Trophic innovations fuel reef fish diversification

Siqueira, Alexandre C.; Morais, Renato A.; Bellwood, David R.; Cowman, Peter F.

doi:10.1038/s41467-020-16498-w

Cited by 67 publications

(92 citation statements)

References 89 publications

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“…Our findings add to recent evidence that evolutionary history (i.e., phylogenetic relatedness) is essential to evaluate the ecological traits of fishes (c.f. [ 86 – 88 ]). Recently, taxonomy and body size have been revealed as important predictors of fish diet composition and size structure [ 89 , 90 ], and in the highest resolution analyses of coral reef fish diet, taxonomic family was a better predictor of fish diet than broad trophic guilds [ 83 ].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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“…In recent years, we have gained an increasingly clear picture of the phylogenetic relationships among coral reef fishes through the pursuit of densely sampled species phylogenies for diverse reef fish families (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). By combining species-rich phylogenies with rich data layers of functional and ecological traits, significant advances have been made in our understanding of the diversification of fish lineages in coral reef ecosystems (14)(15)(16)(17)(18)(19)(20)(21)(22). The project presented here aims to enhance the species richness present in the phylogeny of the reef fish family Pomacentridae and examine the evolutionary history of key structural and ecological traits of the damselfishes, with a focus on the transitions in body size and dietary ecotype throughout pomacentrid diversification.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of the Damselfishes (Pomacentridae) and Patterns of Asymmetrical Diversification in Body Size and Feeding Ecology

McCord

Nash

Cooper

et al. 2021

Preprint

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The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages with ecological and economic importance for coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 330 of the 422 damselfish species. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships and the monophyly of genera, including Chromis, Chrysiptera, Parma and Stegastes. A time-calibrated phylogenetic tree scaled using fossil data and recent estimated ovalentarian clade ages, yields an older root age for the family (55.3 mya) than previously proposed, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 30 times and with asymmetric rates of transition. We tested the hypothesis that transitions among three dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that dietary ecotype is significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between a small number of feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific.

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“…TACT is similar to another two-stage approach known as PASTIS (Thomas et al, 2013), which was used in previous studies to provide large-scale trees of several taxa, including birds (Jetz et al, 2012), squamates (Tonini et al, 2016), and sigmodontine rodents (Maestri et al, 2017). The main advantage of TACT in relation to PASTIS is that it provides branch lengths based on local diversification rates, as opposed to global rates, thus being more suitable for large phylogenies with heterogeneous rate regimes (Rabosky et al, 2018;Chang et al, 2020;Siqueira et al, 2020). Our backbone trees were obtained by combining information on 252 mitogenomes and 177 COI sequences available on GenBank and BOL (Table S1).…”

Section: Methodsmentioning

confidence: 99%

The diversification of termites: inferences from a complete species-level phylogeny

Pie

Caron

Carrijo

2020

Preprint

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Termites play a major role in a variety of ecological processes in tropical and subtropical biomes worldwide, such as decomposition, soil formation and aeration, and nutrient cycling. These important ecosystem services were achieved through their highly complex societies and remarkable adaptations, including the evolution of sterile worker castes, the acquisition of endosymbionts, and the capacity for extensive environmental engineering, yet the causes and consequences of their ecological success are still poorly understood. The goals of our study were (1) to provide the first complete, species-level phylogeny of all currently recognized termite species by integrating the available genetic and taxonomic data, as well as methods of phylogenetic imputation and divergence time estimation; and (2) to explore variation in speciation rates among termite lineages. We provide the inferred relationships as a set of 1,000 pseudo-posterior trees, which can be used in future comparative analyses. We demonstrate that speciation rates have been relatively constant throughout the history of termites, with two positive shifts in speciation rates: one at their origin of Euisoptera and the other concordant with evolution of Termitidae. On the other hand, there was no obvious trend towards deceleration in speciation rates for termites as a whole, nor within the most species-rich families. The provided trees might represent a valuable resource for termite comparative studies by summarizing the available phylogenetic information, while accounting for uncertainty in the inferred topologies.

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Trophic innovations fuel reef fish diversification

Cited by 67 publications

References 89 publications

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

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

Phylogeny of the Damselfishes (Pomacentridae) and Patterns of Asymmetrical Diversification in Body Size and Feeding Ecology

The diversification of termites: inferences from a complete species-level phylogeny

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