Neotropics as a Cradle for Adaptive Radiations.

Neotropical ecosystems are renowned for numerous examples of adaptive radiation in both plants and animals resulting in high levels of biodiversity and endemism. However, we still lack a comprehensive review of the abiotic and biotic factors that contribute to these adaptive radiations. To fill this gap, we delve into the geological history of the region, including the role of tectonic events such as the Andean uplift, the formation of the Isthmus of Panama, and the emergence of the Guiana and Brazilian Shields. We also explore the role of ecological opportunities created by the emergence of new habitats, as well as the role of key innovations, such as novel feeding strategies or reproductive mechanisms. We discuss different examples of adaptive radiation, including classic ones like Darwin's finches and Anolis lizards, and more recent ones like bromeliads and lupines. Finally, we propose new examples of adaptive radiations mediated by ecological interactions in their geological context. By doing so, we provide insights into the complex interplay of factors that contributed to the remarkable diversity of life in the Neotropics and highlight the importance of this region in understanding the origins of biodiversity.

Leaf metabolic traits reveal hidden dimensions of plant form and function.

The metabolome is the biochemical basis of plant form and function, but we know little about its macroecological variation across the plant kingdom. Here, we used the plant functional trait concept to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five metabolic functional traits reveals that plants vary on two major axes of leaf metabolic specialization-a leaf chemical defense spectrum and an expression of leaf longevity. Axes are similar for tropical and temperate species, with many trait combinations being viable. However, metabolic traits vary orthogonally to life-history strategies described by widely used functional traits. The metabolome thus expands the functional trait concept by providing additional axes of metabolic specialization for examining plant form and function.

Diversity and divergence: evolution of secondary metabolism in the tropical tree genus Inga.

Plants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. We explore the evolutionary patterns and processes by which plants generate chemical diversity, from evolving novel compounds to unique chemical profiles. We characterized the chemical profile of one-third of the species of tropical rainforest trees in the genus Inga (c. 100, Fabaceae) using ultraperformance liquid chromatography-mass spectrometry-based metabolomics and applied phylogenetic comparative methods to understand the mode of chemical evolution. We show: each Inga species contain structurally unrelated compounds and high levels of phytochemical diversity; closely related species have divergent chemical profiles, with individual compounds, compound classes, and chemical profiles showing little-to-no phylogenetic signal; at the evolutionary time scale, a species' chemical profile shows a signature of divergent adaptation. At the ecological time scale, sympatric species were the most divergent, implying it is also advantageous to maintain a unique chemical profile from community members; finally, we integrate these patterns with a model for how chemical diversity evolves. Taken together, these results show that phytochemical diversity and divergence are fundamental to the ecology and evolution of plants.

Accelerating the discovery of rare tree species in Amazonian forests: integrating long monitoring tree plot data with metabolomics and phylogenetics for the description of a new species in the hyperdiverse genus Inga Mill.

In species-rich regions and highly speciose genera, the need for species identification and taxonomic recognition has led to the development of emergent technologies. Here, we combine long-term plot data with untargated metabolomics, and morphological and phylogenetic data to describe a new rare species in the hyperdiverse genus of trees Inga Mill. Our combined data show that Inga coleyana is a new lineage splitting from their closest relatives I. coruscans and I. cylindrica. Moreover, analyses of the chemical defensive profile demonstrate that I. coleyana has a very distinctive chemistry from their closest relatives, with I. coleyana having a chemistry based on saponins and I. cylindrica and I. coruscans producing a series of dihydroflavonols in addition to saponins. Finally, data from our network of plots suggest that I. coleyana is a rare and probably endemic taxon in the hyper-diverse genus Inga. Thus, the synergy produced by different approaches, such as long-term plot data and metabolomics, could accelerate taxonomic recognition in challenging tropical biomes.

Herbivores as drivers of negative density dependence in tropical forest saplings.

Ecological theory predicts that the high local diversity observed in tropical forests is maintained by negative density-dependent interactions within and between closely related plant species. By using long-term data on tree growth and survival for coexisting Inga (Fabaceae, Mimosoideae) congeners, we tested two mechanisms thought to underlie negative density dependence (NDD): competition for resources and attack by herbivores. We quantified the similarity of neighbors in terms of key ecological traits that mediate these interactions, as well as the similarity of herbivore communities. We show that phytochemical similarity and shared herbivore communities are associated with decreased growth and survival at the sapling stage, a key bottleneck in the life cycle of tropical trees. None of the traits associated with resource acquisition affect plant performance, indicating that competition between neighbors may not shape local tree diversity. These results suggest that herbivore pressure is the primary mechanism driving NDD at the sapling stage.

Physical, but not chemical, antiherbivore defense expression is related to the clustered spatial distribution of tropical trees in an Amazonian forest.

The conspecific negative density dependence hypothesis states that mortality of young trees (seedlings and saplings) is higher near conspecific adults due to mechanisms such as allelopathy, intraspecific competition, and pest facilitation, explaining why in the tropics, most of plant species tend to be rare and live dispersed. However, there are some tree species that defy this expectation and grow in large clusters of conspecific juveniles and adults. We hypothesize that conspecifics living in clusters show higher and/or more variable defensive profiles than conspecifics with dispersed distributions.We evaluated our hypothesis by assessing the expression of physical leaf traits (thickness, and the resistance to punch, tear and shear) and leaf chemical defenses for six clustered and six non-clustered tree species in Yasuní National Park, Ecuadorian Amazon. We ask ourselves whether (a) clustered species have leaves with higher physical resistance to damage and more chemical defenses variability than non-clustered species; (b) saplings of clustered species may show higher physical resistance to damage and higher variation on chemical leaf defenses than their conspecific adults, and (c) saplings of non-clustered species show lower resistance to physical damage and lower variation in chemical defenses compared to conspecific adults.Overall, our study did not support any of our hypotheses. Remarkably, we found that soluble metabolites were significantly species-specific.Our study suggests that plants physical but not chemical leaf antiherbivore defenses may be a crucial strategy for explaining survivorship of clustered species. Trees in Yasuní may also fall along a suite of tolerance/escape/defense strategies based on limitations of each species physiological constraints for survival and establishment. We conclude that other mechanisms, such as those related to indirect defenses, soil nutrient exploitation efficiency, volatile organic compounds, delayed leaf-greening, and seed dispersal mechanisms, shall be evaluated to understand conspecific coexistence in this forest.

Tracking of Host Defenses and Phylogeny During the Radiation of Neotropical Inga-Feeding Sawflies (Hymenoptera; Argidae).

Coevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny in the evolution of host range and species divergence in leaf-feeding sawflies of the family Argidae associated with Neotropical trees in the genus Inga throughout the Amazon, the Guiana Shield and Panama. Our analyses show that the phylogenies of both the sawfly herbivores and their Inga hosts are congruent, and that sawflies radiated at approximately the same time, or more recently than their Inga hosts. Analyses controlling for phylogenetic effects show that the evolution of host use in the sawflies associated with Inga is better correlated with Inga chemistry than with Inga phylogeny, suggesting a pattern of delayed host tracking closely tied to host chemistry. Finally, phylogenetic analyses show that sister species of Inga-sawflies are dispersed across the Neotropics, suggesting a role for allopatric divergence and vicariance in Inga diversification. These results are consistent with the idea that host defensive traits play a key role not only in structuring the herbivore assemblages at a single site, but also in the processes shaping host association and species divergence at a regional scale.

Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study.

The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.

Consequences of interspecific variation in defenses and herbivore host choice for the ecology and evolution of Inga, a speciose rainforest tree.

We summarize work on a speciose Neotropical tree genus, Inga (Fabaceae), examining how interspecific variation in anti-herbivore defenses may have evolved, how defenses shape host choice by herbivores and how they might regulate community composition and influence species radiations. Defenses of expanding leaves include secondary metabolites, extrafloral nectaries, rapid leaf expansion, trichomes, and synchrony and timing of leaf production. These six classes of defenses are orthogonal, supporting independent evolutionary trajectories. Moreover, only trichomes show a phylogenetic signature, suggesting evolutionary lability in nearly all defenses. The interspecific diversity in secondary metabolite profiles does not arise from the evolution of novel compounds, but from novel combinations of common compounds, presumably due to changes in gene regulation. Herbivore host choice is determined by plant defensive traits, not host phylogeny. Neighboring plants escape each other's pests if their defenses differ enough, thereby enforcing the high local diversity typical of tropical forests. Related herbivores feed on hosts with similar defenses, implying that there are phylogenetic constraints placed on the herbivore traits that are associated with host use. Divergence in defensive traits among Inga appears to be driven by herbivore pressure. However, the lack of congruence between herbivore and host phylogeny suggests that herbivores are tracking defenses, choosing hosts based on traits for which they already have adaptations. There is, therefore, an asymmetry in the host-herbivore evolutionary arms race.

Coevolutionary arms race versus host defense chase in a tropical herbivore-plant system.

Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus Inga and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between Inga species was correlated with similarity in defenses. There was no correlation with phylogeny, a result consistent with our observations that the expression of defenses in Inga is independent of phylogeny. Furthermore, host defensive traits explained 40% of herbivore community similarity. Analyses at finer taxonomic scales showed that different lepidopteran clades select hosts based on different defenses, suggesting taxon-specific histories of herbivore-host plant interactions. Finally, we compared the phylogeny and defenses of Inga to phylogenies for the major lepidopteran clades. We found that closely related herbivores fed on Inga with similar defenses rather than on closely related plants. Together, these results suggest that plant defenses might be more evolutionarily labile than the herbivore traits related to host association. Hence, there is an apparent asymmetry in the evolutionary interactions between Inga and its herbivores. Although plants may evolve under selection by herbivores, we hypothesize that herbivores may not show coevolutionary adaptations, but instead "chase" hosts based on the herbivore's own traits at the time that they encounter a new host, a pattern more consistent with resource tracking than with the arms race model of coevolution.

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

Trait-based community assembly of understory palms along a soil nutrient gradient in a lower montane tropical forest.

Two opposing niche processes have been shown to shape the relationship between ecological traits and species distribution patterns: habitat filtering and competitive exclusion. Habitat filtering is expected to select for similar traits among coexisting species that share similar habitat conditions, whereas competitive exclusion is expected to limit the ecological similarity of coexisting species leading to trait differentiation. Here, we explore how functional traits vary among 19 understory palm species that differ in their distribution across a gradient of soil resource availability in lower montane forest in western Panama. We found evidence that habitat filtering influences species distribution patterns and shifts community-wide and intraspecific trait values. Differences in trait values among sites were more strongly related to soil nutrient availability than to variation in light or rainfall. Soil nutrient availability explained a significant amount of variation in site mean trait values for 4 of 15 functional traits. Site mean values of leaf nitrogen and phosphorus increased 37 and 64%, respectively, leaf carbon:nitrogen decreased 38%, and specific leaf area increased 29% with increasing soil nutrient availability. For Geonoma cuneata, the only species occurring at all sites, leaf phosphorus increased 34% and nitrogen:phosphorus decreased 42% with increasing soil nutrients. In addition to among-site variation, most morphological and leaf nutrient traits differed among coexisting species within sites, suggesting these traits may be important for niche differentiation. Hence, a combination of habitat filtering due to turnover in species composition and intraspecific variation along a soil nutrient gradient and site-specific niche differentiation among co-occurring species influences understory palm community structure in this lower montane forest.