Henrique Eduardo Mendonça Nascimento’s research while affiliated with Amazon Environmental Research Institute (IPAM) and other places

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Publications (101)


Figure 1. Spatial allocation of forest inventory plots across distinct forest types within the state of Amapá and extending up to 100 km beyond its borders. The forest areas represent those still standing in 2018.
Figure 2. Flowchart illustrating the methodological steps for estimating forest biomass in the state of Amapá. BDIA = Environmental Information Database. BDGP = database of georeferenced plots. ANA = National Water Agency.
Figure 3. Flowchart illustrating the application of kriging to the georeferenced database, incorporating five auxiliary environmental variables. BDGP = database of georeferenced plots; OLS = ordinary least squares; R = map of residuals; V = vegetation map; P = precipitation map; La = latitude map; Lo = longitude map; Ord-krig = ordinary kriging; Co-krig = co-kriging; KED = kriging with external drift. For co-kriging, three auxiliary variables were employed (V, P, and Lo), and for KED, five variables were utilized (R, V, P, La, and Lo). The colors in the small maps represent the gradients of R, V, P, La, and Lo, ranging from lower values (yellowish to reddish tones) to higher values (greenish to bluish tones).
Figure 4. Reference map showing the spatial distribution of forest biomass (Mg ha −1 ) in the state of Amapá, generated using kriging with external drift (KED). White areas represent non-forest vegetation.
Forest types and their respective areas in the state of Amapá.

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Dense Forests in the Brazilian State of Amapá Store the Highest Biomass in the Amazon Basin
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June 2025

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48 Reads

M Da Costa

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Eleneide D Sotta

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Citation: da Costa, J.D.M.; Barni, P.E.; Sotta, E.D.; Carim, M.d.J.V.; da Cunha, A.C.; Guedes, M.C.; Aparicio, P.d.S.; de Oliveira, L.L.; Barbosa, R.I.; Fearnside, P.M.; et al. Dense Forests in the Brazilian State of Amapá Store the Highest Biomass in the Amazon Basin. Sustainability 2025, 17, 5310. https:// Abstract: The Amazonian forests located within the Guiana Shield store above-average levels of biomass per hectare. However, considerable uncertainty remains regarding carbon stocks in this region, mainly due to limited inventory data and the lack of spatial datasets that account for factors influencing variation among forest types. The present study investigates the spatial distribution of original total forest biomass in the state of Amapá, located in the northeastern Brazilian Amazon. Using data from forest inventory plots, we applied geostatistical interpolation techniques (kriging) combined with environmental variables to generate a high-resolution map of forest biomass distribution. The stocks of biomass were associated with different forest types and land uses. The average biomass was 536.5 ± 64.3 Mg ha −1 across forest types, and non-flooding lowland forest had the highest average (619.1 ± 38.3), followed by the submontane (521.8 ± 49.8) and the floodplain (447.6 ± 45.5) forests. Protected areas represented 84.1% of Amapá's total biomass stock, while 15.9% was in agriculture and ranching areas, but the average biomass is similar between land-use types. Sustainable-use reserves stock more biomass (40%) than integral-protection reserves (35%) due to the higher average biomass associated with well-structured forests and a greater density of large trees. The map generated in the present study contributes to a better understanding of carbon balance across multiple spatial scales and demonstrates that forests in this region contain the highest carbon stocks per hectare (260.2 ± 31.2 Mg ha −1 , assuming that 48.5% of biomass is carbon) in the Amazon. To conserve these stocks, it is necessary to go further than merely maintaining protected areas by strengthening the protection of reserves, restricting logging activities in sustainable-use areas, promoting strong enforcement against illegal deforestation, and supporting the implementation of REDD+ projects. These actions are critical for avoiding substantial carbon stock losses and for reducing greenhouse-gas emissions from this region.

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Results of model selection for the height-diameter allometry for two forest types (terra-firme and várzea) in northeastern Amazonia.
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Tree height-diameter allometry and implications for biomass estimates in Northeastern Amazonian forests

March 2025

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64 Reads

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1 Citation

The relationship between tree height and diameter varies across forest types, introducing uncertainties in height that can affect aboveground biomass estimates in tropical forests. Here, we used a four-step approach to assess whether incorporating height estimates from local height-diameter models, compared to two published equations, improves biomass estimates across spatial scales. First, we measured the diameter and height of 1,962 trees in two representative forest types in the Northeastern Amazon: non-flooded terra-firme and seasonally-flooded várzea forests. Second, we selected the best height-diameter models from a set of 10 candidates to establish local allometric equations. Third, we applied these best local models and two previously published height models (the regional Guyana shield, and the pantropical model) to estimate tree height, and compared these estimates to measured height. Finally, we computed tree biomass using equations that both included and excluded height, and compared these biomass estimates to those calculated using directly measured height. Asymptotic height-diameter models provided the best fit at local and regional scales. The Quadratic model was the best choice for terra-firme and várzea forests separately, while the Weibull and Michaelis-Menten models performed best for both forests. Local models closely matched measured heights, with deviations of only 0.1%, outperforming the regional and pantropical models within each forest type. The regional model underestimated height in terra-firme by 3% and overestimated it in várzea by 29%, while the pantropical model underestimated height in terra-firme by 19% and overestimated it in várzea by 6%. Using local asymptotic models to estimate height improved the accuracy of biomass estimates, with differences of around 1% between biomass computed using measured heights and estimated heights for terra-firme and várzea forests. In contrast, the biomass calculated using estimated heights from both the regional and pantropical models overestimated the biomass in várzea by 41% and 17%, respectively, while the pantropical model underestimated biomass in terra-firme by 17%. The estimated height and biomass of large trees using regional and pantropical models showed the highest deviations from the observed values. Our findings underscore the necessity for height-diameter modeling for different forest types, and highlight the need to increase sampling of large trees to improve biomass estimation accuracy in Northeastern Amazonia.


Trait space of 353 Amazonian tree genera on 2253 plots with genus level identification
Only genera with complete trait data were used (353 genera, of the 812 in our plots). PC1 has an Eigenvalue of 2.98 and represents the leaf economic spectrum (SLA, N, P, C:N). PC2 (Eigenvalue 1.62) represents the stature-recruitment trade-off (WD, SM) and is strongly linked to short lived pioneers (SLP, negatively) and old-growth species and maximum diameter (OGS, Max, positively). Legend: Colours indicate the probability of trait combinations in the trait space defined by the PCA (red = high probability; yellow = low probability). Contour lines indicate 0.99, 0.50, and 0.25 quantiles of the probability distribution. N leaf nitrogen concentration, C:N ratio of leaf carbon to leaf nitrogen, SLA specific leaf area, SM seed mass, P leaf phosphorus concentration, AA aluminium accumulation, Nfix atmospheric N-fixation, WD wood density (overlapping with OGS), C leaf carbon content, FF fleshy fruit, EM ectomycorrhiza, Her hermaphroditic, Nectar nectar producing. Life histories (dark green): OGS old-growth species, LLP long-lived pioneer, SLP short-lived pioneer⁶⁴; Max, maximum diameter¹⁶⁵. For description of the traits and units, see Supplementary box 1.
Trait space of 2054 tree communities with traits at genus and species level
PC1 has an Eigenvalue of 4.39 (explained variance 33.3%), and appears to be related to the ‘leaf economic spectrum’ (SLA, N, P, C:N) but also WD, SMC, and hermaphroditism contribute to this axis. Life-history forms SLP and LLP are also positively correlated with PC1. Environmental factors sum of bases and pH are strongly positively correlated to this axis. PC2 is linked to nodulation of Fabaceae and fleshy fruits and poorly correlated to the climatic factors used. Legend: Colours indicate the probability of trait combinations in the trait space defined by the PCA (red = high probability; yellow = low probability). Contour lines indicate 0.99, 0.50, and 0.25 quantiles of the probability distribution. N leaf nitrogen concentration, C:N ratio of leaf carbon to leaf nitrogen, SLA specific leaf area, SM seed mass, P leaf phosphorus concentration, AA aluminium accumulation, Nfix atmospheric N-fixation, WD wood density, C leaf carbon content, FF fleshy fruit, EM ectomycorrhiza, Her hermaphroditic, Nectar nectar producing. Life histories (dark green): OGS old-growth species, LLP long-lived pioneer, SLP short-lived pioneer⁶⁴; Environmental variables: Annual, Annual precipitation (Bioclim12)¹⁶⁶; CWD cumulative water deficit, CAPE Convective atmospheric potential energy⁶⁵, WTC Windthrow count⁶⁵; PZ podzol, white-sand forest, FL flooded (swamp forest; várzea; igapó); pH, soil acidity; SB, log(sum of bases)¹⁵⁴; G.prob, geoglyph probability⁵⁸; DSpp, domesticated species⁵⁷. Note that SLA, N and P are overlapping, as are DSpp, G.prob, pH and SB. For description of the traits and units, see Supplementary box 1.
PC1 plot scores of community trait values related to forest types and Amazon regions. a ‘The fast-slow forest spectrum’ as determined by forest type
‘The fast-slow forest spectrum’ is associated mostly with the economic spectra, and the order of forest types appears determined by general soil fertility (see Supplementary Fig. 29a). Note the very high value of the poorest soils in Amazonia (lowest sum of bases (Supplementary Fig. 29a), white sand podzol (PZ). b‘The fast-slow forest spectrum’ as determined by Amazonian region. The order of regions also appears follow general soil fertility (Supplementary Fig 29b). From rich to poor: TFPB terra firme Pebas Formation, VA várzea, SW swamp forest, TFBS terra firme Brazilian Shield, IG igapó, TFGS terra firme Guiana Shield, PZ white sand forest, SWA south west Amazonia, NWA northwest Amazonia, SA southern Amazonia, EA eastern Amazonia, CA central Amazonia, GS Guiana Shield. Colours follow the major forest type (SWA, NWA: TFPB; SA: TFBS; CA, GS: TFGS; EA: mix of TFBS, TFGS). Red dotted line: mean of all data.
Functional characterisation of Amazonian forests
Forest with positive score on the ‘fast-slow forest spectrum’ (yellow, beige) are forests at the “slow”, tough side of economic spectra (high CN ratio, low SLA, N and P), high wood density, low numbers of fleshy fruit, high levels of hermaphroditism, high in nectar producing individuals, occurring mainly on low to very low nutrient soils. Forests with negative score on the ‘fast-slow forest spectrum’ (blue, purple) are the opposite in terms of trait values and occur mainly on nutrient rich soils. The isolines divide Amazonia into three regions, tough-slow (PC1 > 0.65, yellow-beige), soft-fast (PC1 < -1.2 blue-purple) and intermediate (green). Colouring the plots based on their PC1 scores shows that their colour mostly matches the area colour, except if they are white sand plots (PZ) in a green area, and várzea plots (blue dots) in green and yellow areas. Note that the legend has been truncated at 2 standard deviations. Red polygon: Amazonian Biome limit¹⁶⁷. Base map source (country.shp, rivers.shp), ESRI (http://www.esri.com/data/basemaps, © Esri, DeLorme Publishing Company).
The ‘fast-slow forest spectrum’ and soil fertility as potential drivers of aboveground biomass and biomass productivity
a ‘Slow’ forests (positive value) have much higher above ground woody biomass (AWB) than ‘fast’ forests (negative values) b Absolute above ground woody productivity (AGWP) does not vary significantly with the ‘fast-slow forest spectrum’. c Biomass produced per biomass standing (= Relative AGWP [100*AGWP/AGB]) is highest in ‘fast’ forests (negative values for slow-fast forest spectrum). d Relative AGWP is positively correlated with predicted sum of bases¹⁶. Red lines indicate 95% confidence intervals. Biomass data from sources55,83,168. Colours: Red, terra firme Pebas formation; brown, terra firme Brazilian Shield; orange, terra firme Guiana Shield; yellow, white sand forest; purple, swamp forest; light blue, várzea.
Functional composition of the Amazonian tree flora and forests

March 2025

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996 Reads

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1 Citation

Communications Biology

Plants cope with the environment by displaying large phenotypic variation. Two spectra of global plant form and function have been identified: a size spectrum from small to tall species with increasing stem tissue density, leaf size, and seed mass; a leaf economics spectrum reflecting slow to fast returns on investments in leaf nutrients and carbon. When species assemble to communities it is assumed that these spectra are filtered by the environment to produce community level functional composition. It is unknown what are the main drivers for community functional composition in a large area such as Amazonia. We use 13 functional traits, including wood density, seed mass, leaf characteristics, breeding system, nectar production, fruit type, and root characteristics of 812 tree genera (5211 species), and find that they describe two main axes found at the global scale. At community level, the first axis captures not only the ‘fast-slow spectrum’, but also most size-related traits. Climate and disturbance explain a minor part of this variance compared to soil fertility. Forests on poor soils differ largely in terms of trait values from those on rich soils. Trait composition and soil fertility exert a strong influence on forest functioning: biomass and relative biomass production.


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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973 Reads

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2 Citations

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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1,969 Reads

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2 Citations

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.


Technical-scientific production and knowledge networks about medicinal plants and herbal medicines in the Amazon

June 2024

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160 Reads

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4 Citations

Frontiers in Research Metrics and Analytics

Introduction: This paper explores the role of Brazilian research institutions in the global and national context of study of medicinal plants. Most of these plants have ethnopharmacological use and herbal medicines related to the Amazon. It highlights Brazil's position in scientific production and the importance of Amazonian resources in developing phytomedicines. The study aims to provide an overview of the technical-scientific production of medicinal plants and herbal medicines related to the Amazon, focusing on scientific impact, collaboration, Technology Readiness Level (TRL) of scientific production, and innovation system maturity. Methods: The study employs a comprehensive methodological approach, including data collection from Scopus covering the period from 2002 to 2022. The data was cleaned and analyzed using bibliometric and network analysis techniques. Advanced natural language processing techniques, such as Latent Dirichlet Allocation and Jaccard distance measure, were used for TRL classification. Results: The findings reveal a predominant contribution from Brazilian institutions and authors, with 1,850 publications analyzed. Key areas identified include Pharmacology, Toxicology, Pharmaceuticals, Medicine, and Biochemistry. The study also uncovers various collaborative networks and technological maturity levels, with a significant focus on early-stage development phases. Discussion: The research concludes that Brazilian institutions, particularly those in the Amazon region, play a significant role in the scientific exploration and development of medicinal plants and herbal medicines. Despite this, countries like the USA were proportionally more productive in clinical trial research. The study underscores the potential of Brazil's rich biodiversity and traditional knowledge in the pharmaceutical industry, particularly for neglected diseases. It suggests the need for stronger research systems and international collaboration to leverage these resources for global health benefits.



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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1,254 Reads

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18 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.


The evolutionary space is occupied by Amazonian tree communities. Scatterplots of the first two evoPCA axes mapping the tree communities' scores according to geographic regions and forest types. The first axis of the evoPCA recovered a longitudinal gradient in the differentiation of the phylogenetic composition of Amazonian tree communities that mirrors terra‐firme and the wetland forest differentiation. The second axis mainly separates terra‐firme from white‐sand and wetland forests. The contour lines show the central tendency (50% of plots) for each forest type in each geographic region. Contour lines could not be calculated for subsets of plots with low sample size (e.g., in wetland and white‐sand forests of the southern Amazonia). Forest types: TF – Terra‐Firme; PZ – White‐Sand; VA – Várzea; IG – Igapó; SW – Swamp.
First two axes of variation in the phylogenetic composition of tree communities across Amazonia. The maps show scores for the first two evoPCA axes together describing 21.6% of the overall variation. The colour of the circles reflects values for evoPCA scores with similar colours indicating tree communities with similar phylogenetic composition. The location of the communities was slightly jittered to reduce circles overlapping. Please see Figure S7 for maps for each of the first 13 evoPCA axes and Figure S8 for spatially constrained phylogenetic composition patterns corresponding to the significantly constrained axes from a redundancy analysis of the evoPCA axes against selected spatial eigenvectors (MEMs).
The percentage of significant indicator species and higher‐level evolutionary lineages for (a) geographic regions or (b) forest types. A total of 5082 species and 1980 higher‐level evolutionary lineages were tested as indicators for geographic regions or forest types numbers inside bars correspond the totals of species and lineages determined as indicators for a given geographic region or forest type. Geographic regions: NWA – Northwestern Amazonia; CA – Central Amazonia; SWA – Southwestern Amazonia; GS – Guiana Shield; EA – Eastern Amazonia; SA – Southern Amazonia. Forest types: TF – Terra‐Firme; PZ – White‐Sand; VA – Várzea; SW – Swamp; IG – Igapó. For a complete list of significant indicator lineages, please refer to Table S1 and Figure S11 for the mapping of indicator lineages onto the phylogeny of Amazonian trees.
The proportion of indicator lineages in different time bins for geographic regions (a) and forest types (b). Bar plots represent the proportion of lineages with significant indicator values in each time bin. Time slice 0–0 represents the tips of the phylogeny (i.e., species) whereas the other time slices represent internal nodes of the phylogeny (i.e., higher‐level evolutionary lineages). The width of the time bins is distributed in an approximately logarithmic manner. Among regions, the Southwestern and Central Amazonian regions show a greater proportion of indicator lineages going deep in evolutionary time (higher‐level lineages that were determined as indicators). Among forest types, terra‐firme and white‐sand forests show a greater proportion of higher‐level indicator lineages.
Geography and ecology shape the phylogenetic composition of Amazonian tree communities

February 2024

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1,178 Reads

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9 Citations

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.


Consistent patterns of common species across tropical tree communities

January 2024

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2,124 Reads

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37 Citations

Nature

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1–6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories⁷, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.


Citations (78)


... These forests often contain a higher proportion of large (DBH > 30 cm) and tall trees (reaching over 70 m in height; [64]). For instance, large trees in lowland forests of the Amapá National Forest have an average height of 32 m [65], whereas trees of similar diameter typically reach lower heights in the dense forests of the southwestern (24 m) and central (27 m) Amazon [66]. Dominant large-tree species in the region, such as Dinizia excelsa, Manilkara spp., and Vouacapoua americana, are characterized by high wood density, which contributes substantially to the aboveground biomass in Amapá ′ s forests [28,29]. ...

Reference:

Dense Forests in the Brazilian State of Amapá Store the Highest Biomass in the Amazon Basin
Tree height-diameter allometry and implications for biomass estimates in Northeastern Amazonian forests

... However, it has been suggested that isoprene synthase has evolved from terpene synthases (Sharkey et al., 2013;Li et al., 2017). Considering the high species richness and complexity of ecological interactions observed in Amazonian tree communities (Cardoso et al., 2017;ter Steege et al., 2025), and the importance of monoterpenes for plant signaling (Gershenzon and Dudareva, 2007;Fineschi and Loreto, 2012;Xiao et al., 2012), we argue that it would be highly advantageous for an isoprene-emitting species to retain terpene synthase genes and be able to produce both compounds. Moreover, the fact that we have observed many species emitting both isoprene and monoterpenes (12 species) or only monoterpenes (15 species) versus two species that only emitted isoprene and two species that did not emit any VIs further supports this, but more research would be needed to test this hypothesis. ...

Functional composition of the Amazonian tree flora and forests

Communications Biology

... Plants increase their productivity and tend to die younger because they have invested all their energy in growth rather than defense and longevity. For example, plants of the same species in fertile soils tend to grow faster and have lower wood density, so they are more likely to break in stronger winds (23,56,71,72). ...

Phylogenetic conservatism in the relationship between functional and demographic characteristics in Amazon tree taxa

... Additionally, the considerable diversity of species in certain plant families like Melostomataceae, which produce small fruits important for many frugivore species, may also play a key role in sustaining high values of β-diversity (Messeder et al. 2021). The elevated β-diversity observed may reflect the elevated functionality of the systems (Mori et al. 2018), highlighting the immense complexity of megadiverse regions (Valiente-Banuet et al. 2015, Solar et al. 2015, Bruno et al. 2024. ...

The biogeography of the Amazonian tree flora

Communications Biology

... Floodplains are characterized by tropical forests, regionally known as "mata-de-várzea," which host approximately 17% of the tree species found in the Amazon basin (Householder et al. 2024), of which a group of 301 tree species have been identified as floodplain specialists. Most tree species exhibit a strong preference for a specific floodplain habitat type: 51% (154 species) favored várzea, while 38% (115 species) preferred igapó. ...

One sixth of Amazonian tree diversity is dependent on river floodplains

Nature Ecology & Evolution

... The concept of biome conservatism (the tendency of organisms to remain in the same broad environmental conditions over evolutionary time, with low biome shift rates) and phylogenetic niche conservatism (the tendency of species to retain their ecological requirements and related functional traits) have emerged as consensus explanations for understanding patterns of phylogenetic clustering within regions in global analyses (Fine and Lohmann 2018;Segovia et al. 2020). Recent findings suggest that environmental associations of lineages may be the primary force organising the course of diversification, but a key knowledge gap is in studies comparing the degree of evolutionary similarity among species assemblages at large geographic scales (Luize et al. 2024;Rezende et al. 2020a). ...

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

... for example, done by Lenoir et al. 2020). Such analyses could include investigations of global latitudinal trends in biodiversity (Nishizawa et al. 2022), trends for the CMI or MCWD (Zuidema et al. 2022), patterns in hyperdominance (Cooper et al. 2024), or the 'odd man out' pattern of lower tree diversity in Africa (Hagen et al. 2021). As a large fraction of terrestrial plant species are rare (Enquist et al., 2019;Dinerstein et al. 2020), it was interesting to find that 20,732 (43.1%) of tree species occurred in a single botanical country (and thus were found to be endemic to that country), while 39,591 (82.3%) of species occurred in five or fewer such countries. ...

Consistent patterns of common species across tropical tree communities

Nature

... His revised ideas on speciation, emphasizing local adaptation and specialization (Gentry, 1989), seem to have been quietly validated in the decades since he reformulated them. Ecological and evolutionary studies across the Amazon are identifying local edaphic conditions as strong predictors for the diversity of these rainforests (Fortunel et al., 2014;ter Steege et al., 2023). While this process is acknowledged to most likely contribute to the diversification across Amazonia (Antonelli et al., 2018a), very few studies explicitly test this hypothesis. ...

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

Communications Biology

... Nos últimos anos, o sensoriamento remoto tem se tornado uma ferramenta essencial para investigar os efeitos históricos dessa interação entre o homem e o ecossistema. Mesmo em sítios arqueológicos amplamente conhecidos e estudados, o uso de sensores ativos como o Radar de Abertura Sintética (SAR), e o Light Detection and Ranging (LiDAR), tem revolucionado o conhecimento desses vestígios que persistem ao longo do tempo e revelam novas descobertas e conexões [5][6][7][8][9][10][11][12][13]. O caso da floresta Amazônica é um exemplo icônico, onde sociedades pré-colombianas moldaram a paisagem de maneiras ainda visíveis e mensuráveis por tecnologias de sensoriamento remoto [13]. ...

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

Science

... Data quality in prioritization is hampered by biases in knowledge about Amazonian species, favoring certain taxonomic groups and accessible regions (Carvalho et al., 2023). Over half of the upland areas in the Amazon remain poorly studied, particularly those within indigenous lands and more conserved regions (Carvalho et al., 2023). ...

Pervasive gaps in Amazonian ecological research

Current Biology