Paul V. A. Fine’s research while affiliated with University of California, Berkeley and other places

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Publications (191)


Figure 1. (A) We found significant differences in compound richness between roots and leaves across our 31 focus Protium species. (B) Differences in structural diversity between roots and leaves across our 31 experimental Protium species. (C) Even when ranking Protium species based on metab-
Figure 3. (A) We sampled roots and leaves from 31 species in the Protium phylogeny (including two
Evolutionary Trajectories of Shoots vs. Roots: Plant Volatile Metabolomes Are Richer but Less Structurally Diverse Belowground in the Tropical Tree Genus Protium
  • Article
  • Full-text available

January 2025

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36 Reads

Plants

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Paul V. A. Fine

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Italo Mesones

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The breadth and depth of plant leaf metabolomes have been implicated in key interactions with plant enemies aboveground. In particular, divergence in plant species chemical composition—amongst neighbors, relatives, or both—is often suggested as a means of escape from insect herbivore enemies. Plants also experience strong pressure from enemies such as belowground pathogens; however, little work has been carried out to examine the evolutionary trajectories of species’ specialized chemistries in both roots and leaves. Here, we examine the GCMS detectable phytochemistry (for simplicity, hereafter referred to as specialized volatile metabolites) of the tropical tree genus Protium, testing the hypothesis that phenotypic divergence will be weaker belowground compared to aboveground due to more limited dispersal by enemies. We found that, after controlling for differences in chemical richness, roots expressed less structurally diverse compounds than leaves, despite having higher numbers of specialized volatile metabolites, and that species’ phylogenetic distance was only positively correlated with compound structural distance in roots, not leaves. Taken together, our results suggest that root specialized volatile metabolites exhibit significantly less phenotypic divergence than leaf specialized metabolites and may be under relaxed selection pressure from enemies belowground.

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When zombies go vegan: Ophiocordyceps unilateralis hosts are selecting to bite palm leaves before dying?

January 2025

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32 Reads

Acta Oecologica

Some parasites that modify hosts' behavior can receive reproductive advantages. For instance, when infected by Ophiocordyceps unilateralis s.l., ants climb understory plants, lock their jaws into the plant tissue, and die in stable microclimatic conditions that favor the reproductive stage of the fungus. However, the so-called “zombie ants” could die on different species of plants, subject to varying environmental pressures. Here, we investigated whether infected ants lock their jaws on particular species of understory plants more often than expected before dying from the infection. We hypothesize that there may be different reproductive advantages to the parasite based on the plant species on which its hosts die. Our findings reveal that 36.3% of the infected ants died on palm trees, specifically Attalea sp. and Euterpe catinga, more frequently than expected by chance. Also, we found that cadavers tend to persist longer on palms than other plants. Our results suggest that there may be a reproductive advantage for the parasite when its hosts die on palm leaves. Palms generally have long leaf durability, which can reduce parasite cadaver loss by foliar abscission and increase cumulative spore dispersal. Furthermore, we propose abundant plant species with no observance of cadavers potentially have traits like trichome coating and antifungal compounds that may influence the arrival and permanence of new zombie ants. Our results show that infected ants dying on certain understory palm species may increase the fungus’ fitness.


Functional, demographic, and integrative axis of variation. First principal components using leaf (specific leaf area; nitrogen, phosphorous, and carbon content, N, P, and C) wood (wood density, and maximum diameter, Diametermax) and demographic characteristics (maximum growth rate, Growth R.max; mortality rate, Mortality R. and seed mass). Only genera with complete data for all variables are represented (197 genera). Variable contributions are shown as arrows, coloured in light blue (leaf and wood functional traits) and red (demographic characteristics). Principal‐axis interpretation is shown in bold letters. Pictures of seeds (fruit when no seed images are available), leaves and whole trees for four species representing the four extreme strategies are shown. Phylogenetic signal and amount of variance explained by each axis in percentage are shown for each axis.
Variance–covariance networks. Trait correlation networks among leaf (specific leaf area; nitrogen, phosphorous and carbon content, N, P, and C), wood (wood density, and maximum diameter, Diametermax) and demographic characteristics (maximum growth rate, Growth R.max; mortality rate, Mortality R. and seed mass). Leaf and wood functional traits are represented as nodes (circles) in light blue and demographic functional traits are shown in light red. Edges (lines connecting nodes) represent (a) total correlation, (b) phylogenetically conserved portion of the correlation and (c) non‐phylogenetically conserved portion of the total correlation. Solid green lines represent statistically significant positive correlation coefficients and dashed red lines represent significant negative correlation coefficients. Line width is proportional to the absolute value of the correlation coefficient. Pie charts in b and c represent trait variance related to the phylogeny (i.e., phylogenetic signal) and trait variance not related to the phylogeny, respectively. Node size is proportional to the number of connections per node (i.e., degree). Three network metrics are shown in each case.
Functional and demographic axis correlations. Total, phylogenetically conserved and non‐phylogenetically conserved correlation portions between functional and demographic principal components. Phylogenetic signal is also shown and represented as pie charts for each principal component. Values for genera with complete observations are plotted on the genus‐level phylogeny. Bars are coloured by taxonomic order and the most important taxonomic order names are shown. Signif. codes: “***”: p < 0.001; “ns”: p > 0.1.
Phylogenetic conservatism in the relationship between functional and demographic characteristics in Amazon tree taxa

November 2024

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755 Reads

Leaf and wood functional traits of trees are related to growth, reproduction, and survival, but the degree of phylogenetic conservatism in these relationships is largely unknown. In this study, we describe the variability of strategies involving leaf, wood and demographic characteristics for tree genera distributed across the Amazon Region, and quantify phylogenetic signal for the characteristics and their relationships. Leaf and wood traits are aligned with demographic variables along two main axes of variation. The first axis represents the coordination of leaf traits describing resource uptake and use, wood density, seed mass, and survival. The second axis represents the coordination between size and growth. Both axes show strong phylogenetic signal, suggesting a constrained evolution influenced by ancestral values, yet the second axis also has an additional, substantial portion of its variation that is driven by functional correlations unrelated to phylogeny, suggesting simultaneously higher evolutionary lability and coordination. Synthesis. Our results suggest that life history strategies of tropical trees are generally phylogenetically conserved, but that tree lineages may have some capability of responding to environmental changes by modulating their growth and size. Overall, we provide the largest‐scale synopsis of functional characteristics of Amazonian trees, showing substantial nuance in the evolutionary patterns of individual characteristics and their relationships. Read the free Plain Language Summary for this article on the Journal blog.


Variation in composition and relative abundance of 5188 tree species in 2023 forest-inventory plots (1 ha) across Amazonian forests
Ordination biplots showing the two first principal components with inventory plots coloured by (a) ecological forest categories based on hydrology and soil characteristics and (b) geographic regions. a Ecological categories: VA, Várzea forests; SW, swamp forests; IG, igapó forests; PZ, white-sand (podzol) forests; TFGS, terra-firme on the Guiana Shield; TFBS terra-firme on the Brazilian Shield, TFPB terra-firme on the Pebas sedimentary basin. b Geographical regions: CA Central Amazonia, EA Eastern Amazonia, SA Southern Amazonia, GS Guiana Shield, NWA Northwestern Amazonia, SWA Southwestern Amazonia. Arrows indicate vectors constructed with envfit()⁸¹ for 14 environmental predictors: Flooded flooding vs. non-flooding terrains, WTD water table depth, Temp_avg average annual temperature, MCWD maximum climatological water deficit), Annal_ppt Annual Rainfall, Podzol White Sand vs. Clay-Silt terrains, ALOS_MTPI Multiscale Topographic Position Index, TopoDiver Topographic Diversity Index, Ppt_sea precipitation seasonality, ALOS_3D elevation, Temp_range temperature range, Temp_seas temperature seasonality, pH soil pH, SB soil sum of bases.
Variation in interpolated composition and relative abundance of 5,188 tree species in 47,441 grid cells (0.1-degree squares) across Amazonian forests
Ordination biplots showing the two first DCA axes with grid cells coloured by geographic region: CA Central Amazonia, EA Eastern Amazonia, GS Guiana Shield, NWA Northwestern Amazonia, SWA Southwestern Amazonia, SA Southern Amazonia. Black marks show the average position for the abundance distribution of the 20 tree species with the highest interpolated total abundance. The distributions of these species in geographical and ordination space are shown in Supplementary Figs. 5–24.
Maps of the broad-scale spatial variation of tree species composition across Amazonia
Scores of (a) DCA Axis 1, (b) DCA Axis2 (both from Fig. 2). In both maps, grey lines are the isolines linking equal levels of DCA scores, with the spatial distance between consecutive isolines being inversely related to the rate of compositional change across space and used to mark sharp compositional turnover zones (if closer together) or smoother compositional turnover (consecutive isolines further apart). In (a), the blue isoline corresponds to DCA score of 1.0 and the red isoline to soil pH = 5 (west of that line having a soil pH >5). In (b), the red isoline corresponds to maximum climatological water deficit (MCWD) = − 275 mm (south of that line having MCWD < −275), and the blue isoline to MCWD = −100 (west that line having MCWD > −100). The dark green line delimits the Amazonian tropical forests⁹⁵, with white areas within these limits corresponding to montane areas (above 500 m elevation) and non-forested habitats such as savannas. Major river courses are shown in blue. Base map source for countries: https://www.naturalearthdata.com/; rivers⁶¹. Maps created with custom R⁸⁸ script.
Niche positions and niche breadths of 5188 tree species along environmental and compositional gradients in Amazonia as calculated with data from 2023 1-ha forest-inventory plots
Gradients along the x axis: (a) Annual rainfall (mm); (b) maximum climatological water deficit (mm); (c) log(soil sum of bases (Ca+Mg+K)); (d) soil acidity (pH); (e) DCA1 scores from Fig. 2; and (f) DCA2 scores from Fig. 2. The black dots mark the mean niche position or optimum (weighted average value) for each species and the grey lines depict the niche breadths or tolerance (±standard deviation for the variable in sites where the species was observed). The red lines show the mean niche breadth (determined by loess regression). Coloured lines correspond to the lines also visible in Fig. 3 (DCA1, DCA2, pH, MCWD). Species are shown from bottom to top in the order of increasing niche position. (See supplementary data 1 for the niche breadth and position values of all tree species).
The associations of species niche positions on compositional and environmental gradients
In the first row the species niche positions on the DCA1 scores gradient in relation to edaphic niche position gradients: (a) Soil sum of bases, (b) Soil pH. The second row shows the species niche positions along the DCA2 scores gradient in relation to climatic gradients: (c) Annual Rainfall, (d) Maximum climatological water deficit. Plot colours correspond to colours in Fig. 3. Coloured lines correspond to the lines (DCA1, pH, MCWD) also visible in Fig. 3.
The biogeography of the Amazonian tree flora

October 2024

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1,692 Reads

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1 Citation

Communications Biology

We describe the geographical variation in tree species composition across Amazonian forests and show how environmental conditions are associated with species turnover. Our analyses are based on 2023 forest inventory plots (1 ha) that provide abundance data for a total of 5188 tree species. Within-plot species composition reflected both local environmental conditions (especially soil nutrients and hydrology) and geographical regions. A broader-scale view of species turnover was obtained by interpolating the relative tree species abundances over Amazonia into 47,441 0.1-degree grid cells. Two main dimensions of spatial change in tree species composition were identified. The first was a gradient between western Amazonia at the Andean forelands (with young geology and relatively nutrient-rich soils) and central–eastern Amazonia associated with the Guiana and Brazilian Shields (with more ancient geology and poor soils). The second gradient was between the wet forests of the northwest and the drier forests in southern Amazonia. Isolines linking cells of similar composition crossed major Amazonian rivers, suggesting that tree species distributions are not limited by rivers. Even though some areas of relatively sharp species turnover were identified, mostly the tree species composition changed gradually over large extents, which does not support delimiting clear discrete biogeographic regions within Amazonia.



Distribution of inventory data used to create habitat-specific compositional grids
Sampled sites include 1,705 mostly 1-ha tree inventory plots with full information on species composition and abundances. Plots were classified as terra firme (n = 1,250, 73%), várzea (n = 271, 16%), or igapó (n = 184, 11%), following habitat designations of ATDN contributors.
Schematic of the methods used to compare floodplain and terra firme tree compositions, illustrated for two grid cells
(a) Forest plot inventories (colored dots) were separated into várzea, igapó and terra firme categories, and species abundance information for separate várzea, igapó and terra firme grids was calculated at each 1-degree cell (only two shown), using distance-weighted interpolations of inventory plot data from an approximately 300 km circular window (red lines). (b) Floodplain and terra firme grids were overlaid and species turnover computed at analogous (vertically overlapping) cells. (c) Spatially-continuous grids of species turnover for várzea-terra firme and igapó-terra firme comparisons. The number of cells where species turnover is calculated depends on the spatial distribution of floodplain inventories and how it overlaps with terra firme inventories. This included 301 cells and 347 cells for várzea-terra firme and igapó-terra firme comparisons, respectively. In an alternative procedure of calculating species turnover, the interpolation step was excluded and cell compositional data was pooled only from plots located inside cells. For this second approach, the resulting number of cells where species turnover was calculated was 25 and 22 for várzea-terra firme and igapó-terra firme comparisons, respectively.
Comparison of flooding relationships with species turnover using two alternative procedures for populating cell compositional data
While interpolating species abundances maximizes the number of cells where species turnover can be calculated, it introduces spatial autocorrelation. On the other hand, pooling inventories within grid cells reduces the number of cells where species turnover can be calculated, but it maintains spatial independence among cells. We compared both methods to assess the robustness of our results to spatial dependencies. For the approach based on pooling, species cell abundance information was pooled only from inventories located inside individual grid cells, rather than interpolated from inventories from a larger 300 km circular window, in order to avoid residual spatial autocorrelation. Quantile regression slopes (at tau = 0.1) and their 95% confidences intervals are shown for várzea- and igapó-terra firme. The lower bounds of várzea-terra firme species turnover with flooding are statistically equivalent between pooled compositional data (slope ± 95% CI = 1.29 × 10⁻² ± 1.21 × 10⁻², t = 2.20, n = 25, p = 0.038) and interpolated data (slope ± 95% CI = 1.21 × 10⁻² ± 2.48 × 10⁻³, t = 9.57, n = 301, p < 0.001). The lower bounds for igapó-terra firme are likewise similar between pooled (slope ± 95% CI = 1.54 × 10⁻² ± 1.19 × 10⁻², t = 2.66, n = 22, p = 0.015) and interpolated methods (slope ± 95% CI = 1.05 × 10⁻² ± 2.60 × 10⁻³, t = 7.86, n = 347, p < 0.001). Slopes from all comparisons were significant (p < 0.05) and had overlapping 95% confidence intervals.
Broad-scale geographic and environmental patterning of species turnover across floodplain and adjacent terra firme forest habitats, for várzea–terra firme and igapó–terra firme comparisons
a, Spatial patterns of species turnover for várzea and igapó, showing a concentration of high species turnover located centrally within the fluvial network. Grey rivers are masked out because they either correspond to a different floodplain habitat or did not meet minimum sampling criteria for analysis. b, Regional differences in seasonal flooding are described as an annual flood wave that originates in Andean headwaters, peaks in central Amazonia and dissipates near the Amazon mouth. Floodplains positioned at the peak of this flood wave are seasonally inundated by the highest-amplitude and longest-lasting floods. LWT, land water thickness. c, Patterning of species turnover of várzea and igapó with surrounding terra firme along the flood wave. The black dashed line shows the lower bound of species turnover with flooding, assessed with quantile regression at τ = 0.1. d, Mapped residuals from quantile regression modelling for várzea and igapó. Throughout much of western Amazonia, species turnover is relatively higher than expected given the lower flooding implied by its headwater position on the flood wave.
Relationships between species turnover and the relative abundance and richness of floodplain specialists, habitat generalists and spillover from terra firme (terra firme specialists) in várzea and igapó
With increasing levels of species turnover, floodplain specialists become more dominant, while spillover from terra firme species decreases. The proportions are derived from interpolated compositional grids of várzea and igapó after cross-referencing with the names of the 1,666 species tested for habitat association. The relationships with species turnover are derived from simple least squares models. The coloured boxes indicate the proportion of explained variance (r²) and P values. The trend lines (black) are bounded by coloured bands showing the 95% CIs. Density plots for the relative abundance and richness of each species group are shown in the right margins.
One sixth of Amazonian tree diversity is dependent on river floodplains

March 2024

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1,173 Reads

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10 Citations

Nature Ecology & Evolution

Amazonia’s floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region’s floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon’s tree diversity and its function.


Geography and ecology shape the phylogenetic composition of Amazonian tree communities

February 2024

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1,072 Reads

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6 Citations

Journal of Biogeography

Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and várzea forest types, the phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.


Map of the study sites in western Amazonia (Colombia, Ecuador, Peru and Bolivia) represented on a digital elevation model (Shuttle Radar Topography Mission [SRTM]) in WGS84 datum, latitude‐longitude coordinate reference system, including 100 × 100 km grid‐cells.
Model predictions for the best‐fit beta regression model showing the relationship between the mean local abundance and regional frequency of dominant species by habitat types. Lines represent mean generalized model fits, and shading represents 95% confidence intervals of model fits.
Species‐level rank abundance distribution graphs of dominant species by habitat type: (a) terra firme, (b) floodplain, (c) swamp and (d) white sand forests. Upper panels represent local abundance—regional frequency relationship of dominant species within each habitat type, with their quartiles. Numbers refer to each of the combination of quartiles of the two variables, local abundance and regional frequency.
Relative spatial aggregation curves to dominant species by habitat type: (a) terra firme, (b) floodplain, (c) swamp and (d) white sand forests. Upper panels represent local abundance—regional frequency relationship of dominant species within each habitat type, with their quartiles. Numbers refer to each of the combination of quartiles of the two variables, local abundance and regional frequency. Each curve represents the probability of finding a conspecific of a species at each distance compared to the probability of finding conspecifics of any other species at that distance.
Conceptual framework of different dominance patterns inside the set of dominant species in four main habitat types of western Amazonia.
Understanding different dominance patterns in western Amazonian forests

December 2023

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540 Reads

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1 Citation

Ecology Letters

Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥2.5 cm diameter, 2609 species) to explore the relationships between local abundance, regional frequency and spatial aggregation of dominant species in four main habitat types in western Amazonia. Although the abundance‐occupancy relationship is positive for the full dataset, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade‐off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unravelling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests.


Tree alpha-diversity (Fisher’s alpha) in Amazonia
A Histogram of tree alpha-diversity in 2046 ATDN plots. Red lines, mean and mean ± 2 sd. B Tree alpha-diversity by major forest type. C Map of tree alpha-diversity across Amazonia. Legend truncated at 0 and mean + 2 standard deviation of the mean. Amazonian Biome limit - red⁷⁹. D Observed values of tree diversity vs modelled values of tree diversity on the 2046 plots used for mapping. The significance or Moran’s I was tested with the function Moran.I() of ape⁶¹. Marker colours: Red: Terra Firme Pebas Formation; Brown: Terra Firme Brazilian Shield; Orange: Terra Firme Guyana Shield; Yellow: White sand forest; Light blue: Varzea; Dark blue: Igapo; Purple: Swamp. Map created with custom R⁸⁰ script. Base map source (country.shp, rivers.shp): ESRI (http://www.esri.com/data/basemaps, © Esri, DeLorme Publishing Company).
Tree species-richness (species/ha) in Amazonia
A Histogram of tree species-richness in 2046 ATDN plots. B Tree species-richness by major forest type. C Map of tree species-richness across Amazonia. Legend truncated at mean ± 2 standard deviations of the mean. Amazonian Biome limit - red⁷⁹. D Observed values of tree species-richness vs modelled values of tree species-richness on the 2046 plots used for mapping. The significance or Moran’s I was tested with the function Moran.I() of ape⁶¹. Marker colours: Red: Terra Firme Pebas Formation; Brown: Terra Firme Brazilian Shield; Orange: Terra Firme Guyana Shield; Yellow: White sand forest; Light blue: Varzea; Dark blue: Igapo; Purple: Swamp. Map created with custom R⁸⁰ script. Base map source (country.shp, rivers.shp): ESRI (http://www.esri.com/data/basemaps, © Esri, DeLorme Publishing Company).
Tree alpha-diversity and tree species-richness of terra-firme forest in Amazonia
A Map of interpolated tree alpha-diversity (Fisher’s alpha), based on 1441 terra firme plots. B Map of tree species-richness (number of species/ha by plot), based on 1441 terra firme plots. Red polygon: Amazonian Biome limit⁷⁹. Map created with custom R⁸⁰ script. Base map source (country.shp, rivers.shp): ESRI (http://www.esri.com/data/basemaps, © Esri, DeLorme Publishing Company).
The effect of cumulative water deficit (mm), tree density, and temperature seasonality on tree species-richness
A Tree species-richness observed. B Tree species-richness as predicted by cumulative water deficit, regional tree density, and temperature seasonality. C Model performance, showing predicted and observed tree species-richness. D Residuals of tree species-richness predicted by cumulative water deficit, regional tree density, and temperature seasonality (A, B). All figures based on 1441 terra firme plots. Amazonian Biome limit - red⁷⁹. Map created with custom R⁸⁰ script. Base map source (country.shp, rivers.shp): ESRI (http://www.esri.com/data/basemaps, © Esri, DeLorme Publishing Company).
Mapping density, diversity and species-richness of the Amazon tree flora

November 2023

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2,139 Reads

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13 Citations

Communications Biology

ARTICLE Mapping density, diversity and species-richness of the Amazon tree flora Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.


Fig. 1. Geographical distribution of known and newly discovered pre-Columbian geometric earthworks in Amazonia. (A) Map of previously reported and newly discovered earthworks (purple circles and yellow stars, respectively) reported in this study across six Amazonian regions: central Amazonia (CA), eastern Amazonia (EA), Guiana Shield (GS), northwestern Amazonia (NwA), southern Amazonia (SA), and southwestern Amazonia (SwA). (B) Newly discovered earthworks in SA. (C to F) Newly discovered earthworks in SwA. (G to I) Newly discovered earthworks in GS. (J and K) Newly discovered earthworks in CA. Scale bars, 100 m.
More than 10000 pre-Columbian earthworks are still hidden throughout Amazonia

October 2023

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2,184 Reads

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24 Citations

Science

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state


Citations (71)


... The large variability across space of the Amazon forest is observed for species (Luize et al., 2024) as well as forest structure and biomass (de Conto et al., 2024;Saatchi et al., 2011), and the large-scale patterns of height observed in our data reinforce that the Amazon forest is not a uniform and homogeneous forest, for example with the hotspot of high trees in the Guiana Shield, found in this study and in Gorgens et al. (2019). This is particularly concerning for conservation efforts because deforestation that still occurs in the Amazon operates mostly by removing almost entirely large patches of continuous areas of forest, Fig. 14, which is likely the best manner to remove forests that are unique. ...

Reference:

High Resolution Tree Height Mapping of the Amazon Forest using Planet NICFI Images and LiDAR-Informed U-Net Model
The biogeography of the Amazonian tree flora

Communications Biology

... Several species have evolved adaptations to the ecological cycles and physiological conditions driven by seasonal flooding 158,181 , defining the unique vegetation 182 and associated fauna seen in Amazonian floodplains 5 . Specialization in seasonally flooded habitats is known in Amazonian trees 183,184 , birds 185,186 , primates 159 , butterflies 187 , amphibians and squamate reptiles 147,188,189 , and even in soil organisms 190 . Thus, the seasonal flooding cycle and fluvial sedimentation-erosion patterns dictate the geographic distribution of Amazonian ecosystems and their associated biota. ...

One sixth of Amazonian tree diversity is dependent on river floodplains

Nature Ecology & Evolution

... ref. 45). However, quantitative tests of the biogeographical pattern of Amazonian tree communities are scarce and based on incomplete presence/absence data 44,48 or on genus-level identifications and very coarse spatial resolution 29 ; but see Luize et al. 49 , unveiling the role of dispersal and phylogenetic niche conservatism on phylogenetic compositional changes over Amazonia. ...

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

Journal of Biogeography

... Normally, these two variables are positively related, but the absence of a relationship has also been found [1][2][3]. At present, the factors driving the shape of the AOR are incompletely understood and include, for example, niche breadth, vital rates, body size, migration, dispersal, successional stage, and urbanization [4][5][6][7][8][9][10][11][12][13][14][15]. ...

Understanding different dominance patterns in western Amazonian forests

Ecology Letters

... It has substantial economic and social repercussions in remote regions and urban complexes. Specifically, the Brazilian Amazon has dense forests [6,7], numerous rivers [8][9][10][11], and lakes, which pose a barrier to the construction of highways and railways. ...

Mapping density, diversity and species-richness of the Amazon tree flora

Communications Biology

... The authors also suggest a second major east-to-west cultural expansion of maize traditions, associated with geometric enclosures in the Upper Tapajós 74 and Upper Xingu 26 dating to ce ~800-1000. Furthermore, the predicted geographic distribution of earthworks is influenced by the sum of exchangeable base cation concentration in the surface soil 75 across the Amazon Basin, with a higher probability of earthworks in areas with higher overall soil fertility 75,76 . This wide area covers most of the southern rim of the Amazon biome, from Acre/Peru to the Xingu/Tocantins basin, hinting at a possible relationship between maize, urbanism and earthworks in the Southern Amazon. ...

More than 10000 pre-Columbian earthworks are still hidden throughout Amazonia

Science

... The richness, or number of compounds that a plant produces, has long been a key measure of chemical diversity [41] and has been shown to be a strong predictor of the diversity of associations between plants and herbivores in Protium [42]. It is yet to be determined whether the differences in chemical richness between above-and belowground tissues in Protium mirror the diversity and richness differences in plant-enemy interactions. ...

A test of the Geographic Mosaic Theory of Coevolution: investigating widespread species of Amazonian Protium (Burseraceae) trees, their chemical defenses, and their associated herbivore faunas

... Rather, flower resource allocation must ensure reproduction while avoiding herbivory and resisting abiotic stress (Roddy et al., 2021). Because flowers are typically shortlived compared to leaves, selection may have favored making them cheap with a relatively low-biomass investment but a high-water mass investment for a given display area (Zhang et al., 2017;An et al., 2023;Roddy et al., 2023). However, to attract pollinators, flowers are typically displayed at the outer edge of the plant canopy, a placement that exposes them to the hottest, driest, sunniest, and windiest conditions experienced by the plant, all of which can elevate water loss and impair flower water status, potentially precluding successful pollination (Patiño & Grace, 2002;Bourbia et al., 2020;Carins-Murphy et al., 2023;Aun et al., 2024). ...

Flowers are leakier than leaves but cheaper to build

... These efforts have long relied on observations of plant presence and abundance along environmental gradients (Dufrêne & Legendre, 1997;Futuyma & Moreno, 1988). Through these studies, soil nutrients and water availability have been identified as strong drivers of plant species distributions across scales (Esquivel-Muelbert et al., 2017;Vleminckx et al., 2023). While some species are restricted to specific portions of these gradients (so-called specialist species), others are widely distributed (so-called generalist species; Dennis et al., 2011;Kassen, 2002). ...

Niche breadth of Amazonian trees increases with niche optimum across broad edaphic gradients

... The use of the term 'information entropy' is frequent in contemporary ecology (e.g., Harte, 2011;Singh et al., 2019;Mattos et al., 2022;Zhang et al., 2023;Pos et al., 2023;Xu, 2023). The equation of Josiah Willard Gibbs for entropy in statistical mechanics (Tolman, 1938, p. 539, Eq. (122.10)) ...

Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology