Phylogenetic Analyses of Andean and Amazonian Tree Communities in Ecuador

The forests of Ecuador are known for their high levels of diversity and endemism, classifying the country as a biodiversity hotspot. Both the western Amazon and Andean montane forests are richly populated with tropical tree species that have been little studied in a community phylogenetic context. The implementation of elevational transects and trait based analyses having proven useful in gaining a better understanding ofhow environmental factors are affecting the tree community structure in these habitats. The goal of this research was to evaluate the magnitude ofDNA barcode diversity among Amazonian and Andean tree species. Specifically, the objectives were to (1) evaluate community phylogenetic structure and correlate phylogenetic analyses with diversity metrics among Andean tree species along an elevational gradient at Siempre Verde Reserve, Ecuador, and to (2) construct a tropical tree community phylogeny using DNA barcodes and to test for phylogenetic signal in the occurrence of phytochemicals among tree species within Yasuni National Park, Ecuador. In the montane forest at Siempre Verde, 595 individuals were tagged, collected and identified, comprising 36 families, 53 genera, and 88 species. Analyses revealed that species richness was decreasing with elevation but the number of stems of common species was increasing causing phylogenetic clumping at higher elevations. Evidence implies that habitat filtering of species due to cloud inundation is behind this observed pattern contributing to the community structure. In the upland Amazonian forest of Yasuni, 337 common tree species making up 181 genera and 56 families were sent for sequencing, and the trait distribution of phytochemical presence was determined. Metrics of phylogenetic trait distribution all supported a random distribution of the medicinal trait within the Yasuni tree community. In the future, having higher sequence recovery and resolution along with complete floristic sampling will improve statistical power and the ability to detect fine scale community structure patterns in both of these forests. Studies like this, which include taxonomic, functional, and phylogenetic diversity, will allow for more comparisons to better understand these unique biodiversity hotspots

Functional perspectives on tropical tree demography and forest dynamics

Abstract Disentangling the processes that drive population, community and whole forest structure and dynamics is a challenge. It becomes a grand challenge in the tropics where there are a large number of species, small population sizes, less research infrastructure, and a relatively smaller number of researchers compared to the temperate zone. Tackling this grand challenge, we argue, requires detailed knowledge of the functioning of individuals and species. To this end, researchers frequently employ plant functional traits to study tree populations and communities. Here, we review this approach by first providing a basic background regarding the major trait axes generally of interest. We then discuss how these axes may be or have been applied from ecosystem to community and population studies. In doing so, we highlight where the functional trait research program has failed in tropical tree ecology and where it can be improved or strengthened. Finally, we provide a perspective regarding how functional trait and emerging ‘omics approaches can be integrated to address large questions facing the field. Our intention throughout is to provide an entryway into this literature for an early career researcher rather than a comprehensive review of all possible studies that have taken place in tropical forests

Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance

Data from: Intra-specific relatedness, spatial clustering and reduced demographic performance in tropical rainforest trees

Intra-specific negative density dependence promotes species coexistence by regulating population sizes. Patterns consistent with such density dependence are frequently reported in diverse tropical tree communities. Empirical evidence demonstrating whether intra-specific variation is related to these patterns, however, is lacking. The present study addresses this important knowledge gap by genotyping all individuals of a tropical tree in a long-term forest dynamics plot in tropical China. We show that related individuals are often spatially clustered, but having closely related neighbors reduces the growth performance of focal trees. We infer from the evidence, that dispersal limitation and negative density dependence are operating simultaneously to impact the spatial distributions of genotypes in a natural population. Furthermore, dispersal limitation decreases local intra-specific genetic diversity and increases negative density dependence thereby promoting niche differences and species co-existence as predicted by theory

Aristolochia mishuyacensis (Aristolochiaceae), a new record for Ecuador, with taxonomic notes

© 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Aristolochia mishuyacensis is recorded for the first time in the Ecuadorian Amazon. Two specimens were collected in two banks of black water tributaries of the Yasuní river, Yasuní National Park. This species is currently distributed in Bolivia, Brazil, Colombia, Ecuador, and Peru, below 200 m. An updated description and images of the species are provided, and its relationships with other species are discussed

Aristolochia mishuyacensis (Aristolochiaceae), a new record for Ecuador, with taxonomic notes

Aristolochia mishuyacensis is recorded for the first time in the Ecuadorian Amazon. Two specimens were collected in two banks of black water tributaries of the Yasuní river, Yasuní National Park. This species is currently distributed in Bolivia, Brazil, Colombia, Ecuador, and Peru, below 200 m. An updated description and images of the species are provided, and its relationships with other species are discussed

Data from: Neighborhood defense gene similarity effects on tree performance: a community transcriptomic approach

The structure and dynamics of ecological communities are ultimately the outcome of the differential demographic rates of individuals. Individual growth and mortality rates largely result from the interaction between an organism's phenotype and the abiotic and biotic environment. Functional traits have been used extensively over the past decade to elucidate links among phenotypes, demography and community dynamics. A fundamental weakness of most functional trait approaches is the use of ‘soft’ traits associated with resource acquisition to examine how neighbourhood similarity affects tree survival and growth. However, these ‘soft’ traits are unlikely to be good predictors of similarities among co-occurring species. Less easily measured aspects of organismal function – such as those related to defence – have frequently gone unmeasured. This is particularly problematic for testing important hypotheses in forest ecology, such as the Janzen–Connell hypothesis where focal trees are expected to be at a disadvantage if their neighbours share the same natural enemies. A potential alternative to functional trait approaches is to quantify the transcriptomic or functional genomic similarity of species. Such analyses are now possible in natural systems where de novo transciptome assemblies can be used to conduct functional phylogenomic analyses where homologous gene trees are produced. Using demographic plot data for 21 species from a North American forest dynamic plot, we conduct a community functional phylogenomic analysis of a plant community to elucidate the similarity in defence response genes across species. This similarity was then used to ask whether the similarity in defence genes of heterospecific species in the local neighbourhood of a focal individual tree influences its growth and mortality rates. The results show that individual growth rates are higher when surrounded by dissimilar heterospecific species for 16 of 27 defence genes analysed. Additionally, survival rates are increased when an individual is in a neighbourhood with dissimilar species for 4 of the 27 defence genes studied. Lastly, strong conspecific effects were found in all analyses, underscoring that future analyses investigating the genetic variation and differential expression of defence-related genes in neighbourhoods may prove important. Synthesis. In summary, this research leverages recent advances in RNA sequencing and bioinformatics to conduct community-wide transcriptomic analyses and analyses of defence-related gene similarity across a tree community. The results demonstrate that defence gene similarity in neighbourhoods often does have negative effects on individual demographic performance as predicted by the Janzen–Connell hypothesis

Tree crown overlap improves predictions of the functional neighbourhood effects on tree survival and growth

1. Investigations of forest community structure and dynamics have been facilitated by the use of neighbourhood models that examine the interactions between a focal tree and its neighbours using a fixed radius. However, different studies have chosen different radii without clear reasons, hampering the understanding of mechanisms structuring tree communities. 2. Using functional trait and tree demography data from the Luquillo subtropical forest in Puerto Rico, we compared fixed‐neighbourhood models with a canopy overlap model, in which tree crown overlap is used as an indicator of neighbourhood crowding. Analyses that combine functional trait and demographic data provide a mechanistic understanding of observed patterns of community structure and dynamics as they provide insights into the linkages between phenotypes and the environment. 3. Overall, canopy overlap models had better support when compared to neighbourhood models using a fixed radius, suggesting that the fixed radius approach does not capture the full extent of competitive interactions among trees. Moreover, the effects of functional neighbourhood on tree survival and growth differ depending on the type of approach used and lead to different conclusions with respect to the drivers of tree community dynamics. 4. Synthesis. In summary, our findings highlight the utility of neighbourhood models based on tree crown overlap, and suggest that applying this same approach to different plots and forests will facilitate comparisons across systems and improve our understanding of the mechanisms that drive the structure and dynamics of tree communities