, Hoegh-Guldberg O (2014)

Marine Biodiversity

Article DOI

Call to protect all coral reefs

Bridge TC, Hughes TP, Guinotte JM, Bongaerts P (2013)

Nat Clim Chang

Article DOI

Cyclone damage at mesophotic depths on Myrmidon Reef (GBR)

Bongaerts P, Muir P, Englebert N, Bridge TCL, Hoegh-Guldberg O (2013)

Coral Reefs

Article DOI

Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic h...

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

Article Open Access DOI

Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia

Bridge TCL, Fabricius KE, Bongaerts P, Wallace CC, Muir PR, Done TJ, Webster JM (2012)

Coral Reefs

Article DOI

The first record of Hippocampus denise (Syngnathidae) from Australia

Foster R, Bridge TCL, Bongaerts P (2012)

Aqua Int J Ichthyol

Article

The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west...

van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF (2011)

Mol Ecol

Article DOI

Symbiodinium diversity in mesophotic coral communities on the Great Barrier Reef: a first assessment

Bongaerts P, Sampayo EM, Bridge TCL, Ridgway T, Vermeulen F, Englebert N, Webster JM, Hoegh-Guldberg O (2011)

Mar Ecol Prog Ser

Article DOI

Mesophotic coral ecosystems on the walls of Coral Sea atolls

Bongaerts P, Bridge TCL, Kline DI, Muir PR, Wallace CC, Beaman RJ, Hoegh-Guldberg O (2011)

Coral Reefs

Article DOI

Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep ree...

Bongaerts P, Riginos C, Hay KB, van Oppen MJH, Hoegh-Guldberg O, Dove S (2011)

BMC Evol Biol

Article Open Access DOI

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O (2010)

PLoS ONE

Article Open Access DOI

Assessing the 'deep reef refugia' hypothesis: focus on Caribbean reefs

Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010)

Coral Reefs

Review DOI

In situ photobiology of corals over large depth ranges: A multivariate analysis on the roles of environment, host, an...

Frade PR, Bongaerts P, Winkelhagen AJS, Tonk L, Bak RPM (2008)

Limnol Oceanogr

Article DOI