Phylogenetic diversity of Amazonian tree communities

This is the peer reviewed version of the following article: Honorio Coronado, E. N., Dexter, K. G., Pennington, R. T., Chave, J., Lewis, S. L., Alexiades, M. N., Alvarez, E., Alves de Oliveira, A., Amaral, I. L., Araujo-Murakami, A., Arets, E. J. M. M., Aymard, G. A., Baraloto, C., Bonal, D., Brienen, R., Cerón, C., Cornejo Valverde, F., Di Fiore, A., Farfan-Rios, W., Feldpausch, T. R., Higuchi, N., Huamantupa-Chuquimaco, I., Laurance, S. G., Laurance, W. F., López-Gonzalez, G., Marimon, B. S., Marimon-Junior, B. H., Monteagudo Mendoza, A., Neill, D., Palacios Cuenca, W., Peñuela Mora, M. C., Pitman, N. C. A., Prieto, A., Quesada, C. A., Ramirez Angulo, H., Rudas, A., Ruschel, A. R., Salinas Revilla, N., Salomão, R. P., Segalin de Andrade, A., Silman, M. R., Spironello, W., ter Steege, H., Terborgh, J., Toledo, M., Valenzuela Gamarra, L., Vieira, I. C. G., Vilanova Torre, E., Vos, V., Phillips, O. L. (2015), Phylogenetic diversity of Amazonian tree communities. Diversity and Distributions, 21: 1295–1307. doi: 10.1111/ddi.12357, which has been published in final form at 10.1111/ddi.12357Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.FINCyT - PhD studentshipSchool of Geography of the University of LeedsRoyal Botanic Garden EdinburghNatural Environment Research Council (NERC)Gordon and Betty Moore FoundationEuropean Union's Seventh Framework ProgrammeERCCNPq/PELDNSF - Fellowshi

Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies

The Spectranomics approach to tropical forest remote sensing has established a link between foliar reflectance spectra and the phylogenetic composition of tropical canopy tree communities vis-à-vis the taxonomic organization of biochemical trait variation. However, a direct relationship between phylogenetic affiliation and foliar reflectance spectra of species has not been established. We sought to develop this relationship by quantifying the extent to which underlying patterns of phylogenetic structure drive interspecific variation among foliar reflectance spectra within three Neotropical canopy tree communities with varying levels of soil fertility. We interpreted the resulting spectral patterns of phylogenetic signal in the context of foliar biochemical traits that may contribute to the spectral-phylogenetic link. We utilized a multi-model ensemble to elucidate trait-spectral relationships, and quantified phylogenetic signal for spectral wavelengths and traits using Pagel’s lambda statistic. Foliar reflectance spectra showed evidence of phylogenetic influence primarily within the visible and shortwave infrared spectral regions. These regions were also selected by the multi-model ensemble as those most important to the quantitative prediction of several foliar biochemical traits. Patterns of phylogenetic organization of spectra and traits varied across sites and with soil fertility, indicative of the complex interactions between the environmental and phylogenetic controls underlying patterns of biodiversity

A generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

Aim: The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Innovation: Here, we present a completely generalized and flexible framework to expand incomplete phylogenies. The framework is implemented in the R package “randtip”, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip can generate fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the “blind” expansion of phylogenies using “quick-and-dirty” approaches often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step tutorial that was designed to provide guidelines to non-specialist users. Main Conclusions: Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete phylogenies and thereby account for phylogenetic uncertainty in quantitative analysesMinistry of Science and Innovation of Spain, Grant/Award Number: CGL2017- 86926-P; Regional Government of Madrid, Spain, Grant/Award Number: CM/ JIN/2019-00

Phylogenetic and Biogeographic Controls of Plant Nighttime Stomatal Conductance

The widely documented phenomenon of nighttime stomatal conductance (gsn) could lead to substantial water loss with no carbon gain, and thus it remains unclear whether nighttime stomatal conductance confers a functional advantage. Given that studies of gsn have focused on controlled environments or small numbers of species in natural environments, a broad phylogenetic and biogeographic context could provide insights into potential adaptive benefits of gsn. We measured gsn on a diverse suite of species (n = 73) across various functional groups and climates‐of‐origin in a common garden to study the phylogenetic and biogeographic/climatic controls on gsn and further assessed the degree to which gsn co‐varied with leaf functional traits and daytime gas exchange rates. Closely related species were more similar in gsn than expected by chance. Herbaceous species had higher gsn than woody species. Species that typically grow in climates with lower mean annual precipitation – where the fitness cost of water loss should be the highest – generally had higher gsn. Our results reveal the highest gsn rates in species from environments where neighboring plants compete most strongly for water, suggesting a possible role for the competitive advantage of gsn

ORGANIZAÇÃO DA COMUNIDADE E ESTRUTURA FILOGENÉTICA DO COMPONENTE ARBÓREO DE UM FRAGMENTO DE FLORESTA NEBULAR NO PLANALTO CATARINENSE

This study aimed to survey the community organization and the phylogenetic structure of tree species component in a nebular forest, in the municipality of Urubici, Santa Catarina state. A total of 25 plots (400 m2) were allocated, where all trees with circumference at breast height (cbh) equal or superior than 15.7 cm were measured (cbh) and identified. The Shannon index and phytosociological descriptors were determined. The dispersal syndromes of propagules were determined and the spatial distribution of each species was analyzed. The phylogenetic structure was evaluated by the values of ‘Mean Pairwise Distance’ (MPD) and Net Relatedness Index (NRI), determined through a phylogenetic tree built in function of the species sampled, an abundance matrix of species by plots and 1,000 simulations of a community with phylogenetic randomness organization. The spatial structure of the phylogenetic metrics was analyzed through I Moran Index. A total of 1,579 trees were sampled, belonging to 33 species, with Myrtaceae as the richest family. The low value of diversity (2.43), associated to low richness, is expected for nebular forest, where the environment is typically selective. The most representative species in the forest was Myrceugenia euosma (O.Berg) D.Legrand (VI = 24.51%). The predominant dispersal syndrome was zoochory (84.85%), followed by anemochory (15.15%); and the species showed predominantly a clustered spatial distribution. The community had variation in relation to the phylogenetic structure, with most plots showing no significant difference from the null model of complete randomness.O presente estudo teve como objetivos conhecer a organização da comunidade e a estruturação filogenética do componente arbóreo de um fragmento de Floresta Nebular em Urubici - SC. Para isso, foram alocadas 25 parcelas de 400 m2, nas quais foi medida a circunferência a altura do peito – CAP, e identificadas todas as árvores com CAP igual ou superior a 15,7 cm. Foram calculados o índice de diversidade de Shannon-Wiener e os descritores fitossociológicos. A síndrome de dispersão de propágulos e a distribuição espacial de cada espécie foram determinadas. A estruturação filogenética foi avaliada por meio dos valores de Mean pairwise distance (MPD) e de Net Relatedness Index (NRI), calculados a partir de uma árvore filogenética construída em função das espécies amostradas, de uma matriz de abundância das espécies por parcelas e 1.000 simulações de uma comunidade organizada filogeneticamente de forma aleatória. A estruturação espacial das métricas filogenéticas foi analisada por meio do Índice I de Moran. Foram amostrados 1.579 indivíduos, pertencentes a 33 espécies, sendo Myrtaceae a família de maior riqueza de espécies. O baixo valor de diversidade (2,43), associado à baixa riqueza na área, é esperado em Florestas Nebulares, cujo ambiente é tipicamente seletivo. A maior representação na floresta foi de Myrceugenia euosma (O.Berg) D.Legrand (VI = 24,51%). A síndrome de dispersão predominante foi a zoocoria (84,85%), seguida pela anemocoria (15,15%), e a distribuição espacial foi predominantemente agregada. A comunidade apresentou variação em relação à estruturação filogenética, sendo que, para a maioria das parcelas, o padrão não diferiu do modelo nulo de completa aleatoriedade

Effects of plant invasions on ecosystem processes: Linking above- and below-ground resource-use strategies of native and invasive species in Eastern U.S. forests

Despite the increasing number of non-native invasive species worldwide and their potential impacts on ecosystems, the mechanisms that invaders alter ecosystem nutrient processes remain elusive. Invaders are often more productive than native species which suggests invaders may have different above- and below-ground resource-use strategies that can profoundly alter ecosystem processes. Here I investigated above- and below-ground plant traits and soil properties associated with resource-use strategies and soil nitrogen (N) dynamics for multiple native and non-native forest understory species in the Eastern U.S. to better understand invader impacts on ecosystem processes. In the first study, performed in a common garden, I examined the linkage between above- and below-ground resource-use strategies for native and invasive species that allow invaders to be more productive than co-occurring natives. Results showed that, despite invaders losing a significant amount of N from litter, they had greater root production and specific root length associated with a greater soil nutrient uptake capacity than natives. In the second study, I examined whether the different tissue traits are associated with litter decomposition rate and if invaders can increase nutrient cycling through faster litter decomposition than natives. Results revealed no differences in leaf and root decomposition rates between native and non-native forest understory woody species, suggesting that litter decomposition rate is not a process that invasive species affect with regard to soil nutrient processes in the Eastern U.S. forests. Finally, I investigated invader impacts on soil N processes in a monoculture experiment. After two growing seasons, invaders had greater above- and below-ground productivity. Invaders facilitated N cycling via greater litter N input into the soil that increased soil N availability, and had greater fine root production and SRL that increased plant N uptake. Although the greater aboveground production of invaders reduced soil temperature and moisture, which can reduce soil microbial activity, the stimulatory effects of a greater flow of litter N to the soil appeared to overwhelm any negative effects that invaders had on the soil microclimate. Taken together, my results suggest that invaders have different above-and below-ground resource-use strategies and invaders\u27 greater productivity is one of the major drivers that can significantly change ecosystem processes