Supporting Material for “Assessing coral fish diversity: the need for a change in
methods”
Loiseau N., Gaertner J-C.
Appendix 1 List of reviewed papers
Ackerman, J. L., & Bellwood, D. R. (2000). Reef fish assemblages: a re-evaluation using
enclosed rotenone stations. Marine ecology Progress Series, 206, 227-237.
Acosta, C. A., & Robertson, D. N. (2002). Diversity in coral reef fish communities: the effects
of habitat patchiness revisited. Marine ecology Progress Series, 227, 87-96.
Albins, M. A. (2013). Effects of invasive Pacific red lionfish Pterois volitans versus a native
predator on Bahamian coral-reef fish communities. Biological Invasions, 15(1), 29-43.
Almany, G. R. (2004). Does increased habitat complexity reduce predation and competition in
coral reef fish assemblages? Oikos, 106(2), 275-284.
Almany, G. R., Peacock, L. F., Syms, C., McCormick, M. I., & Jones, G. P. (2007). Predators
target rare prey in coral reef fish assemblages. Oecologia,152(4), 751-761.
Alvarez‐Filip, L., Reyes‐Bonilla, H., & Calderon‐Aguilera, L. E. (2006). Community
structure of fishes in Cabo Pulmo reef, Gulf of California. Marine ecology, 27(3), 253262.
Alvarez‐Filip, L., Reyes‐Bonilla, H., & Calderon‐Aguilera, L. E. (2006). Community
structure of fishes in Cabo Pulmo reef, Gulf of California. Marine ecology, 27(3), 253262.
Andréfouët, S., & Wantiez, L. (2010). Characterizing the diversity of coral reef habitats and
fish communities found in a UNESCO World Heritage Site: The strategy developed for
Lagoons of New Caledonia. Marine Pollution Bulletin,61(7), 612-620.
Araújo, F. G., & De Azevedo, M. C. (2001). Assemblages of Southeast-South Brazilian
Coastal Systems based on the distribution of fishes. Estuarine, Coastal and Shelf
Science, 52(6), 729-738.
Arias‐González, J. E. (1998). Trophic models of protected and unprotected coral reef
ecosystems in the South of the Mexican Caribbean. Journal of fish Biology, 53(sA),
236-255.
Arias-González, J. E., Done, T. J., Page, C. A., Cheal, A. J., Kininmonth, S., & Garza-Pérez,
J. R. (2006). Towards a reefscape ecology: relating biomass and trophic structure of fish
assemblages to habitat at Davies Reef, Australia. Marine ecology Progress Series, 320,
29-41.
Arias-González, J. E., Legendre, P., & Rodríguez-Zaragoza, F. A. (2008). Scaling up beta
diversity on Caribbean coral reefs. Journal of Experimental Marine Biology and
Ecology, 366(1), 28-36.
Ashworth, J. S., Bruce, O. E., & Hellw, M. E. (2006). Fish assemblages of Red Sea backreef
biotopes. Aquatic Conservation: Marine and Freshwater Ecosystems, 16(6), 593-609.
Ault, T. R., & Johnson, C. R. (1998). Spatial variation in fish species richness on coral reefs:
habitat fragmentation and stochastic structuring processes.Oikos, 354-364.
Balasubramanian, H., Foster, R.S. (2007) Species and space: role of volume in organizing
coral reef fish assemblages in SE Cuba. Marine ecology Progress Series, 345, 229-236
Barjau-González, E., Rodríguez-Romero, J., Galván-Magaña, F., & López-Martínez, J.
(2012). Changes in the taxonomic diversity of the reef fish community of San José
Island, Gulf of California, Mexico. Biodiversity and Conservation, 21(14), 3543-3554.
Baron, R. M., Jordan, L. K., & Spieler, R. E. (2004). Characterization of the marine fish
assemblage associated with the nearshore hardbottom of Broward County, Florida,
USA. Estuarine, Coastal and Shelf Science, 60(3), 431-443.
Bauman, A. G., Burt, J. A., Feary, D. A., Marquis, E., & Usseglio, P. (2010). Tropical
harmful algal blooms: An emerging threat to coral reef communities? Marine Pollution
Bulletin, 60(11), 2117-2122.
Bejarano, S., Golbuu, Y., Sapolu, T., & Mumby, P. J. (2013). Ecological risk and the
exploitation of herbivorous reef fish across Micronesia. Marine ecology Progress
Series, 482, 197-215.
Bellwood, D. R., Baird, A. H., Depczynski, M., González-Cabello, A., Hoey, A. S., Lefèvre,
C. D., & Tanner, J. K. (2012). Coral recovery may not herald the return of fishes on
damaged coral reefs. Oecologia, 170(2), 567-573.
Bellwood, D. R., Hoey, A. S., Ackerman, J. L., & Depczynski, M. (2006). Coral bleaching,
reef fish community phase shifts and the resilience of coral reefs. Global Change
Biology, 12(9), 1587-1594.
Bellwood, D. R., Wainwright, P. C., Fulton, C. J., & Hoey, A. (2002). Assembly rules and
functional groups at global biogeographical scales. Functional Ecology, 16(5), 557-562.
Belmaker, J., Shashar, N., & Ziv, Y. (2005). Effects of small-scale isolation and predation on
fish diversity on experimental reefs. Marine ecology Progress Series, 289, 273-283.
Belmaker, J., Ziv, Y., & Shashar, N. (2011). The influence of connectivity on richness and
temporal variation of reef fishes. Landscape ecology, 26(4), 587-597.
Bergman, K. C., Svensson, S., & Öhman, M. C. (2001). Influence of algal farming on fish
assemblages. Marine Pollution Bulletin, 42(12), 1379-1389.
Beukers-Stewart, B. D., Beukers-Stewart, J. S., & Jones, G. P. (2011). Behavioural and
developmental responses of predatory coral reef fish to variation in the abundance of
prey. Coral reefs, 30(3), 855-864.
Booth, D. J., & Beretta, G. A. (2002). Changes in a fish assemblage after a coral bleaching
event. Marine ecology Progress Series, 245, 205-212.
Bouchon-Navaro, Y., Bouchon, C., Louis, M., & Legendre, P. (2005). Biogeographic patterns
of coastal fish assemblages in the West Indies. Journal of Experimental Marine Biology
and Ecology, 315(1), 31-47.
Brewer, T. D., Cinner, J. E., Fisher, R., Green, A., & Wilson, S. K. (2012). Market access,
population density, and socioeconomic development explain diversity and functional
group biomass of coral reef fish assemblages. Global Environmental Change, 22(2),
399-406.
Bridge, T., Scott, A., & Steinberg, D. (2012). Abundance and diversity of anemonefishes and
their host sea anemones at two mesophotic sites on the Great Barrier Reef,
Australia. Coral reefs, 31(4), 1057-1062.
Brokovich, E., Ayalon, I., Einbinder, S., Segev, N., Shaked, Y., Genin, A., ... & Kiflawi, M.
(2009). Grazing pressure on coral reefs decreases across a wide depth gradient in the
Gulf of Aqaba, Red Sea. Marine ecology Progress Series,399, 69.
Burgess, S. C., Osborne, K., & Caley, M. J. (2010). Similar regional effects among local
habitats on the structure of tropical reef fish and coral communities. Global Ecology and
Biogeography, 19(3), 363-375.
Burt, J., Bartholomew, A., Usseglio, P., Bauman, A., & Sale, P. F. (2009). Are artificial reefs
surrogates of natural habitats for corals and fish in Dubai, United Arab Emirates? Coral
reefs, 28(3), 663-675.
Caley, M. J. (1995). Reef-fish community structure and dynamics: an interaction between
local and larger-scale processes? Marine ecology Progress Series, 129(1), 19-29.
Cappo, M., De'ath, G., & Speare, P. (2007). Inter-reef vertebrate communities of the Great
Barrier Reef Marine Park determined by baited remote underwater video
stations. Marine ecology Progress Series, 350, 209-221.
Cappo, M., Speare, P., & De'ath, G. (2004). Comparison of baited remote underwater video
stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in
inter-reefal areas of the Great Barrier Reef Marine Park. Journal of Experimental
Marine Biology and Ecology, 302(2), 123-152.
Carassou, L., & Ponton, D. (2007). Spatio-temporal structure of pelagic larval and juvenile
fish assemblages in coastal areas of New Caledonia, southwest Pacific. Marine
Biology, 150(4), 697-711.
Carassou, L., Léopold, M., Guillemot, N., Wantiez, L., & Kulbicki, M. (2013). Does
herbivorous fish protection really improve coral reef resilience? A case study from New
Caledonia (South Pacific). PloS one, 8(4), e60564.
Chabanet, P., Ralambondrainy, H., Amanieu, M., Faure, G., & Galzin, R. (1997).
Relationships between coral reef substrata and fish. Coral reefs, 16(2), 93-102.
Chaves, L. D. C. T., Ormond, C. G. A., McGinty, E. S., & Ferreira, B. P. (2012). Space
partitioning among damselfishes in the Caribbean coast of Panama: the role of habitat
preferences. Neotropical Ichthyology, 10(3), 633-642.
Cheal, A. J., Emslie, M., MacNeil, M. A., Miller, I., & Sweatman, H. (2013). Spatial variation
in the functional characteristics of herbivorous fish communities and the resilience of
coral reefs. Ecological Applications, 23(1), 174-188.
Cheal, A. J., MacNeil, M. A., Cripps, E., Emslie, M. J., Jonker, M., Schaffelke, B., &
Sweatman, H. (2010). Coral–macroalgal phase shifts or reef resilience: links with
diversity and functional roles of herbivorous fishes on the Great Barrier Reef. Coral
reefs, 29(4), 1005-1015.
Cheal, A. J., Wilson, S. K., Emslie, M. J., Dolman, A. M., & Sweatman, H. (2008).
Responses of reef fish communities to coral declines on the Great Barrier Reef. Marine
ecology Progress Series, 372, 211-223.
Cheal, A., Emslie, M., Miller, I., & Sweatman, H. (2012). The distribution of herbivorous
fishes on the Great Barrier Reef. Marine Biology, 159(5), 1143-1154.
Chittaro, P. M. (2002). Species-area relationships for coral reef fish assemblages of St. Croix,
US Virgin Islands. Marine ecology Progress series,233, 253-261.
Chittaro, P. M., & Sale, P. F. (2003). Structure of patch-reef fish assemblages at St. Croix, US
Virgin Islands, and One Tree Reef, Australia. Marine ecology Progress series, 249,
277-287.
Chong-Seng, K. M., Mannering, T. D., Pratchett, M. S., Bellwood, D. R., & Graham, N. A.
(2012). The influence of coral reef benthic condition on associated fish
assemblages. PloS one, 7(8), e42167.
Cinner, J. E., McClanahan, T. R., Graham, N. A., Pratchett, M. S., Wilson, S. K., & Raina, J.
B. (2009). Gear‐based fisheries management as a potential adaptive response to climate
change and coral mortality. Journal of Applied Ecology, 46(3), 724-732.
Clark, S., & Edwards, A. J. (1994). Use of artificial reef structures to rehabilitate reef flats
degraded by coral mining in the Maldives. Bulletin of Marine Science, 55(2-3), 724744.
Coker, D. J., Graham, N. A. J., & Pratchett, M. S. (2012). Interactive effects of live coral and
structural complexity on the recruitment of reef fishes. Coral reefs, 31(4), 919-927.
Côté, I. M., Mosqueira, I., & Reynolds, J. D. (2001). Effects of marine reserve characteristics
on the protection of fish populations: a meta‐analysis. Journal of fish Biology, 59(sA),
178-189.
Depczynski, M., & Bellwood, D. R. (2005). Wave energy and spatial variability in
community structure of small cryptic coral reef fishes. Marine ecology Progress
Series, 303, 283-293.
Dickens, L. C., Goatley, C. H., Tanner, J. K., & Bellwood, D. R. (2011). Quantifying relative
diver effects in underwater visual censuses. PloS one,6(4), e18965.
Dominici-Arosemena, A., & Wolff, M. (2006). Reef fish community structure in the Tropical
Eastern Pacific (Panamá): living on a relatively stable rocky reef
environment. Helgoland Marine Research, 60(4), 287-305.
Dorenbosch, M., Grol, M. G. G., Christianen, M. J. A., Nagelkerken, I., & Van Der Velde, G.
(2005). Indo-Pacific seagrass beds and mangroves contribute to fish density and
diversity on adjacent coral reefs. Marine ecology Progress Series, 302, 63-76.
Dorenbosch, M., Grol, M. G. G., Nagelkerken, I., & Van der Velde, G. (2006). Different
surrounding landscapes may result in different fish assemblages in East African
seagrass beds. Hydrobiologia, 563(1), 45-60.
Dorenbosch, M., Verberk, W. C. E. P., Nagelkerken, I., & Van der Velde, G. (2007).
Influence of habitat configuration on connectivity between fish assemblages of
Caribbean seagrass beds, mangroves and coral reefs. Marine ecology Progress
Series, 334, 103-116.
Dorman, S. R., Harvey, E. S., & Newman, S. J. (2012). Bait effects in sampling coral reef fish
assemblages with stereo-BRUVs. PloS one, 7(7), e41538.
Dulvy, N. K., Freckleton, R. P., & Polunin, N. V. (2004). Coral reef cascades and the indirect
effects of predator removal by exploitation. Ecology letters,7(5), 410-416.
Dulvy, N. K., Mitchell, R. E., Watson, D., Sweeting, C. J., & Polunin, N. V. (2002). Scaledependant control of motile epifaunal community structure along a coral reef fishing
gradient. Journal of Experimental Marine Biology and Ecology, 278(1), 1-29.
Dulvy, N. K., Stanwell-Smith, D., Darwall, W. R., & Horrill, C. J. (1995). Coral mining at
Mafia Island, Tanzania: a management dilemma. Ambio, 358-365.
Dustan, P., Doherty, O., & Pardede, S. (2013). Digital reef rugosity estimates coral reef
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Ebersole, J. P. (2001). Recovery of fish assemblages from ship groundings on coral reefs in
the Florida Keys National Marine Sanctuary. Bulletin of Marine Science, 69(2), 655671.
Edwards, H. J., Elliott, I. A., Pressey, R. L., & Mumby, P. J. (2010). Incorporating
ontogenetic dispersal, ecological processes and conservation zoning into reserve
design. Biological Conservation, 143(2), 457-470.
Emslie, M., Cheal, A., Sweatman, H., & Delean, J. (2008). Recovery from disturbance of
coral and reef fish communities on the Great Barrier Reef, Australia. Marine ecology
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Fabricius, K., De’ath, G., McCook, L., Turak, E., & Williams, D. M. (2005). Changes in
algal, coral and fish assemblages along water quality gradients on the inshore Great
Barrier Reef. Marine Pollution Bulletin, 51(1), 384-398.
Ferreira, C. E. L., & Gonçalves, J. E. A. (2006). Community structure and diet of roving
herbivorous reef fishes in the Abrolhos Archipelago, south‐western Atlantic. Journal of
fish Biology, 69(5), 1533-1551.
Fitzpatrick, B. M., Harvey, E. S., Heyward, A. J., Twiggs, E. J., & Colquhoun, J. (2012).
Habitat specialization in tropical continental shelf demersal fish assemblages. PloS
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Floeter, S. R., Behrens, M. D., Ferreira, C. E. L., Paddack, M. J., & Horn, M. H. (2005).
Geographical gradients of marine herbivorous fishes: patterns and processes. Marine
Biology, 147(6), 1435-1447.
Floeter, S. R., Guimaraes, R. Z., Rocha, L. A., Ferreira, C. E. L., Rangel, C. A., & Gasparini,
J. L. (2001). Geographic variation in reef‐fish assemblages along the Brazilian
coast. Global Ecology and Biogeography, 10(4), 423-431.
Fowler, A. M., & Booth, D. J. (2012). How well do sunken vessels approximate fish
assemblages on coral reefs? Conservation implications of vessel-reef
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Francisco-Ramos, V., & Arias-González, J. E. (2013). Additive partitioning of coral reef fish
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Fulton, C. J., & Bellwood, D. R. (2004). Wave exposure, swimming performance, and the
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Graham, N. A., McClanahan, T. R., MacNeil, M. A., Wilson, S. K., Polunin, N. V., Jennings,
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Andrefouet, S. (2012). Multi-taxa coral reef community structure in relation to habitats
in the Baa Atoll Man and Biosphere UNESCO Reserve (Maldives), and implications for
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Knudby, A., Brenning, A., & LeDrew, E. (2010). New approaches to modelling fish–habitat
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Kulbicki, M., Sarramégna, S., Letourneur, Y., Wantiez, L., Galzin, R., Mou-Tham, G., ... &
Thollot, P. (2007). Opening of an MPA to fishing: Natural variations in the structure of
a coral reef fish assemblage obscure changes due to fishing. Journal of Experimental
Marine Biology and Ecology, 353(2), 145-163.
Ley, J. A. (2005). Linking fish assemblages and attributes of mangrove estuaries in tropical
Australia: criteria for regional marine reserves. Marine ecology Progress series, 305,
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Lindahl, U. L. F., Öhman, M. C., & Schelten, C. K. (2001). The 1997/1998 mass mortality of
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Lindsay, M. J., Patterson, H. M., & Swearer, S. E. (2008). Habitat as a surrogate measure of
reef fish diversity in the zoning of the Lord Howe Island Marine Park, Australia. Marine
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Appendix 2 Codes, formula and references of the indices mentioned in figure 3.
Indices
Formula
R packages
S
Species density
Vegan. Oksanen et al.
2013
Dmg: Margalef 1958
𝐷𝑚𝑔 = ln⁡(𝑛)
Chao 1: Chao 1984
𝑆𝐶ℎ𝑎𝑜1 = 𝑆
Number of species
Chao 2: Chao 1984
Nrare
𝑆−1
Vegan for S. Oksanen
et al. 2013
Vegan. Oksanen et al.
2013
Vegan. Oksanen et al.
2013
𝑓1 (𝑓1 −1)
2(𝑓2 +1)
𝑚−1 𝑞1 (𝑞1 −1)
𝑆𝐶ℎ𝑎𝑜2 = 𝑆 + (
𝑚
)
2(𝑞2 +1)
Number of rare species
Evenness
Ehulbert = 𝐻 ′ 𝑚𝑎𝑥−𝐻′𝑚𝑖𝑛
Eheip: Heip 1974
Eheip =
E1/D: Smith and Wilson 1996
EBG: Berger and Parker 1970
Vegan for H’.
Oksanen et al. 2013
𝐻 ′ −𝐻′𝑚𝑖𝑛
Ehulbert: Hulbert 1971
E1/D =
EBG=
Vegan for H’.
Oksanen et al. 2013
𝑒 𝐻′ −1
𝑆−1
1/𝐷
Vegan for D. Oksanen
et al. 2013
𝑆
𝑁𝑚𝑎𝑥
𝑁
Functional diversity
Functional richness
FRic: Villéger et al. 2008
FD. Laliberté et al.
2014
Convex hull algorithm
Functional evenness
𝑑𝑖𝑗 ⁄𝑝𝑖 +𝑝𝑗
1
FD. Laliberté et al.
2014
𝑝𝑗
∑𝑁
𝑗≠𝑖1−𝑝𝑖 𝑑𝑖𝑗
1
𝑁
∑𝑖 𝑚𝑖𝑛{𝑝𝑖 ∗
, }−1/𝑁
𝑝𝑗
𝑁
𝑁
∑𝑁
∑
𝑖 𝑝𝑖 𝑗≠𝑖1−𝑝𝑖 𝑑𝑖𝑗
Ricotta et al. 2014
provided the script
FEve: Villéger et al. 2008
𝐹𝐸𝑣𝑒 =
Ru: Ricotta et al. 2014
𝑅𝑢 =
Functional divergence
1
∑𝑆−1
𝑖=1 min(∑𝑠−1𝑑 ⁄𝑝 +𝑝 ,𝑆−1)−𝑆−1
𝑖=1 𝑖𝑗 𝑖 𝑗
1−
1
𝑆−1
1−1/𝑁
Q: Rao 1982
𝑄 = ∑𝑆𝑖=1 ∑𝑆𝑗=1 𝑝𝑖 𝑝𝑗 𝑑𝑖,𝑗
FD. Laliberté et al.
2014
FDiv: Villéger et al. 2008
FDiv = Δ|d|+dG
̅̅̅̅
Δd+dG
FD. Laliberté et al.
2014
FDis: Laliberté and Legendre. 2010
FDis =
∑ pi zi
∑ pi
FD. Laliberté et al.
2014
S : number of species in the community, N : total abundance, 𝐻′ = − ∑𝑆𝑖 𝑝𝑖 𝑙𝑛𝑝𝑖 , D= Simpson index with
1 − 𝐷 = 1 − ∑𝑆𝑖 𝑝𝑖 ², f1 is the number of singleton species, f2 is the number of doubleton species, , q1 is the
number of unique species, q2 is the number of duplicate species, z : barycenter of the community, dij : distance
between species i and j, pi et pj : abundance between species i and j, dG: distance to gravity center. Δd: sum of
abundance-weighted deviances, Δ|d|: absolute abundance-weighted deviances.
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