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Abstract The structure and dynamics of forest ecosystems are the outcome of differential performance playing out at the individual level. Interactions between the traits of an organism and its environment determine performance. Thus, our ability to understand and, ultimately, model forest dynamics critically relies on knowledge regarding the functional biology of the organisms. In tropical forests, this is a daunting challenge due to the diversity of the systems. This has driven ecologists to focus on identifying a handful of fundamentally important trade‐offs and a few traits that may indicate where a species falls along that trade‐off axis. In other cases, some ecologists have argued that species can be roughly binned into a handful of functional groups or guilds that capture most of the information needed to generate realistic models of forest dynamics. Here, we discuss the functional biology of tropical forest dynamics. We identify a series of key trade‐offs that should underpin forest dynamics and the traits ecologists have attempted to link to these trade‐offs. We then explore how far we can get by using functional groups or guilds to model tropical forest dynamics, the conceptual frameworks used for promoting such approaches, and what this modeling framework does not capture. We then use this to identify key gaps that should motivate the future of tropical tree functional ecology. 

Abstract Tropical tree communities are among the most diverse in the world. A small number of genera often disproportionately contribute to this diversity. How so many species from a single genus can co‐occur represents a major outstanding question in biology. Niche differences are likely to play a major role in promoting congeneric diversity, but the mechanisms of interest are often not well‐characterized by the set of functional traits generally measured by ecologists.To address this knowledge gap, we used a functional genomic approach to investigate the mechanisms of co‐occurrence in the hyper‐diverse genusFicus. Our study focused on over 800 genes related to drought and defence, providing detailed information on how these genes may contribute to the diversity ofFicusspecies.We find widespread and consistent evidence of the importance of defence gene dissimilarity in co‐occurring species, providing genetic support for what would be expected under the Janzen‐Connell mechanism. We also find that drought‐related gene sequence similarity is related toFicusco‐occurrence, indicating that similar responses to drought promote co‐occurrence.Synthesis. We provide the first detailed functional genomic evidence of how drought‐ and defence‐related genes simultaneously contribute to the local co‐occurrence in a hyper‐diverse genus. Our results demonstrate the potential of community transcriptomics to identify the drivers of species co‐occurrence in hyper‐diverse tropical tree genera. 

Abstract Metabolomics provides an unprecedented window into diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying species coexistence. Here, we used untargeted metabolomics to evaluate chemical composition of 358 tree species and its relationship with phylogeny and variation in light environment, soil nutrients, and insect herbivore leaf damage in a tropical rainforest plot. We report no phylogenetic signal in most compound classes, indicating rapid diversification in tree metabolomes. We found that locally co‐occurring species were more chemically dissimilar than random and that local chemical dispersion and metabolite diversity were associated with lower herbivory, especially that of specialist insect herbivores. Our results highlight the role of secondary metabolites in mediating plant–herbivore interactions and their potential to facilitate niche differentiation in a manner that contributes to species coexistence. Furthermore, our findings suggest that specialist herbivore pressure is an important mechanism promoting phytochemical diversity in tropical forests. 

Abstract Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity are key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of 20 co-occurring forest trees species from genera including Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, and Ulmus sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant–pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies. 

Abstract Forest tree communities are largely structured by interactions between phenotypes and their environments. Functional traits have been popularized as providing key insights into plant functional tradeoffs. Similarly, tree crown—stem diameter and tree height—stem diameter allometric relationships are likely to be strongly coordinated with functional trait tradeoff axes. Specifically, species with functional traits indicative of conservative strategies (i.e., dense wood, heavy seeds) should be related to tree architectures that have lower heights and wider crowns for a given stem diameter. For example, shade‐tolerant species in tropical forests are typically characterized as having dense wood, large seeds, and relatively broad crowns at early ontogenetic stages. Here, we focus on 14 dominant dicot tree species in a tropical forest. We utilized hierarchical Bayesian models to characterize species‐specific height and crown size allometric parameters. We sampled from the posterior distributions for these parameters and correlated them with six functional traits. We also characterize the expected height and crown size for a series of reference stem diameters to quantify the relationship between traits and tree architecture across size classes. We find little interspecific variation in allometric slopes, but clear variation in allometric intercepts. Allometeric height intercepts were negatively correlated with wood density and crown size intercepts were positively related to wood density and seed mass and negatively related to leaf percent phosphorus. Thus, interspecific variation in tree architecture is generated by interspecific variation in allometric intercepts and not slopes. These intercepts could be predicted using a handful of functional traits where conservative traits were indicative of trees that are relatively short and have larger crown sizes. This demonstrates a coordination of tropical tree life histories that can be characterized simultaneously with functional traits and tree allometries. 

SUMMARY Maples (the genusAcer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. AmongAcerspecies, several stand out in their importance to economic interest. Here we report the first two chromosome‐scale genomes for North American species,Acer negundoandAcer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, withA. negundoat a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, andA. saccharumat a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, thoughA. saccharumhas local gene duplication and more recent bursts of transposable elements, as well as a large‐scale translocation between two chromosomes. Genomic comparison revealed thatA. negundohas a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained fromA. saccharumgiven long‐term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.