Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

Understanding species' roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator-prey interactions in highly diverse ecosystems.Peer reviewe

Restoring the reef: Coral restoration yields rapid impacts on certain fish assemblages

International audienceCoral reefs harbor one of the highest biodiversity on Earth but increasing disturbances have often led to rapid shifts from coral to algal states, prompting the development of conservation methods, including coral restoration. While most studies have focused on the medium and long-term effects of restoration on fish assemblages, less is known about its short-term effects (i.e., within one month) on associated communities. This study explored the short-term impacts (<1 month) of coral restoration, including four restoration conditions, on fish abundance, diversity, and assemblages in a marine educational area (a small coastal area managed by a scholl in the frame of an eco-citizen pedagogical program) in Bora, French Polynesia. Sixteen dead reef patches previously covered by macroalgae were grouped into four conditions as follows: four were non-restored (control condition), four were restored to 25% living coral cover (condition 25%), four to 50% living coral cover (condition 50%), and four were restored to 75% living coral cover (condition 75%). The abundance of fish at adult and juvenile stages was assessed, before and after coral restoration, using the fixed-point method for a period of 5 min on each of the 16 reef patches. Two successive observation periods were conducted for each patch: one focusing on more visible and mobile fish, and another on more cryptic species. Surveys were conducted one day and three days prior to restoration, and then 24 days and 28 days post-restoration. For adults, the difference in abundance, number of species, and diversity before and after restoration were not significant between the conditions. Similarly, for juveniles, no significant differences were observed when considering the conditions and restoration. Before restoration, the fish assemblages were randomly distributed between the four conditions for both adults and juveniles. After the restoration, the inter-conditions similarity decreased significantly for adults, but not for juveniles. Some species were associated with the more restored patches (Chaetodon citrinellus, Halichoeres trimaculatus, and Zanclus cornutus). Finaly, the restoration seemed to have variable effects depending on the trophic groups. Coral restoration has short-term effects on fish assemblages, indicating the effectiveness of restoration efforts even within a brief period. These rapid changes underscore the remarkable ability of adult fish to adapt to rapidly changing environments

Mesophotic depths hide high coral cover communities in French Polynesia

The rapid decline of shallow coral reefs has increased the interest in the long-understudied mesophotic coral ecosystems (MCEs). However, MCEs are usually characterised by rather low to moderate scleractinian coral cover, with only a few descriptions of high coral cover at depth. Here, we explored eight islands across French Polynesia over a wide depth range (6 to 120 m) to identify coral cover hotspots at mesophotic depths and the co-occurrent biotic groups and abiotic factors that influence such high scleractinian cover. Using Bayesian modelling, we found that 20 out of 64 of studied deep sites exhibited a coral cover higher than expected in the mesophotic range (e.g. as high as 81.8 % at 40 m, 74.5 % at 60 m, 53 % at 90 m and 42 % at 120 m vs the average expected values based on the model of 31.2 % at 40 m, 22.8 % at 60 m, 14.6 % at 90 m and 9.8 % at 120 m). Omitting the collinear factors light-irradiance and depth, these ‘hotspots’ of coral cover corresponded to mesophotic sites and depths characterised by hard substrate, a steep to moderate slope, and the dominance of laminar corals. Our work unveils the presence of unexpectedly and unique high coral cover communities at mesophotic depths in French Polynesia, highlighting the importance of expanding the research on deeper depths for the potential relevance in the conservation management of tropical coral reefs

Scaling up calcification, respiration, and photosynthesis rates of six prominent coral taxa

Coral reefs provide a range of important services to humanity, which are underpinned by community-level ecological processes such as coral calcification. Estimating these processes relies on our knowledge of individual physiological rates and species-specific abundances in the field. For colonial animals such as reef-building corals, abundance is frequently expressed as the relative surface cover of coral colonies, a metric that does not account for demographic parameters such as coral size. This may be problematic because many physiological rates are directly related to organism size, and failure to account for linear scaling patterns may skew estimates of ecosystem functioning. In the present study, we characterize the scaling of three physiological rates — calcification, respiration, and photosynthesis — considering the colony size for six prominent, reef-building coral taxa in Mo'orea, French Polynesia. After a seven-day acclimation period in the laboratory, we quantified coral physiological rates for three hours during daylight (i.e., calcification and gross photosynthesis) and one hour during night light conditions (i.e., dark respiration). Our results indicate that area-specific calcification rates are higher for smaller colonies across all taxa. However, photosynthesis and respiration rates remain constant over the colony-size gradient. Furthermore, we revealed a correlation between the demographic dynamics of coral genera and the ratio between net primary production and calcification rates. Therefore, intraspecific scaling of reef-building coral physiology not only improves our understanding of community-level coral reef functioning but it may also explain species-specific responses to disturbances