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  Daniel Cleary  
  Phone: +351 234 370700 (ext. 22726)  
  e-mail: send email  
  Category: Principal Researcher  
  Department: Biology  
  Research group: Marine & Estuarine Ecology
ISI Web of KnowledgeSM search factor: AU=(Cleary DFR)  
  Direct URL for this page: http://www.cesam.ua.pt/cleary  
Short history

Principal researcher of Marine and Estuarine Ecology. I studied biology at the University of Amsterdam. During my study I spent half a year in the Caribbean where I studied aggressive interactions among coral species. After this I spent a year in France at the Université de Provence. For my PhD (also in Amsterdam), I spent two and a half years in the jungles of Borneo, mainly studying butterflies but I was also interested in many other organisms in the rainforest and how disturbances such as logging and forest fires affected them. After my PhD, I did postdocs in Amsterdam and Leiden. Author of more than 100 papers in leading international journals in the areas of Ecology, Tropical Biology and Marine Biology. Principal Researcher or team member of national and international research projects on terrestrial and marine ecology. Research advisor of several Msc students, PhD students and Postdocs. Has refereed several leading journals in the fields of ecology, conservation biology, zoology and marine biology. My major interests include corals, sponges, butterflies, odonates, microbial ecology, biostatistics (particularly using R) and relating community structure to spatial, environmental and temporal processes.

Reviewer for International Journals

Acta Oecologica

Biodiversity and Conservation

• Contributions to Zoology

Conservation Biology

Diversity and Distributions


Ecological Entomology


Entomological Science

Estuarine, Coastal and Shelf Science

FEMS Microbiology Ecology

Journal of Applied Ecology

Journal of Biogeography

Journal of Tropical Ecology

Journal of Tropical Forest Science

Landscape Ecology

Marine Ecology Progress Series

Molecular Ecology



Western North American Naturalist

Scientific Supervision
PhD (Co-supervisor): Thomas Swierts
(not a CESAM member)
PhD (Co-supervisor): Diogo Pinho
PhD (Co-supervisor): Esther van der Ent
(not a CESAM member)

Post-doc (Co-supervisor): Francisco Coelho

PhD (Main Supervisor): Ana Rita Moura Polónia
PhD (Co-supervisor): Lisa Becking
(not a CESAM member)
PhD (Co-supervisor): Ana Cecília da Cruz Pires

Master (Main Supervisor): Dille Wielakker
(not a CESAM member)
Master (Main Supervisor): Annemieke Bijlmer
(not a CESAM member)
Master (Main Supervisor): Andreia Gonçalves Sousa
(not a CESAM member)
Master (Main Supervisor): Ana Cecília da Cruz Pires
Master (Main Supervisor): Lisa Becking
(not a CESAM member)
Master (Main Supervisor): Paola Rachello-Dolmen
(not a CESAM member)
Master (Co-supervisor): Pedro Miguel Pinheiro Saraiva
(not a CESAM member)
Master (Co-supervisor): Gomes, Hélder Alexandre Campos
(ex-CESAM member)

AquaHeal: Microbial modulation in aquacultures with recirculation system: towards a production system suppressor of diseases [see details]

EcoTech-SPONGE- Assessing the ecological functions and potential biotechnological applications of plasmid assemblages from microbial symbionts of marine sponges [see details]

eLTER H2020 project - Integrated European Long-Term Ecosystem & Socio-Ecological Research Infrastructure (LTER Ria de Aveiro is one of the Virtual Access (VA) sites in the H2020 project eLTER) [see details]

STEP - Integrated System for Managing Fishfarm Effluents [see details]

LTER-RAVE - Long term monitoring in the Ria de Aveiro: towards a deeper understanding of ecological, environmental and economic processes [see details]

LAGOONS - Integrated water resources and coastal zone management in European lagoons in the context of climate change [see details]

AQUASAFE - Development of new technologies to anticipate and diagnose disease outbreaks in aquaculture [see details]

RASTREMAR - Use of molecular tools in the traceability of marine food products [see details]

LESS CORAL: The impact of human settlLEmentS on CORAL reef ecosystems [see details]

DiverseShores - Testing associations between genetic and community diversity in European rocky shore environments [see details]

DOMINO EFFECT - Degradation of lOtic ecosysteMs assocIated with plaNtation fOrestry: An Evaluation of plantation Forest Food-wEb CommuniTies [see details]

Global climate change and pollution: a synergy designed for disaster? [see details]

  1. Coelho F.J.R.C., Cleary D.F.R., Gomes N.C.M., Polonia A.R.M., Huang Y.M., Liu L.L., de Voogd N.J. (2018) Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems. Microbial Ecology. 75, 1, 239-254. (see details) ISI paper
    Link: https://link.springer.com/article/10.1007/s00248-017-1023-x
  2. Monteiro M., Seneca J., Torgo L., Cleary D.F.R., Gomes N.C.M., Santoro A.E., Magalhaes C. (2018) Environmental controls on estuarine nitrifying communities along a salinity gradient. Aquatic Microbial Ecology. 80, 2, 167-180. (see details) ISI paper
  3. Boaventura C.M., Coelho F.J.R.C., Martins P.T., Pires A.C.C., Duarte L.N., Uetanabaro A.P.T., Cleary D.F.R., Gomes N.C.M. (2018) Micro-eukaryotic plankton diversity in an intensive aquaculture system for production of Scophthalmus maximus and Solea senegalensis. Aquaculture. 490, 321-328. (see details) ISI paper
    Link: https://www.sciencedirect.com/science/article/pii/S0044848617303095
  4. Martins P., Coelho F.J.R.C., Cleary D.F.R., Pires A.C.C., Marques B., Rodrigues A.M., Quintino V., Gomes N.C.M. (2018) Seasonal patterns of bacterioplankton composition in a semi-intensive European seabass (Dicentrarchus labrax) aquaculture system. Aquaculture. 490, 240-250. (see details) ISI paper
    Link: https://www.sciencedirect.com/science/article/pii/S0044848617322020
  5. Cleary D.F.R., Polonia A.R.M. (2018) Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes. Antonie Van Leeuwenhoek International Journal Of General And Molecular Microbiology. 111, 2, 237-257. (see details) ISI paper
  6. Cleary D.F.R., Polonia A.R.M., de Voogd N.J. (2018) Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes. Fems Microbiology Ecology. 94, 2, (see details) ISI paper
  7. Cleary D.F.R., Coelho F.J.R.C., Oliveira V., Gomes N.C.M., Polonia A.R.M. (2017) Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment. Marine Ecology. 38, 2, -e12411. (see details) ISI paper
    Link: http://dx.doi.org/10.1111/maec.12411
  8. Polonia A.R.M., Cleary D.F.R., Freitas R., Gomes N.C.M., de Voogd N.J. (2017) Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment. Journal Of Sea Research. 119, 37-53. (see details) ISI paper
    Link: http://dx.doi.org/10.1016/j.seares.2016.10.007
  9. Sousa A.I., Santos D.B., da Silva E.F., Sousa L.P., Cleary D.F.R., Soares A.M.V.M., Lillebo A.I. (2017) 'Blue Carbon' and Nutrient Stocks of Salt Marshes at a Temperate Coastal Lagoon (Ria de Aveiro, Portugal). Scientific Reports. 7, 41225, (see details) ISI paper
    Link: http://www.nature.com/articles/srep41225
  10. Sousa A.I., Calado R., Cleary D.F.R., Nunes C., Coimbra M.A., Serodio J., Lillebo A.I. (2017) Effect of spatio-temporal shifts in salinity combined with other environmental variables on the ecological processes provided by Zostera noltei meadows. Scientific Reports. 7, (see details) ISI paper
    Link: https://www.nature.com/articles/s41598-017-01359-2
  11. Polonia A.R.M., Cleary D.F.R., Freitas R., Coelho F.J.R.C., de Voogd N.J., Gomes N.C.M. (2016) Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Marine Genomics. 29, 69-80. (see details) ISI paper
    Link: https://doi.org/10.1016/j.margen.2016.04.014
  12. Cleary D.F.R., Becking L.E., Polonia A.R.M., Freitas R.M., Gomes N.C.M. (2016) Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes. Fems Microbiology Ecology. 92, 5, (see details) ISI paper
  13. Coelho F.J.R.C., Cleary D.F.R., Costa R., Ferreira M., Polonia A.R.M., Silva A.M.S., Simoes M.M.Q., Oliveira V., Gomes N.C.M. (2016) Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution. Molecular Ecology. 25, 18, 4645-4659. (see details) ISI paper
    Link: 10.1111/mec.13779
  14. Cleary D.F.R., Polonia A.R.M., Sousa A.I., Lillebo A.I., Queiroga H., Gomes N.C.M. (2016) Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima. Plant Biology. 18, 5, 824-834. (see details) ISI paper
  15. Coelho F.J.R.C., Louvado A., Domingues P.M., Cleary D.F.R., Ferreira M., Almeida A., Cunha M.R., Cunha A., Gomes N.C.M. (2016) Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz. Scientific Reports. 6, 35272, (see details) ISI paper
    Link: https://www.nature.com/articles/srep35272
  16. Cleary, DFR (2016) Diversity and composition of plants, butterflies and odonates in an Imperata cylindrica grassland landscape in East Kalimantan, Indonesia. Journal Of Tropical Ecology. 32, 555-560. (see details) ISI paper
  17. Cleary D.F.R., Polonia A.R.M., Renema W., Hoeksema B.W., Rachello-Dolmen P.G., Moolenbeek R.G., Budiyanto A., Yahmantoro ., Tuti Y., Giyanto ., Draisma S.G.A., van Reine W.F.P., Hariyanto R., Gittenberger A., Rikoh M.S., de Voogd N.J. (2016) Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex. Marine Pollution Bulletin. 110, 2, 701-717. (see details) ISI paper
  18. Huang Y.S.M., de Voogd N.J., Cleary D.F.R., Li T.H., Mok H.K., Ueng J.P. (2016) Biodiversity pattern of subtidal sponges (Porifera: Demospongiae) in the Penghu Archipelago (Pescadores), Taiwan. Journal Of The Marine Biological Association Of The United Kingdom. 96, 2, 417-427. (see details) ISI paper
  19. Cleary D.F.R., Becking L.E., Polonia A.R.M., Freitas R.M., Gomes N.C.M. (2015) Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes. Antonie Van Leeuwenhoek International Journal Of General And Molecular Microbiology. 107, 3, 821-834. (see details) ISI paper
    Link: http://dx.doi.org/10.1007/s10482-014-0375-1
  20. de Voogd N.J., Cleary D.F.R., Polonia A.R.M., Gomes N.C.M. (2015) Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. Fems Microbiology Ecology. 91, 4, (see details) ISI paper
    Link: http://dx.doi.org/10.1093/femsec/fiv019
  21. Coelho F.J.R.C., Cleary D.F.R., Rocha R.J.M., Calado R., Castanheira J.M., Rocha S.M., Silva A.M.S., Simoes M.M.Q., Oliveira V., Lillebo A.I., Almeida A., Cunha A., Lopes I., Ribeiro R., Moreira-Santos M., Marques C.R., Costa R., Pereira R., Gomes N.C.M. (2015) Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities. Global Change Biology. 21, 5, 1871-1886. (see details) ISI paper
  22. Pegoraro N., Calado R., Duarte L.N., Manco S.C., Fernandes F.J., Polonia A.R.M., Cleary D.E.R., Gomes N.C.M. (2015) Molecular analysis of skin bacterial assemblages from codfish and pollock after dry-salted fish production. Journal Of Food Protection. 78, 5, 983-989. (see details) ISI paper
    Link: http://dx.doi.org/10.4315/0362-028X.JFP-14-390
  23. Polonia A.R.M., Cleary D.F.R., Freitas R., de Voogd N.J., Gomes N.C.M. (2015) The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment. Molecular Ecology. 24, 2, 409-423. (see details) ISI paper
    Link: http://dx.doi.org/10.1111/mec.13024
  24. Cleary D.F.R., de Voogd N.J., Polonia A.R.M., Freitas R., Gomes N.C.M. (2015) Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia. Microbial Ecology. 70, 4, 889-903. (see details) ISI paper
    Link: http://link.springer.com/article/10.1007/s00248-015-0632-5#
  25. Polonia A.R.M., Cleary D.F.R., de Voogd N.J., Renema W., Hoeksema B.W., Martins A., Gomes N.C.M. (2015) Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago. Science Of The Total Environment. 537, 139-151. (see details) ISI paper
    Link: 10.1016/j.scitotenv.2015.07.102
  26. Rotllant G., Simeo C.G., Guerao G., Sastre M., Cleary D.F.R., Calado R., Estevez A. (2014) Interannual variability in the biochemical composition of newly hatched larvae of the spider crab Maja brachydactyla (Decapoda, Majidae). Marine Ecology-an Evolutionary Perspective. 35, 3, 298-307. (see details) ISI paper
    Link: http://dx.doi.org/10.1111/maec.12081
  27. Gomes N.C.M., Cleary D.F.R., Pires A.C.C., Almeida A., Cunha A., Mendonca-Hagler L.C.S., Smalla K. (2014) Assessing variation in bacterial, composition between the rhizospheres of two mangrove tree species. Estuarine Coastal And Shelf Science. 139, 40-45. (see details) ISI paper
    Link: http://dx.doi.org/10.1016/j.ecss.2013.12.022
  28. Polonia A.R.M., Cleary D.F.R., Duarte L.N., de Voogd N.J., Gomes N.C.M. (2014) Composition of Archaea in Seawater, Sediment, and Sponges in the Kepulauan Seribu Reef System, Indonesia. Microbial Ecology. 67, 3, 553-567. 1432-184X. (see details) ISI paper
    Link: http://dx.doi.org/10.1007/s00248-013-0365-2
  29. Cleary D.F.R., Polonia A.R.M., Renema W., Hoeksema B.W., Wolstenholme J., Tuti Y., de Voogd N.J. (2014) Coral reefs next to a major conurbation: a study of temporal change (1985-2011) in coral cover and composition in the reefs of Jakarta, Indonesia. Marine Ecology Progress Series. 501, 89-98. (see details) ISI paper
    Link: http://dx.doi.org/10.3354/meps10678
  30. Oliveira V., Gomes N.C.M., Cleary D.F.R., Almeida A., Silva A.M.S., Simoes M.M.Q., Silva H., Cunha A. (2014) Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons. Fems Microbiology Ecology. 90, 3, 647-662. (see details) ISI paper
  31. Hudson L.N., Newbold T., Contu S., Hill S.L.L., Lysenko I., De Palma A., Phillips H.R.P., Senior R.A., Bennett D.J., Booth H., Choimes A., Correia D.L.P., Day J., Echeverria-Londono S., Garon M., Harrison M.L.K., Ingram D.J., Jung M., Kemp V., Kirkpatrick L., Martin C.D., Pan Y., White H.J., Aben J., Abrahamczyk S., Adum G.B., Aguilar-Barquero V., Aizen M.A., Ancrenaz M., Arbelaez-Cortes E., Armbrecht I., Azhar B., Azpiroz A.B., Baeten L., Baldi A., Banks J.E., Barlow J., Batary P., Bates A.J., Bayne E.M., Beja P., Berg A., Berry N.J., Bicknell J.E., Bihn J.H., Bohning-Gaese K., Boekhout T., Boutin C., Bouyer J., Brearley F.Q., Brito I., Brunet J., Buczkowski G., Buscardo E., Cabra-Garcia J., Calvino-Cancela M., Cameron S.A., Cancello E.M., Carrijo T.F., Carvalho A.L., Castro H., Castro-Luna A.A., Cerda R., Cerezo A., Chauvat M., Clarke F.M., Cleary D.F.R., Connop S.P., D'Aniello B., da Silva P.G., Darvill B., Dauber J., Dejean A., Diekotter T., Dominguez-Haydar Y., Dormann C.F., Dumont B., Dures S.G., Dynesius M., Edenius L., Elek Z., Entling M.H., Farwig N., Fayle T.M., Felicioli A., Felton A.M., Ficetola G.F., Filgueiras B.K.C., Fonte S.J., Fraser L.H., Fukuda D., Furlani D., Ganzhorn J.U., Garden J.G., Gheler-Costa C., Giordani P., Giordano S., Gottschalk M.S., Goulson D., Gove A.D., Grogan J., Hanley M.E., Hanson T., Hashim N.R., Hawes J.E., Hebert C., Helden A.J., Henden J.A., Hernandez L., Herzog F., Higuera-Diaz D., Hilje B., Horgan F.G., Horvath R., Hylander K., Isaacs-Cubides P., Ishitani M., Jacobs C.T., Jaramillo V.J., Jauker B., Jonsell M., Jung T.S., Kapoor V., Kati V., Katovai E., Kessler M., Knop E., Kolb A., Korosi A., Lachat T., Lantschner V., Le Feon V., LeBuhn G., Legare J.P., Letcher S.G., Littlewood N.A., Lopez-Quintero C.A., Louhaichi M., Lovei G.L., Lucas-Borja M.E., Luja V.H., Maeto K., Magura T., Mallari N.A., Marin-Spiotta E., Marshall E.J.P., Martinez E., Mayfield M.M., Mikusinski G., Milder J.C., Miller J.R., Morales C.L., Muchane M.N., Muchane M., Naidoo R., Nakamura A., Naoe S., Nates-Parra G., Navarrete Gutierrez D.A., Neuschulz E.L., Noreika N., Norfolk O., Noriega J.A., Noske N.M., O'Dea N., Oduro W., Ofori-Boateng C., Oke C.O., Osgathorpe L.M., Paritsis J., Parra-H A., Pelegrin N., Peres C.A., Persson A.S., Petanidou T., Phalan B., Philips T.K., Poveda K., Power E.F., Presley S.J., Proenca V., Quaranta M., Quintero C., Redpath-Downing N.A., Reid J.L., Reis Y.T., Ribeiro D.B., Richardson B.A., Richardson M.J., Robles C.A., Rombke J., Romero-Duque L.P., Rosselli L., Rossiter S.J., Roulston T.H., Rousseau L., Sadler J.P., Safian S., Saldana-Vazquez R.A., Samnegard U., Schuepp C., Schweiger O., Sedlock J.L., Shahabuddin G., Sheil D., Silva F.A.B., Slade E.M., Smith-Pardo A.H., Sodhi N.S., Somarriba E.J., Sosa R.A., Stout J.C., Struebig M.J., Sung Y.H., Threlfall C.G., Tonietto R., Tothmeresz B., Tscharntke T., Turner E.C., Tylianakis J.M., Vanbergen A.J., Vassilev K., Verboven H.A.F., Vergara C.H., Vergara P.M., Verhulst J., Walker T.R., Wang Y., Watling J.I., Wells K., Williams C.D., Willig M.R., Woinarski J.C.Z., Wolf J.H.D., Woodcock B.A., Yu D.W., Zaitsev A.S., Collen B., Ewers R.M., Mace G.M., Purves D.W., Scharlemann J.P.W., Purvis A. (2014) The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts. Ecology And Evolution. 4, 24, 4701-4735. (see details) ISI paper
  32. Leal M.C., Nunes C., Kempf S., Reis A., Lopes da Silva T., Serôdio J., Cleary D.F.R., Calado R. (2013) Effect of light, temperature and diet on the fatty acid profile of the tropical sea anemone Aiptasia pallida. Aquaculture Nutrition. 19, 818-826. (see details) ISI paper
  33. Gomes N.C.M., Cruz S.C., Pires A.C.C., Gonçalves S.F., Calado R., Cleary D.F.R., Loureiro S. (2013) Richness and composition of sediment bacterial assemblages in an Atlantic port environment. Science Of The Total Environment. 452-453, 172-180. (see details) ISI paper
    Link: http://dx.doi.org/10.1016/j.scitotenv.2013.02.017
  34. Calado R., Guerao G., Gras N., Cleary D.F.R., Rotllant G. (2013) Contrasting habitats occupied by sibling spider crabs Maja squinado and M. brachydactyla (Brachyura, Majidae) can influence the biochemical variability displayed by newly hatched larvae. Journal Of Plankton Research. 35, 684-688. (see details) ISI paper
  35. Coelho F.J.R.C., Rocha R.J.M., Pires A.C.C., Ladeiro B., Castanheira J.M., Costa R., Almeida A., Cunha A., Lillebo A.I., Ribeiro R., Pereira R., Lopes I., Marques C., Moreira-Santos M., Calado R., Cleary D.F.R., Gomes N.C.M. (2013) Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities. Global Change Biology. 19, 8, 2584-2595. (see details) ISI paper
  36. Cleary D.F.R., Becking L.E., de Voogd N.J., Pires A.C.C., Polónia A.R.M., Egas C., Gomes N.C.M. (2013) Habitat and host related variation in sponge bacterial symbiont communities in Indonesian waters. Fems Microbiology Ecology. 85, 3, 465–482 (see details) ISI paper
    Link: http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12135/abstract
  37. Martins P., Cleary D.F.R., Pires A.C.C., Rodrigues A.M., Quintino V., Calado R., Gomes N.C.M. (2013) Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis. Plos One. 8, 11, (see details) ISI paper
    Link: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080847
  38. Swierts T., Peijnenburg K., de Leeuw C., Cleary D.F.R., Hornlein C., Setiawan E., Worheide G., Erpenbeck D., de Voogd N.J. (2013) Lock, Stock and Two Different Barrels: Comparing the Genetic Composition of Morphotypes of the Indo-Pacific Sponge Xestospongia testudinaria. Plos One. 8, 9, e74396 (see details) ISI paper
    Link: http://dx.doi.org/10.1371/journal.pone.0074396
  39. Becking L.E., Cleary D.F.R., de Voogd N.J. (2013) Sponge species composition, abundance, and cover in marine lakes and coastal mangroves in Berau, Indonesia. Marine Ecology Progress Series. 481, 105-120. (see details) ISI paper
    Link: http://dx.doi.org/10.3354/meps10155
  40. de Voogd N.J., Cleary D.F.R., Dekker F. (2013) The coral-killing sponge Terpios hoshinota invades Indonesia. Coral Reefs. 32, 3, 755-755. (see details) ISI paper
  41. Cleary D.F.R., Oliveira V., Gomes N.C.M., Pereira A. , Henriques I., Marques B., Almeida A., Cunha A., Correia A., Lillebø A.I. (2012) Impact of sampling depth and plant species on local environmental conditions, microbiological parameters and bacterial composition in a mercury contaminated salt marsh. Marine Pollution Bulletin. 64, 2, 263-271. (see details) ISI paper
    Link: http://dx.doi.org/10.1016/j.marpolbul.2011.11.020
  42. Cleary D.F.R., Smalla K., Mendonça-Hagler L.C.S., Gomes N.C.M. (2012) Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. Plos One. 7, 1, e29380 (see details) ISI paper
    Link: http://dx.doi.org/10.1371/journal.pone.0029380
  43. Pires A.C.C., Cleary D.F.R., Almeida A., Cunha A., Dealtry S., Mendonca-Hagler L.C.S., Smalla K., Gomes N.C.M. (2012) Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples. Applied And Environmental Microbiology. 78, 16, 5520-5528. (see details) ISI paper
    Link: http://aem.asm.org/content/early/2012/05/30/AEM.00386-12.abstract
  44. Lillebø A.I., Cleary D.R.F., Marques B., Reis A., Lopes da Silva T., Calado R. (2012) Ragworm fatty acid profiles reveals habitat and trophic interactions with halophytes and with mercury. Marine Pollution Bulletin. 64, 2528-2534. (see details) ISI paper
    Link: http://dx.doi.org/10.1016/j.marpolbul.2012.08.009
  45. Queiroga H., Costa R., Leonardo N., Soares D., Cleary D.F.R. (2011) Morphometric variation in two intertidal littorinid gastropods. Contributions To Zoology. 80, 3, 201-211. (see details) ISI paper
  46. Calado R., Pimentel T., Cleary D.F.R., Dionísio G., Nunes C., Lopes da Silva T., Dinis M.T., Reis A. (2010) Providing a common diet to different marine decapods does not standardize the fatty acid profiles of their larvae – a warning sign for experimentation using invertebrate larvae produced in captivity. Marine Biology. 157, 2427-2434. (see details) ISI paper
  47. Gomes N.C.M., Cleary D.F.R., Pinto F.N., Egas C., Almeida A., Cunha A., Mendonca-Hagler L.C.S., Smalla K. (2010) Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves. Plos One. 5, 11, (see details) ISI paper
    Link: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014065
  48. Cleary DFR, Genner MJ, Koh LP, Boyle TJB, Setyawati T, de Jong R, Menken SBJ (2009) Butterfly species and traits associated with selectively logged forest in Borneo. Basic And Applied Ecology. 10, 237–245 (see details) ISI paper
  49. Marijnissen S.A.E., Michel E., Cleary D.F.R., McIntyre P.B. (2009) Ecology and conservation status of endemic freshwater crabs in Lake Tanganyika, Africa. Biodiversity And Conservation. 18, 1555-1573. (see details) ISI paper
  50. de Voogd NJ, Becking LE, Cleary DFR (2009) Sponge community composition in the Derawan Islands, NE Kalimantan, Indonesia. Marine Ecology Progress Series. 396, 219-230. (see details) ISI paper
  51. de Voogd N.J., Cleary D.F.R. (2009) Variation in sponge composition among Singapore reefs. The Raffles Bulletin Of Zoology. supplement 22, 59-67. (see details) ISI paper
  52. Cleary DFR, DeVantier L, Giyanto, Vail L, Manto P, de Voogd NJ, Rachello-Dolmen PG, Tuti Y, Budiyanto A, Wolstenholme J, Hoeksema BW, Suharsono (2008) Relating variation in species composition to environmental variables: a multi-taxon study in an Indonesian coral reef complex. Aquatic Sciences. 70, 419-431. (see details) ISI paper
  53. Marijnissen SAE, Michel E, Kamermans M, Olaya-Bosch K, Kars M, Cleary DFR, van Loon EE, Rachello Dolmen PG, Menken SBJ (2008) Exploring ecological correlates of species differences in Lake Tanganyika endemic crabs. Hydrobiologia. 615, 81-94. (see details) ISI paper
  54. Grill A, Cleary DFR, Stettmer C, Bräu M, Settele J (2008) A mowing experiment to evaluate the influence of management on the activity of host ants of Maculinea butterflies. Journal Of Insect Conservation. 12, 617-627. (see details) ISI paper
  55. de Voogd NJ, Cleary DFR (2008) An analysis of sponge diversity and distribution at three taxonomic levels in the Thousand Islands/Jakarta Bay reef complex, West-Java, Indonesia. Marine Ecology. 29, 205–215 (see details) ISI paper
  56. Cleary DFR, de Voogd NJ (2007) Environmental determination of sponge assemblages in the Spermonde Archipelago, Indonesia. Journal Of The Marine Biological Association Of The Uk. 87, 1669-1676. (see details) ISI paper
  57. Erpenbeck D, Cleary DFR, Voigt O, Nichols SA, Degnan BM, Hooper JNA, Wörheide G (2007) Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA. Of The Marine Biological Association Of The Uk. 87, 1607-1614. (see details) ISI paper
  58. van Soest RWM, Cleary DFR, de Kluijver MJ, Lavaleye MSS, Maier C, van Duyl FC (2007) Sponge diversity and community composition in Irish bathyal coral reefs. Contributions To Zoology. 76, 121-142. (see details) ISI paper
  59. van Loon E, Cleary DFR, Fauvelot C (2007) ARES: software to compare allelic richness between uneven samples. Molecular Ecology Notes. 7, 579-582. (see details) ISI paper
  60. Cleary DFR, Boyle TJB, Setyawati T, Angraeti CD, Menken SBJ (2007) Bird species richness, composition and ecological traits associated with unlogged and logged Bornean hill forest. Ecological Applications. 17, 1184-1197. (see details) ISI paper
  61. Rachello-Dolmen PG, Cleary DFR (2007) Coral species, traits and environmental conditions in Jakarta Bay/Pulau Seribu reef complex. Estuarine, Coastal And Shelf Science. 73, 816-826. (see details) ISI paper
  62. Cleary DFR, Renema W (2007) Relating species traits of foraminifera to environmental parameters in the Spermonde Archipelago, Indonesia. Marine Ecology Progress Series. 334, 73-82. (see details) ISI paper
  63. de Voogd NJ, Cleary DFR (2007) Relating species traits to environmental parameters in Indonesian coral reef sponge assemblages. Marine And Freshwater Research. 58, 240-249. (see details) ISI paper
  64. Cleary DFR, Suharsono, Hoeksema BW (2006) Coral diversity across a disturbance gradient in the Pulau Seribu reef complex off Jakarta, Indonesia. Biodiversity And Conservation. 15, 3653-3674. (see details) ISI paper
  65. Grill A, Schtickzelle N, Cleary DFR, Nève G, Menken SBJ (2006) Ecological differentiation between the Sardinian endemic Maniola nurag and the pan-European M. urtina. Biological Journal Of The Linnean Society. 89, 561-574. (see details) ISI paper
  66. Charrette NA, Cleary DFR, Mooers AØ (2006) Range-restricted, specialist Bornean butterflies are less likely to recover from ENSO-induced disturbance. Ecology. 87, 2330-2337. (see details) ISI paper
  67. Fauvelot C, Cleary DFR, Menken SBJ (2006) Short-term impact of 1997/1998 ENSO-induced disturbance on abundance and genetic variation in a tropical butterfly. Journal Of Heredity. 97, 367-380. (see details) ISI paper
  68. Cleary DFR, Mooers AØ (2006) Burning and logging differentially affect endemic versus widely distributed butterfly species in Borneo. Diversity And Distributions. 12, 409-416. (see details) ISI paper
  69. Fauvelot C, Cleary DFR, Menken SBJ (2006) Impact of disturbance on butterfly population genetics in East Kalimantan, Indonesia. Molecular Ecology . 15, 2069–2081 (see details) ISI paper
  70. Cleary DFR, Genner MJ (2006) Understanding diversity patterns of Bornean butterfly assemblages. Biodiversity And Conservation. 15, 517-538. (see details) ISI paper
  71. Becking LE, Cleary DFR, de Voogd NJ, Renema W, de Beer M, van Soest RWM, Hoeksema BW (2006) Beta diversity of tropical marine assemblages in the Spermonde Archipelago, Indonesia. Marine Ecology – An Evolutionary Perspective. 27, 76-88. (see details) ISI paper
  72. de Voogd NJ, Cleary DFR, Hoeksema BW, Noor A, van Soest RWM (2006) Sponge beta diversity in the Spermonde Archipelago, Indonesia. Marine Ecology Progress Series. 309, 131-142. (see details) ISI paper
  73. Cleary DFR, Fauvelot C, Genner, MJ, Menken SBJ, Mooers AØ (2006) Parallel responses of species and genetic diversity to El Niño Southern Oscillation-induced environmental destruction. Ecology Letters. 9, 301-307. (see details) ISI paper
  74. Cleary DFR, Priadjati A, Suryokusumo BK, Menken SBJ (2006) Butterfly, sapling, seedling and tree diversity in a fire-affected Bornean rainforest. Austral Ecology. 31, 46-57. (see details) ISI paper
  75. Cleary DFR, Genner MJ, Boyle TJB, Setyawati T, Angraeti CD, Menken SBJ (2005) Dependence of bird species richness and composition upon local- and large-scale environmental factors in Borneo. Landscape Ecology. 20, 989-1001. (see details) ISI paper
  76. Cleary DFR, Becking LE, de Voogd NJ, Renema W, de Beer M, van Soest RWM, Hoeksema BW (2005) Cross-shelf diversity of sea urchins, sponges, mushroom corals and foraminifera in the Spermonde Archipelago, Indonesia. Estuarine, Coastal And Shelf Science. 65, 557-570. (see details) ISI paper
  77. Cleary DFR, Priadjati A (2005) Vegetation responses to burning in a rain forest in Borneo. Plant Ecology. 177, 145-163. (see details) ISI paper
  78. Grill A, Knoflach B, Cleary DFR, Kati V (2005) Butterfly, spider, and plant communities in different land-use types in Sardinia, Italy. Biodiversity And Conservation. 14, 1281-1300. (see details) ISI paper
  79. Cleary DFR, Boyle TJB, Setyawati T, Menken SBJ (2005) The impact of logging on the abundance, species richness and community composition of butterfly guilds in Borneo. Journal Of Applied Entomology. 129, 52-59. (see details) ISI paper
  80. Cleary DFR (2004) Community composition and species richness of parasitoids infesting Yponomeuta species in the Netherlands. Contributions To Zoology. 73, 255-261. (see details) ISI paper
  81. Cleary DFR, Grill A (2004) Butterfly response to severe ENSO-induced forest fires in Borneo. Ecological Entomology. 29, 666-676. (see details) ISI paper
  82. Genner MJ, Taylor MI, Cleary DFR, Hawkins SJ, Knight ME, Turner GF (2004) Beta diversity of rock-restricted cichlid fishes in Lake Malawi: importance of environmental and spatial factors. Ecography. 27, 601-610. (see details) ISI paper
  83. Cleary DFR, Mooers AØ (2004) Butterfly species richness and community composition in forests affected by ENSO-induced burning and habitat isolation in Borneo. Journal Of Tropical Ecology. 20, 359-367. (see details) ISI paper
  84. Cleary DFR, van Ginkel W (2004) Effects of host species and size on brood size and larval mortality of the parasitoid, Ageniaspis fuscicollis (Dalman) (Hymenoptera, Encyrtidae). Environmental Entomology. 33, 528-534. (see details) ISI paper
  85. Cleary DFR, Genner MJ (2004) Changes in rain forest butterfly diversity following major ENSO-induced fires in Borneo. Global Ecology And Biogeography . 13, 129-140. (see details) ISI paper
  86. Cleary DFR (2004) Assessing the use of butterflies as indicators of logging in Borneo at three taxonomic levels. Journal Of Economic Entomology . 97, 429-435. (see details) ISI paper
  87. Cleary DFR, Mooers AØ, Eichhorn KAO, van Tol J, de Jong R, Menken SBJ (2004) Diversity and community composition of butterflies and odonates in an ENSO-induced fire affected habitat mosaic: a case study from East Kalimantan, Indonesia. Oikos. 105, 426-446. (see details) ISI paper
  88. Hoeksema BW, Cleary DFR (2004) The sudden death of a coral reef. Science . 303, 1293-1293. (see details) ISI paper
  89. Genner MJ, Seehausen O, Cleary DFR, Knight ME, Michel E, Turner GF (2004) How does the taxonomic status of allopatric populations influence species richness within African cichlid fish assemblages?. Journal Of Biogeography. 31, 93-102. (see details) ISI paper
  90. Grill A, Cleary DFR (2003) Diversity patterns in butterfly communities of the Greek nature reserve Dadia. Biological Conservation. 114, 427-436. (see details) ISI paper
  91. Cleary DFR (2003) An examination of scale of assessment, logging and ENSO-induced fires on butterfly diversity in Borneo. Oecologia . 135, 313-321. (see details) ISI paper
  92. Cleary DFR, Descimon H, Menken SBJ (2002) Genetic and ecological differentiation between the butterfly sisterspecies Colias alfacariensis and Colias hyale. Contributions To Zoology. 71, 131-139. (see details) ISI paper
  1. Gomes N.C.M., Cleary D.F.R., Calado R., Costa R. (2011) Mangrove bacterial richness. Communicative And Integrative Biology. 4, 4, 1-5. (see details)
    Link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181510/pdf/cib0404_0419.pdf
  2. de Voogd NJ, Cleary DFR (2007) Sponge biodiversity near Asian conurbations. Global Marine Environment. 6, 6-7. (see details)
  3. Cleary DFR, Tichelaar I (2003) Bosbranden en El Niño. Ecologie & Ontwikkeling. 2, 14-15. (see details)
  4. Cleary DFR, Menken SBJ (2002) Branden maken bossen extra kwetsbaar. Natuur En Techniek. 3, 57 (see details)
  5. ACC Pires, DFR Cleary, ARM Polónia, SC Lim, NJ de Voogd, V Oliveira, NCM Gomes Comparison of bacterial communities associated with Xestospongia testudinaria, sediment and seawater in a Singaporean coral reef ecosystem. Journal Of The Marine Biological Association Of The United Kingdom. (see details)
    Link: https://doi.org/10.1017/S0025315418000188
  1. Cleary D.F.R (2008) Biodiversity conservation in Borneo and the threat of large scale disturbance events. In: Tropenbos Series. (EDS.), Reflections on the Heart of Borneo. Wageningen, the Netherlands. Tropenbos International. 24, (see details)
  2. Cleary D.F.R (2008) Biodiversity conservation in Borneo and the threat of large scale disturbance events. In: Tropenbos Series. (EDS.), Reflections on the Heart of Borneo. Wageningen, the Netherlands. Tropenbos International. 24, (see details)
  3. Mooers A, Meuser E, Cleary DFR (2007) El Niño and Biodiversity. In: Encyclopedia of Biodiversity. Oxford. Elsevier. (see details)
  1. Gomes, Hélder Alexandre Campos (2015) Ecological and biotechnological potential of sponge microbiome. MSc Thesis. [co-supervisor] (see details)
  2. Pires A.C.C. (2010) Estudo do Efeito "rizosfera" nas Comunidades de Archaea em Plantas de Mangal. MSc Thesis. (see details)
  3. de Sousa AG (2010) Análise de padrões de arrojamentos de cetáceos na costa continental portuguesa. MSc Thesis. (see details)
  4. Cleary DFR (2002) Biodiversity and environmental change in the rainforests of Borneo. PhD Thesis. (see details)
    Link: http://dare.uva.nl/record/102576
  1. Oliveira V., Pires A.C.C., Cleary D.F.R., Pólonia A.R.M., Lim S.C., de Voogd N.J., Gomes N.C.M. (2017) Bacterial communities of Xestospongia testudinaria, sediment and water in a singaporean coral reef ecosystem. (see details)
  2. Coelho FJRC, Cleary DFR, Ferreira M, Gomes NCM (2015) Response of sediment archaeal communities to ocean acidification and oil pollution. (see details)
  3. Sousa A.I., Santos D.B., Ferreira da Silva E., Cleary D.F.R., Lillebø A.I. (2015) Salt marsh species- and zonation-specificities in regulation ecosystem services provided. (see details)
  4. Sousa A.I., Polónia A.R., Calado R., Serôdio J., Cleary D.F.R., Lillebø A.I. (2014) Zostera noltii functioning and dynamics along a salinity gradient: Ria de Aveiro (Portugal). (see details)
  5. Sousa AI, Marques B, Santos DB, Cleary DFR, Lillebø AI (2014) Ecosystem functions supported by salt marshes: coastal C and N sinks. (see details)
  6. de Figueiredo D.R., Cleary D., Saraiva P., Gomes N., Gonçalves A.M.M., Reboleira A.S., Gonçalves F., Oliveira J., Condesso de Melo M.T., Abrantes N. (2014) Metagenomic overview of bacterioplankton diversity from Estremenho karst massif aquifer (Portugal). (see details)
  7. Sousa A.I., Polónia A.R., Calado R., Serôdio J., Cleary D.F.R., Lillebø A.I. (2013) Zostera noltii dynamics along a salinity gradient: Ria de Aveiro (Portugal). (see details)
  8. Sousa AI, Santos DB, Marques B, Serôdio J, Ferreira da Silva E, Cleary DFR, Soares A, Lillebø AI. (2013) Ecological processes and ecosystem services in coastal wetlands: seagrass meadows and salt marshes. (see details)
  9. Polónia ARM, Cleary DRF, Duarte LN, de Voogd NJ, Gomes NCM Composition of Archaea in seawater, sediment and sponges in the Kepulauan Seribu reef system, Indonesia. (see details)
  10. Polónia ARM, Figueiredo M, Cleary DFR, de Voogd NJ, Martins A. Sea surface temperature and ocean colour (MODIS/AQUA) space and time variability in Indonesian Sea coral reef systems from 2002 to 2011. (see details)
  11. Oliveira, V., Gomes, N.C.M., Cleary, D.F.R., Almeida, A., Silva, A., Simões, M.M.Q., Silva, H., Cunha, A. In depth molecular analysis of bacterial communities in salt marshes chronically exposed to oil hydrocarbons. (see details)
  1. Lillebø A.I., Queiroga H., Dias J.M., Alves F., Cleary D.F.R. (2011) Ria de Aveiro: Uma Visão dos Processos Ambientais, Ecológicos e Socioeconómicos. In: Almeida, A., Alves, F.L., Bernardes, C., Dias, J.M., Gomes, N.C.M., Pereira, E., Queiroga, H., Serôdio, J., Vaz, N. (Eds). Actas das Jornadas da Ria de Aveiro, Universidade de Aveiro, CESAM-Centro de Estudos do Ambiente e do Mar, pp.334-339. (see details)