DOI: 10.5061/dryad.ns1rn8q03
title: Variation in functional composition of reef fishes along a tropical to temperate gradient

description: AimsTransformations of species and functional compositions on subtropical
 reefs are ongoing due to poleward range shifts of some tropical species,
 with largely unknown consequences to ecosystem functioning. Trait-based
 approaches are powerful tools to quantify such changes. Here, we evaluated
 changes in the trait composition of coral-associated fish communities
 along a tropical to a temperate environmental gradient of ca.1400 km in
 southern Japan with abundance-weighted trait expression to assess how
 trait complexity changes with increasing latitude. LocationRyukyu Islands
 and southern Pacific coast of Japan TaxonReef fish MethodsWe tested for
 shifts in trait space and functional redundancy, based on five
 morphological, life history, and behavioural traits: maximum length,
 pelagic larval duration, trophic level, substrate preference, and
 reproductive mode. Our trait database was coded with two approaches,
 first, by attributing a single value to each trait per species, and
 second, by fuzzy coding that allows more than one value per trait and
 hence considers some intraspecific trait variation. ResultsWe found a
 reduction in specialist habitat traits (coral substrate preference,
 nesters, herbivores) and an increase in generalist traits (predators) with
 increasing latitude, along with a contraction in trait space from tropical
 to temperate reefs. Functional redundancy declined with increasing
 latitude. These trends were closely linked with latitudinal gradients in
 temperature, along with changes in other environmental factors such as
 turbidity and photosynthetically active radiation. Main
 ConclusionFunctional turnover and contractions are thus likely due to the
 marginal conditions for coral-associated fishes at higher latitudes,
 favouring generalist species, whereas increased resources at lower
 latitudes favour high redundancy and niche partitioning. Accounting for
 intraspecific trait variation indicated the same trends but highlighted
 increased functional vulnerability across all sites. We show that trait
 complexity in coral-associated fish communities decreases from tropical to
 temperate reefs, highlighting the reduced functional scope that comes with
 marginal environmental conditions.
description: <strong>Study sites & data
 collection</strong><br>Visual census fish surveys were carried
 out at 31 sites along the Pacific coast of Japan, located between
 24<sup>o</sup> and 35<sup>o</sup> northern
 latitude, with climates ranging from tropical to temperate. This thermal
 gradient creates several areas with different environmental properties
 which were clustered into regions: tropical, warm subtropical, cold
 subtropical and warm temperate. Surveys were carried out along
 belt-transects (25m x 5m) in coral habitat, at a standardised depth of
 8-12m during the northern summers in 2015 for all sites except sites
 20-31, which were surveyed in 2016. At our most northern site (Tateyama),
 surveys were conducted at 3m depth as the coral habitat did not extend to
 deeper depths. We recorded individual fish lengths estimated to the
 nearest cm of all target species along the transects, whilst swimming
 along 5 replicate transects per site. The abundance of each species was
 counted visually and standardised using log(1+x) to meet normality
 assumptions. <strong>Fuzzy set
 theory</strong><br>Unlike traditional trait-based approaches,
 the fuzzy coding method allows species to be placed in more than one
 category per trait to account for uncertainty in ecological
 characteristics (Chevene et al., 1994; Cheung et al., 2005; Jones and
 Cheung, 2018), and some degree of intraspecific trait variation. For
 example, it is difficult to know whether a fish species is of medium or
 large size, as size may vary with environment or habitat. Cheung et al.
 (2005) therefore used fuzzy set theory when describing the maximum length
 of fish, allowing fish species to be placed in more than one category,
 whereby in some communities a species is classed as a medium fish and as a
 large fish in others, with the degree of membership to each category
 (i.e., small, medium or large) defined by relative abundance. For example,
 a fish species with a maximum size of 68 cm can be classified as large or
 medium, with a degree of membership of 0.7 (large) and 0.3 (medium),
 therefore within 70% of hypothetical populations the species is classed as
 large but in the other 30%, it is medium (Cheung et al., 2005). Here, we
 used this fuzzy approach such that fishes whose traits vary within a
 species could be placed into several categories for the same
 trait. <strong>Species
 Traits</strong><br>Species traits were compiled from the
 primary literature and FishBase (Froese and Pauly, 2021). Five traits were
 selected to describe the morphological, behavioural, and biological
 functional niches of the reef fish species surveyed (Brandl et al., 2019;
 Miller et al., 2023). Two different trait databases were created from the
 trait information: a categorical single trait value database, and a
 fuzzy-coded trait database. The categorical single-trait database followed
 traditional trait-based techniques and allowed for one value per trait per
 species. These values were obtained from FishBase, where the mean
 (numerical traits) or the dominant reported value (categorical traits)
 were assigned (Cook et al., 2022; Anderson et al., 2022; Clay et al.,
 2023; Miller et al., 2023). Traits for the categorical trait database
 included two numerical (maximum length and pelagic larval duration (PLD))
 and three categorical (trophic level, substrate preference, and
 reproductive method) data formats. The maximum length and PLD were
 assigned to four categories to make them comparable to the fuzzy database.
 The fuzzy trait database applied the same categories as the categorical
 database but allowed species traits to be placed in more than one category
 (Chevene et al., 1994, Cheung et al., 2005, Jones and Cheung, 2018).
 Values for the fuzzy database were obtained from FishBase (Froese and
 Pauly, 2021) and other literature (Craig, 1996; Shibukawa and Suzuki,
 2002; Wilson et al., 2008), capturing a range of trait values per species.
 Each trait value was assigned a weighting between 0 and 3, relating to the
 affinity of the species for the trait value, where 0 indicated no affinity
 and 3 complete affinity. These were then standardised so that the sum of
 each trait was equal to 1. These weightings were assigned depending on the
 abundance of the trait value within the literature and thus were not
 site-specific, e.g., where a secondary trait value was available, the most
 dominant reported value was assigned a 2, and the secondary value 1. This
 strategy allowed for some intraspecific variability along the temperature
 gradient in response to different environmental pressures to be estimated
 based on abundance-weighted trait expression.  
 <strong>Community Weighted Means</strong><br>To
 calculate community weighted means (CWM) a site-by-species abundance and
 species-by-trait matrices were combined through the “functcomp” function
 from the “FD” package in R (Laliberté et al., 2014). For categorical data,
 the CWM represents the abundance of each trait at each site (Lavorel et
 al., 2008). 
 <strong>References</strong><br>Anderson, L.,
 McLean, M., Houk, P., Graham, C., Kanemoto, K., Terk, E., McLeod, E. and
 Beger, M. 2022. Decoupling linked coral and fish trait structure. Marine
 Ecology Progress Series. 689, pp.19–32. Brandl, S.J.,
 Rasher, D.B., Côté, I.M., Casey, J.M., Darling, E.S., Lefcheck, J.S. and
 Duffy, J.E. 2019. Coral reef ecosystem functioning: eight core processes
 and the role of biodiversity. Frontiers in Ecology and the Environment.
 17(8), pp.445–454. Cheung, W.W.L., Pitcher, T.J. and
 Pauly, D. 2005. A fuzzy logic expert system to estimate intrinsic
 extinction vulnerabilities of marine fishes to fishing. Biological
 Conservation. 124(1), pp.97–111. Chevene, F., DolÉAdec,
 S. and Chessel, D. 1994. A fuzzy coding approach for the analysis of
 long-term ecological data. Freshwater Biology. 31(3),
 pp.295–309. Clay, C.G., Reimer, J.D., Cook, K.M.,
 Yamagiwa, H., Gravener, E., Theodora, L.H.Y. and Beger, M. 2023. Temporal
 functional changes in coral and fish communities on subtropical coastal
 coral reefs. Marine and Freshwater Research. Cook,
 K.M., Yamagiwa, H., Beger, M., Masucci, G.D., Ross, S., Lee, H.Y.T.,
 Stuart‐Smith, R.D. and Reimer, J.D. 2022. A community and functional
 comparison of coral and reef fish assemblages between four decades of
 coastal urbanisation and thermal stress. Ecology and Evolution. 12(3),
 p.e8736. Craig, P. 1996. Intertidal territoriality and
 time-budget of the surgeonfish, Acanthurus lineatus, in American Samoa.
 Environmental biology of fishes. 46, pp.27–36. Froese,
 R. and Pauly, D. 2021. FishBase. Jones, M.C. and
 Cheung, W.W.L. 2018. Using fuzzy logic to determine the vulnerability of
 marine species to climate change. Global change biology. 24(2),
 pp.e719–e731. Laliberté, E., Legendre, P., Shipley, B.
 and Laliberté, M.E. 2014. Package ‘FD’. Measuring functional diversity
 from multiple traits, and other tools for functional ecology.
 Lavorel, S., Grigulis, K., McIntyre, S., Williams, N.S.G.,
 Garden, D., Dorrough, J., Berman, S., Quétier, F., Thébault, A. and Bonis,
 A. 2008. Assessing functional diversity in the field–methodology matters!
 Functional Ecology. 22(1), pp.134–147. Miller, M.,
 Reimer, J.D., Cook, K.M., Pandolfi, J.M., Sommer, B., Obuchi, M. and
 Beger, M. 2023. Temperate functional niche availability not
 resident-invader competition shapes tropicalisation in reef fishes. Nature
 communications. Shibukawa, K. and Suzuki, T. 2002.
 Asterropteryx atripes, a new gobiid fish from the Western Pacific Ocean
 (Perciformes: Gobioidei). Ichthyological Research. 49,
 pp.274–280. Wilson, S.K., Burgess, S.C., Cheal, A.J.,
 Emslie, M., Fisher, R., Miller, I., Polunin, N.V.C. and Sweatman, H.P.A.
 2008. Habitat utilization by coral reef fish: implications for specialists
 vs. generalists in a changing environment. Journal of Animal Ecology.,
 pp.220–228.
description: All data files can be opened in Excel. 
description: # Title of Dataset: Variation in functional composition of reef fishes
 along a tropical-to-temperate gradient --- This file contains the data
 used to evaluate changes in the trait composition of coral-associated fish
 communities along a tropical to a temperate environmental gradient of
 ca.1400 km in southern Japan with abundance-weighted trait expression to
 assess how trait complexity changes with increasing latitude. Our trait
 database was coded with two approaches, first, by attributing a single
 value to each trait per species, and second, by fuzzy coding that allows
 more than one value per trait and hence considers some intraspecific trait
 variation. ## Description of the Data and file structure The csv file
 titled "JAPAN_JBI_LatitudinalGradient_key" contains the trait
 abreviations key and explains the codes used throughout the other files.
 The csv file titled
 "JAPAN_JBI_LatitudinalGradient_CategoricalApproach_TraitDatabase" contains the categorial approach trait values for each species in the study (i.e. one trait value per category per species). The first column contains the 394 reef fish species latin names. The maximum length column indicates which max length category the species is in, where 1 = Si1, 2 = Si2, 3 = Si3, 4 = Si4. The PLD (pelagic larval duration) column indicates the PLD category for each species, where 1 = Pld1, 2 = Pld2, 3 = Pld3, 4 = Pld4. The TrophicLevel column indicates which trophic category each species belongs to (see key.csv for coding). The Substrate column indicates which substrate category each species is in (see key.csv for coding) and the reproduction column indicates which category of reproductive strategy each species belongs to (see key.csv for coding). NULL refers to missing data or NA's. The csv file titled "JAPAN_JBI_LatitundinalGradient_FuzzyApproach_TraitDatabase" contains the fuzzy approach trait values for each species in the study (i.e. multiple trait value per category per species). The first column contains the 394 reef fish species latin names. The remaining columns realte to the fuzzy coding value for each trait (see key.csv for coding). Each trait value was assigned a weighting between 0 and 3, relating to the affinity of the species for the trait value, where 0 indicated no affinity and 3 complete affinity. These were then standardised so that the sum of each trait was equal to 1. These weightings were assigned depending on the abundance of the trait value within the literature and thus were not site-specific, e.g., where a secondary trait value was available, the most dominant reported value was assigned a 2, and the secondary value 1. NULL refers to missing data or NA's. The csv file titled "JAPAN_JBI_LatitudinalGradient_CategoricalApproach_CWM" contains the community weighted mean (CWM) values for each categorical trait value for each of the 31 sites along the Pacific coast of Japan. The first column indicates the site ID, the second relates to which evironmental cluster the site was clustered into. The third and fourth columns are the latutude and longitude of each site. The rest of the columns realte to specific traits. The CWM in this file were obtained by combing the categorical trait database with the species abundances per site (Fish abundance and raw survey data are subject to controlled access to protect the novelty of collaborative papers still in preparation but are available from Maria Beger ([m.beger@leeds.ac.uk](mailto:m.beger@leeds.ac.uk)) upon request. ) The csv file titled "JAPAN_JBI_LatitudinalGradient_FuzzyApproach_CWM" contains the community weighted mean (CWM) values for each categorical trait value for each of the 31 sites along the Pacific coast of Japan. The first column indicates the site ID, the second relates to which evironmental cluster the site was clustered into. The third and fourth columns are the latutude and longitude of each site. The rest of the columns realte to specific traits. The CWM in this file were obtained by combing the fuzzy trait database with the species abundances per site (Fish abundance and raw survey data are subject to controlled access to protect the novelty of collaborative papers still in preparation but are available from Maria Beger ([m.beger@leeds.ac.uk](mailto:m.beger@leeds.ac.uk)) upon request. ) ## Sharing/access Information The data can be downloaded from this link: Was data derived from another source? yes, list source(s): Trait values were obtained from : * Froese, R. and Pauly, D. 2021. FishBase. * Craig, P. 1996. Intertidal territoriality and time-budget of the surgeonfish, Acanthurus lineatus, in American Samoa. Environmental biology of fishes. 46, pp.2736. * Shibukawa, K. and Suzuki, T. 2002. Asterropteryx atripes, a new gobiid fish from the Western Pacific Ocean (Perciformes: Gobioidei). Ichthyological Research. 49, pp.274280. * Wilson, S.K., Burgess, S.C., Cheal, A.J., Emslie, M., Fisher, R., Miller, I., Polunin, N.V.C. and Sweatman, H.P.A. 2008. Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment. Journal of Animal Ecology., pp.220228.