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advances.sciencemag.org/cgi/content/full/1/10/e1500936/DC1

Supplementary Materials for

Estimating the global conservation status of more than 15,000

Amazonian tree species

Hans ter Steege, Nigel C. A. Pitman, Timothy J. Killeen, William F. Laurance, Carlos A. Peres,

Juan Ernesto Guevara, Rafael P. Salomão, Carolina V. Castilho, Iêda Leão Amaral, Francisca Dionízia de

Almeida Matos, Luiz de Souza Coelho, William E. Magnusson, Oliver L. Phillips, Diogenes de Andrade

Lima Filho, Marcelo de Jesus Veiga Carim, Mariana Victória Irume, Maria Pires Martins, Jean-François

Molino, Daniel Sabatier, Florian Wittmann, Dairon Cárdenas López, José Renan da Silva Guimarães,

Abel Monteagudo Mendoza, Percy Núñez Vargas, Angelo Gilberto Manzatto, Neidiane Farias Costa Reis,

John Terborgh, Katia Regina Casula, Juan Carlos Montero, Ted R. Feldpausch, Euridice N. Honorio

Coronado, Alvaro Javier Duque Montoya, Charles Eugene Zartman, Bonifacio Mostacedo,

Rodolfo Vasquez, Rafael L. Assis, Marcelo Brilhante Medeiros, Marcelo Fragomeni Simon, Ana Andrade,

José Luís Camargo, Susan G. W. Laurance, Henrique Eduardo Mendonça Nascimento, Beatriz S.

Marimon, Ben-Hur Marimon Jr., Flávia Costa, Natalia Targhetta, Ima Célia Guimarães Vieira,

Roel Brienen, Hernán Castellanos, Joost F. Duivenvoorden, Hugo F. Mogollón, Maria Teresa Fernandez

Piedade, Gerardo A. Aymard C., James A. Comiskey, Gabriel Damasco, Nállarett Dávila, Roosevelt

García-Villacorta, Pablo Roberto Stevenson Diaz, Alberto Vincentini, Thaise Emilio, Carolina Levis,

Juliana Schietti, Priscila Souza, Alfonso Alonso, Francisco Dallmeier, Leandro Valle Ferreira, David Neill,

Alejandro Araujo-Murakami, Luzmila Arroyo, Fernanda Antunes Carvalho, Fernanda Coelho Souza,

Dário Dantas do Amaral, Rogerio Gribel, Bruno Garcia Luize, Marcelo Petrati Pansonato, Eduardo

Venticinque, Paul Fine, Marisol Toledo, Chris Baraloto, Carlos Cerón, Julien Engel, Terry W. Henkel,

Eliana M. Jimenez, Paul Maas, Maria Cristina Peñuela Mora, Pascal Petronelli, Juan David Cardenas

Revilla, Marcos Silveira, Juliana Stropp, Raquel Thomas-Caesar, Tim R. Baker, Doug Daly, Marcos Ríos

Paredes, Naara Ferreira da Silva, Alfredo Fuentes, Peter Møller Jørgensen, Jochen Schöngart, Miles R.

Silman, Nicolás Castaño Arboleda, Bruno Barçante Ladvocat Cintra, Fernando Cornejo Valverde, Anthony

Di Fiore, Juan Fernando Phillips, Tinde R. van Andel, Patricio von Hildebrand, Edelcilio Marques Barbosa,

Luiz Carlos de Matos Bonates, Deborah de Castro, Emanuelle de Sousa Farias, TheranyGonzales,

Jean-LouisGuillaumet, Bruce Hoffman, YadvinderMalhi, Ires Paula de Andrade Miranda, Adriana Prieto,

Agustín Rudas, Ademir R. Ruschell, Natalino Silva, César I. A. Vela, Vincent A. Vos, Eglée L. Zent,

Stanford Zent, Angela Cano, Marcelo Trindade Nascimento, Alexandre A. Oliveira, Hirma Ramirez-

Angulo, José Ferreira Ramos, Rodrigo Sierra, Milton Tirado, Maria Natalia Umaña Medina, Geertje van

der Heijden, Emilio Vilanova Torre, Corine Vriesendorp, Ophelia Wang, Kenneth R. Young,

Claudia Baider, Henrik Balslev, Natalia de Castro, William Farfan-Rios, Cid Ferreira, Casimiro Mendoza,

Italo Mesones,Armando Torres-Lezama, Ligia Estela Urrego Giraldo, Daniel Villarroel, Roderick Zagt,

Miguel N. Alexiades, Karina Garcia-Cabrera, Lionel Hernandez, Isau Huamantupa-Chuquimaco,

William Milliken, Walter Palacios Cuenca, Susamar Pansini, Daniela Pauletto, Freddy Ramirez Arevalo,

Adeilza Felipe Sampaio, Elvis H. Valderrama Sandoval, Luis Valenzuela Gamarra

Published 20 November 2015, Sci. Adv. 1, e1500936 (2015)

DOI: 10.1126/sciadv.1500936

This PDF file includes:

Use of the IUCN threat criteria

Caveats regarding deforestation scenarios

Caveats regarding population models

Caveats regarding the interaction between tree species populations and forest loss

Fig. S1. Map of Amazonia showing the location of the 1485 ATDN plots that

contributed data to this report.

Fig. S2. Map of lowland forests in the Amazon.

Fig. S3. Total deforestation of the Amazon by 2013.

Fig. S4. Deforestation and tree population declines in the Amazon.

Fig. S5. Deforestation and tree population declines of rare species in the Amazon.

Table S1. Deforestation and tree population declines of rare species in the

Amazon.

Fig. S6. Projected (including historical) deforestation in the Amazon by 2050 in

the BAU scenario.

Fig. S7. Projected (including historical) deforestation in the Amazon by 2050 in

the IGS.

Fig. S8. Protected areas and indigenous territories in the Amazon.

Fig. S9. How much of the Amazon is protected and how many individual trees do

protected areas protect?

Fig. S10. Rare species in protected areas and indigenous territories.

Table S2. Rare species in protected areas and indigenous territories.

Fig. S11. Protected areas and indigenous territories in the Amazon with

deforestation according to BAU scenario 2050.

Fig. S12. Protected areas and indigenous territories in the Amazon with

deforestation according to IGS 2050.

Fig. S13. How much forest loss has taken place and will take place in Amazonian

protected areas?

Fig. S14. Decline in relative population size shows no relationship with original

population size in (A) BAU scenario and (B) IGS.

Fig. S15. Interpolated stem density for the Amazon.

Fig. S16. Interpolated identification level of plots in the Amazon.

Fig. S17. Projected and observed deforestation in Amazonia from 2002 to 2013.

Table S3. IUCN categories, designations, and conversion into SCRs (1) and

SUIRs (2).

Legends for appendixes S1 to S5

References (39–83)

Other Supplementary Material for this manuscript includes the following:

(available at advances.sciencemag.org/cgi/content/full/1/10/e1500936/DC1)

Appendix S1 (Microsoft Excel format). Data by DGC.

Appendix S2 (Microsoft Excel format). Data by species.

Appendix S3 (Microsoft Excel format). Data of individuals by region.

Appendix S4 (Microsoft Excel format). Tree species estimated to occur in

Cristalino State Park in Brazil but not yet recorded there (32) and their estimated

threat status according to historical and projected deforestation.

Appendix S5 (Microsoft Excel format). Plot metadata.

Supplementary Text

Use of the IUCN threat criteria

Of the five different criteria used to determine IUCN Red List threat categories (39) we

focused on Criterion A, which is based on reductions in population size. Within Criterion A

users can select any of four sub-criteria, depending on the type of population loss. We

primarily used Criterion A4, which applies to cases in which a combination of historical and

future loss can be estimated.

Classifying a species as threatened under Criterion A4 requires demonstrating "an

observed, estimated, inferred, projected or suspected population size reduction of ≥30% over

any 10 year or three generation period, whichever is longer (up to a maximum of 100 years

in the future), where the time period must include both the past and the future, and where the

reduction or its causes may not have ceased OR may not be understood OR may not be

reversible, based on (and specifying) any of (a) to (e) under A1" (39). Any reduction of ≥30%

qualifies a species as globally threatened (39). A species qualifies as Vulnerable (VU) if the

reduction is ≥30%, Endangered (EN) if ≥50%, and Critically Endangered (CR) if ≥80% (39).

Applying Criterion A4 to our dataset required us to make two assumptions. First, we

assumed a mean generation time for Amazonian tree species of 50 years. Generation times

are not well documented; our assumption is conservative according to a recent estimate for

Neotropical trees in general (40). Our assumed three-generation period of 150 years

encompasses historic and projected forest loss between 1900 (when we assumed forest cover

to be 100%) and 2050 (1, 2). This is extremely conservative based on the IUCN's definition

of generation: "Generation length is the average age of parents of the current cohort (i.e.

newborn individuals in the population). Generation length therefore reflects the turnover rate

of breeding individuals in a population." (39).

Second, we assumed that a ≥30% population reduction in the Amazon for a given

species implies a ≥30% population reduction at the global scale. We believe this is a

reasonable assumption because all of the biogeographic regions neighboring the Amazon

(where the extra-Amazonian populations of the tree species in our dataset are most likely to

occur) have already suffered rates of forest loss that exceed those of the Amazon (15).

With regard to the five bases (a-e) which must be applied when Criterion A4 is used,

our analysis corresponds to b (an index of abundance appropriate to the taxon). Thus the full

criterion we used is A4b.

While A4b was the primary criterion, we also used Criterion A2b to determine what

the threat status of species would be if only historic forest loss were considered. Criterion

A2b is identical to A4b, except that it only incorporates historic population reductions, not

projected population reductions. In our case species that qualified as threatened under A2b

formed a subset of species that qualify as threatened under A4b.

It is worth noting that Criterion A4 has been used sparingly to date by

conservationists. Of the 19,738 land plant species evaluated so far by the IUCN, just 2% have

been listed based on Criterion A4. A similar figure applies to the most recent Brazilian red

list of threatened plants (19).

After applying Criteria A2 and A4, we asked how many of the species that did not

qualify as globally threatened under those criteria qualified as globally threatened under

Criterion C1. Criterion C1 classifies a species as globally threatened if "Population size [is]

estimated to number fewer than 10,000 mature individuals and…an estimated continuing

decline of at least 10% within 10 years or three generations, whichever is longer, (up to a

maximum of 100 years in the future) [is observed]…."

After applying Criterion C1, we asked how many of the remaining unthreatened

species qualified as globally threatened under Criterion D1. Criterion D1 classifies a species

as globally threatened if "Population size [is] estimated to number fewer than 1,000 mature

individuals."

Because Criteria C1 and D1 refer to global not Amazonian population sizes, applying

them required estimating how many of the species in our dataset do not occur outside of the

Amazon. Given the scarcity of empirical measurements of Amazonian endemism, we used

the figure 50%. This is very conservative, according to a recent paper estimating that the

entire Neotropical region contains 19,000–25,000 tree species (41).

Caveats regarding deforestation scenarios

Estimating how many Amazonian tree species are globally threatened depends to a large

degree on which projected deforestation scenario one uses. The BAU and IGS models were

originally developed to reflect a pessimistic and an optimistic scenario, respectively (2).

However, deforestation rates across the Amazon have declined faster than predicted by both

scenarios (1, 2, 5, 8, 15, 42, 43). Data from the PRODES Project

(http://www.obt.inpe.br/prodes/prodes_1988_2014.htm) show annual forest loss in the

Brazilian Amazon in 2003-2013 to have averaged 12,943 km2, which is 76% of that

predicted by the IGS scenario. This section describes why we believe both scenarios remain

relevant despite lower-than-predicted deforestation rates in recent years.

First, while observed deforestation rates between 2002 and 2013 were lower than

projected, deforestation was geographically concentrated in the areas predicted by IGS 2013

(Fig. S17): southern and eastern Amazonia. IGS predicted slightly lower-than-observed

deforestation in these areas and somewhat higher-than-observed deforestation rates in central

Amazonia. When we look at the difference between observed deforestation and projected

deforestation in individual grid cells (to quantify the error in projected deforestation), the vast

majority of cells show an error of -5 to +5 %, and larger errors are very rare (Fig. S17F). As

road access is of primary importance to deforestation, both actual and predicted deforestation

follow the main access pattern of Amazonia closely. These will also, arguably, be the areas

where deforestation will be concentrated in the very near future.

Second, deforestation rates remain constant or are increasing in the Amazonian

landscapes of the Andean nations, where they are driven by agriculture, illicit crop

production, petroleum exploration, mining and infrastructure development (44-50). A long

list of well-documented drivers threaten forests at the basin-wide scale: ranching (3), legal

and illegal logging (5, 51), dams (52, 53), recurrent fires (6, 54), droughts (55, 56) and the

interaction between climate change and land-use (7, 57-59). Recent policy initiatives in

Bolivia propose to expand agricultural landscapes from 3 to 13 Mha by 2025, a goal that

would triple already high annual deforestation rates (>200,000 ha yr-1) (15, 60, 61).

Similarly, industrial-scale oil palm plantations continue to be established on intact (primary)

forest landscapes in the Peruvian Amazon (62).

Third, after declining for many years, deforestation in the Brazilian Amazon rose by

28% between August 2013 and July 2014, while between August and November 2014

monthly tabulations increased by 100% compared to the previous year (63). The Forest Code

of Brazil stipulates that 80% of private properties should be conserved in the Amazon but this

has proven difficult to enforce and is challenged by a strong agri-business lobby (64).

Fourth, while a substantial portion of the Amazon is protected (2, 65) and PAs have

proven largely effective against deforestation (65-67), they remain vulnerable. For example,

PRODES data show that significant deforestation continues to occur inside PAs in

http://www.obt.inpe.br/prodes/prodes_1988_2014.htm

Amazonian Brazil (http://www.dpi.inpe.br/prodesdigital/prodesuc.php), which is not

predicted by the IGS scenario. Many Amazonian PAs are poorly funded and severely

understaffed (68); illegal mining and agriculture are commonly observed, especially in SUIRs

(69); some reserves face threats of being degazetted, downgraded, or downsized (30, 69); and

new legislation may permit mining in 10% of the area of Brazilian PAs, even SPRs (69).

Funding for protected areas in the non-Brazilian Amazon, which incorporates approximately

40% of the total biome, remains uncertain (69, 70) particularly in light of weak carbon

markets and the still unfulfilled expectations that REDD initiatives would provide revenues to

the PA systems in Andean countries (71).

Fifth, anthropogenic fire is increasing in the Arc of Deforestation in southern and

eastern Brazil, threatening the last intact areas and remnant fragments both inside and outside

PAs (72, 73). This fire-induced erosion of biodiversity is independent of deforestation rates,

jeopardizing the benefits achieved by initiatives to reduce biodiversity losses or greenhouse

gas emission (e.g. REDD) (54).

Sixth, the deforestation scenarios we used do not take into account losses due to dams,

many of which have now been planned in lowland Amazonia and the Andean piedmont (5, 8,

52, 53, 69). Hydroelectric reservoirs will kill substantial fractions of individuals of floodplain

specialists (74) (for a list of floodplain tree species see (14)) and altered hydrological regimes

will impact the recruitment, composition and richness of flooded forests. Most dams will

require road and power line networks creating additional factors that can increase the spatial

scale of forest disruption. Of all nine Amazonian countries Brazil will be most severely

impacted, with 143 dams operational or under construction, and 254 planned (75).

Finally, climate change poses a severe additional threat that was not taken into

account by the BAU and IGS scenarios. Especially in areas most impacted by historical

deforestation, projected decreases in precipitation and increases in forest flammability may

create conditions that are no longer capable of sustaining moist forest and thus accelerate

forest loss (5, 7, 76). This suggests that species that are largely restricted to southern and

eastern Amazonia (Appendix S3) may be even more vulnerable than we estimate.

Caveats regarding population models

As in (14), a fundamental assumption of our analyses is that the population size estimates

generated by spatial models are reasonably accurate. In that paper we argued that for

estimating population sizes the LOESS method was acceptable. Here we used a different

method of spatial interpolation, Inverse Distance Weighting (IDW), in order to prevent model

predictions from becoming negative and resurfacing at large distances from known locations

(as they do in LOESS models, due to polynomial effects). IDW does not have this property as

it is a distance-weighted average and abundances can never fall below zero. To avoid model

output suggesting that all species occur across all of Amazonia (with very low densities over

large areas), we truncated the relative density to zero at 4° (~444 km) from the closest plot

where the species was recorded. This was an arbitrary choice. In summary, the differences

between LOESS and IDW model output are negligible for population size but non-trivial for

spatial pattern.

Although our plot database has grown substantially since 2013, we removed a large

number of plots (those with fewer than 60% of the individuals identified to species). While a

large number of unidentified individuals has little effect on ecological patterns (77) it does

affect the spatial model of individual species because non-identification leads to false

absences. We assume that as species are mainly non-identified where they are rare, this will

have a minor effect of the final estimate of the number of individuals.

http://www.dpi.inpe.br/prodesdigital/prodesuc.php

Most species in the Amazon are rare (14) and did not occur in our plots. Do they exist

and does their pattern follow the diversity pattern of the more common species (36, 78)? We

previously argued that at least 16,000 tree species occur in Amazonia (14) and in fact have

found herbarium collections of ~12,000 species (ter Steege et al. unpublished data). Given the

low collecting intensity in Amazonia (< 500,000 unique collections of trees, i.e. <0.1

collections km-2), the large areas that are virtually unexplored, and the fact that many rare

species are expected to have very restricted ranges (13), we still believe 16,000 species is a

reasonable estimate for tree species in Amazonia (although our data now suggest 15,200).

Assuming a log-series distribution for relative abundances of species, areas with high alpha-

diversity are expected to have more rare species, as higher alpha-diversity theoretically leads

to higher number of singletons, doubletons, etc. This is also what is observed in our plots.

Caveats regarding the interaction between tree species populations and forest loss

Our model is simplistic in that it treats all species as equally impacted by forest loss. Here we

discuss two important exceptions: pioneer tree species (whose populations often increase

with forest loss) and timber species (whose populations often decline in the absence of forest

loss).

Our analyses underestimate population declines of timber species that are selectively

logged in standing forest (51, 79). For example, the forest cover data we used show that

central Guyana remains almost entirely forested, but field surveys there show that the timber

tree Chlorocardium rodiei has lost ~70% of adult individuals in the region (80). Other

valuable timber species in the Amazon whose populations are surely lower than our models

indicate include mahogany (Swietenia macrophylla, (81)), Cedrela spp., Cedrelinga

cateniformis, Dinizia spp., Mezilaurus itauba, Hura crepitans, Ocotea cymbarum, Virola

spp., and Calophyllum brasiliense. We do not know how many Amazonian tree species are

affected by selective logging, but at least 257 of the species in our study are known to be

logged commercially (82). In our threat assessment based on forest loss, 208 (IGS) and 80

(BAU) of these timber taxa were not considered threatened based on Criterion A4b.

Our analyses overestimate population declines in pioneer tree species and secondary

forest specialists, whose populations often increase in areas that are heavily deforested (83).

While these species should probably not be listed as threatened based on Criterion A4b,

removing them is unlikely to change the broader trends we observe for two reasons. First,

relatively few Amazonian tree species are strict pioneers. In a fragmented forest near

Manaus, Brazil that harbors more than 1,000 tree species, 33 pioneer species increased in

abundance following disturbance (83). If that is typical, then only ~3% of tree species in

Amazonian tree communities are expected to see population increases following forest loss.

Assuming 15,200 tree species in the Amazon, this gives 450 pioneer species. Second, after

disturbance pioneer species become especially common in the 50 m-wide strip of forest just

inside the forest edge, which effectively increases habitat loss for non-pioneer species. In

other words, a small pioneer guild may see increased populations following deforestation, but

those increased populations exacerbate population declines for non-pioneers.

Fig. S1. Map of Amazonia showing the location of the 1485 ATDN plots that contributed

data to this report. The white polygon marks our delimitation of the study area and consists of

567 1° grid cells (area = 6.29 million km2). Orange circles indicate plots on terra firme; blue

squares, plots on seasonally or permanently flooded terrain (várzea, igapó, swamps); yellow

triangles, plots on white-sand podzols. Background is from Visible Earth. Regions: CA,

central Amazonia; EA, eastern Amazonia; GS, Guiana Shield; SA, southern Amazonia;

WAN, northwestern Amazonia; WAS, southwestern Amazonia.

Figure S2. Map of lowland forest in the Amazon. The green area represents land area (33)

minus large water bodies (33), areas over 500 m elevation (34), and areas originally without

forest (1). Regions: CA, central Amazonia; EA, eastern Amazonia; GS, Guiana Shield; SA,

southern Amazonia; WAN, northwestern Amazonia; WAS, southwestern Amazonia.

Figure S3. Total deforestation of the Amazon by 2013. Green: original forest area as in Fig.

S2; Red: area of original forest lost by 2013 (1, 15). Regions: CA, central Amazonia; EA,

eastern Amazonia; GS, Guiana Shield; SA, southern Amazonia; WAN, northwestern

Amazonia; WAS, southwestern Amazonia.

Fig S4. Deforestation and tree population declines in the Amazon. Deforestation by 2013 (A),

projected (including historical) deforestation by 2050 with a (B) business-as-usual scenario (2050

BAU), and projected (including historical) deforestation by 2050 with (C) an improved governance

scenario (2050 IGS) (1). The effect of deforestation on the populations of 4953 Amazonian tree

species is given for 2013 (D) and two scenarios for 2050 (E,F). IUCN threat levels are as follows: VU

= Vulnerable (population loss ≥ 30%), EN = Endangered (population loss ≥ 50%), CR = Critically

Endangered (population loss ≥ 80%). Regions as in Fig. S1.

A D

B E

C F

Fig. S5. Deforestation and tree population

declines of rare species in the Amazon*.

The effect of deforestation on simulated

populations of 10,247 rare Amazonian tree

species (population size <106 individuals) in

2013 (A) and two scenarios for 2050:

business-as-usual (2050 BAU) (B) and

improved governance (2050 IGS) (C). IUCN

threat levels are as follows: VU = Vulnerable

(population loss ≥ 30%), EN = Endangered

(population loss ≥ 50%), CR = Critically

Endangered (population loss ≥ 80%). Regions

as in Fig. S1.

* example of one simulation

A

B

C

Table. S1. Deforestation and tree population declines of rare species in the Amazon. The

mean effect and standard deviation of deforestation on simulated populations (500

simulations) of 10,247 rare Amazonian tree species (population size <106 individuals) in

2013 (A) and two scenarios for 2050: business-as-usual (2050 BAU) (B) and improved

governance (2050 IGS) (C). IUCN threat levels are as follows: VU = Vulnerable (population

loss ≥ 30%), EN = Endangered (population loss ≥ 50%), CR = Critically Endangered

(population loss ≥ 80%). Regions as in Fig. S1.

A. 2013 current All sd CA sd EA sd GS sd SA sd WAN sd WAS sd

number of species 10,247 0 2,575 60 605 25 1,757 43 1,586 44 2,643 57 816 31

mean population loss (%) 8.3 0.2 2.0 0.2 44.1 1.8 0.6 0.1 23.7 0.9 2.8 0.3 5.8 0.7

median population loss 0.0 0.0 0.0 0.0 27.7 11.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

# species VU (loss 30-50%) 231 15 30 6 41 6 6 2 103 11 23 5 17 4

# species EN (loss 50-80%) 129 11 7 3 38 7 1 1 58 8 9 3 6 2

# species CR (loss > 80%) 607 23 25 5 219 15 5 2 275 15 49 7 30 5

# species <10,000, loss 10-30% 33 6 4 2 5 2 2 1 17 4 4 2 3 2

# species <1,000 loss < 30% 5,010 20 1,383 34 177 13 961 27 648 25 1,413 33 421 20

# species with IUCN threat class. 6,010 22 1,449 34 479 22 974 27 1,100 32 1,497 33 477 21

B. 2050 BAU All sd CA sd EA sd GS sd SA sd WAN sd WAS sd




# species VU (loss 30-50%) 595 24 140 13 16 4 117 13 109 10 115 12 60 8

# species EN (loss 50-80%) 516 20 116 16 20 5 84 11 125 16 68 9 34 6

# species CR (loss > 80%) 3,354 47 785 27 520 23 426 20 1,035 32 360 19 182 14

# species <10,000, loss 10-30% 76 9 22 5 2 1 12 4 13 4 19 4 8 3

# species <1,000 loss < 30% 3,239 38 872 27 35 6 647 24 205 15 1,171 31 307 18

# species with IUCN threat class. 7,780 36 1,935 46 593 25 1,287 34 1,487 42 1,733 38 591 25

C. 2050 IGS All sd CA sd EA sd GS sd SA sd WAN sd WAS sd




# species VU (loss 30-50%) 693 34 133 15 59 11 89 12 178 17 123 13 60 9

# species EN (loss 50-80%) 364 43 69 21 57 20 36 14 102 22 47 16 27 12

# species CR (loss > 80%) 1,533 37 334 19 317 18 167 12 384 20 214 15 106 11

# species <10,000, loss 10-30% 88 9 17 4 7 3 13 4 21 5 23 5 7 3

# species <1,000 loss < 30% 4,214 31 1,144 31 110 11 819 26 536 22 1,251 31 351 19

# species with IUCN threat class. 6,891 32 1,697 40 550 24 1,124 30 1,221 35 1,657 36 551 23

Figure S6. Projected (including historical) deforestation in the Amazon by 2050 in the

BAU scenario. Green: original forest area as in Fig. S2; Red: area of original forest projected

to be lost by 2050 (1). Regions as in Fig. S1.

Figure S7. Projected (including historical) deforestation in the Amazon by 2050 in the

IGS. Green: original forest area as in Fig. S2; Red: area of original forest projected to be lost

by 2050 (1). Regions as in Fig. S1.

Figure S8. Protected areas and indigenous territories in the Amazon. Green: original

forest area as in Fig. S2; dark blue: Strict Conservation Reserves (IUCN classes I-IV (37));

light blue: Sustainable Use and Indigenous Reserves (IUCN classes V-VI and all other

categories (37)); red: observed deforestation up to 2013 (1) inside reserves.

Fig. S9. How much of the Amazon is protected and how many individual trees do

protected areas protect? A. Fraction of grid cells in strict conservation reserves. B. Fraction

of grid cells in sustainable use and indigenous reserves. C. Fraction of populations of 4953

tree species within strict conservation reserves. D. Fraction of populations of 4953 tree

species within sustainable use and indigenous reserves.

A C

B D

Fig. S10 Rare species in protected areas and

indigenous territories*. Fraction of

populations of 10,247 rare tree species within

conservation reserves. A. strict conservation

reserves, B. sustainable use and indigenous

reserves, C. all reserves combined. Regions as

in Fig. S1.

* example of one simulation.

A

B

C

Table S2. Rare species in protected areas and indigenous territories. Mean and standard

deviation of the fraction of populations of 10,247 rare tree species within conservation

reserves. A. strict conservation reserves, B. sustainable use and indigenous reserves, C. all

reserves combined. Regions as in Fig. S1

A. 2013 Strict conservation All sd CA sd EA sd GS sd SA sd WAN sd WAS sd

number of species 10247 0 2628 47 614 22 1790 36 1620 33 2696 41 833 28

mean population in PA1 7.5 0.2 3.4 0.3 1.8 0.5 11.1 0.7 3.2 0.3 11.0 0.6 14.0 1.0

median population in PA1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

number of species <50% in SCR 9505 23 2546 46 604 22 1594 36 1572 31 2405 43 718 26

number of species 50-70% in SCR 162 14 19 4 2 1 41 6 14 3 68 8 19 4

number of species >70% in SCR 580 21 63 9 8 3 156 13 34 6 223 14 96 9

B. 2013 Sust Util & Ind Res All sd CA sd EA sd GS sd SA sd WAN sd WAS sd







C. 2013 All Reserves All sd CA sd EA sd GS sd SA sd WAN sd WAS sd







Figure S11. Protected areas and indigenous territories in the Amazon with deforestation

according to BAU scenario 2050. Green: Original forest area as in Fig. S1; dark blue: Strict

Conservation Reserves ( IUCN classes I-IV (37)); light blue: Sustainable Use and Indigenous

Reserves (IUCN classes V-VI and all other categories (37)); red: predicted total deforestation

by 2050 (1) inside reserve areas.

Figure S12. Protected areas and indigenous territories in the Amazon with deforestation

according to IGS scenario 2050. Green: original forest area as in Fig. S1; dark blue: Strict

Conservation Reserves ( IUCN classes I-IV (37)); light blue: Sustainable Use and Indigenous

Reserves (IUCN classes V-VI and all other categories (37)); red: predicted total deforestation

by 2050 (1) inside reserve areas.

Fig. S13. How much forest loss has taken place and will take place in Amazonian

protected areas? A. Fraction of grid cells inside protected area deforested by 2013. B. Same

for projected (including historical) deforestation by 2050 with the business-as-usual (BAU)

scenario. C. Same for projected (including historical) deforestation by 2050 with improved

governance (IGS) scenario. D. Fraction of number of individuals lost in portions of protected

areas deforested by 2013. E. Same for projected (including historical) deforestation by 2050

with BAU. F. Same for projected (including historical) deforestation by 2050 with IGS.

A D

B E

C F

Figure S14. Decline in relative population size shows no relationship with original population size in (A)

BAU and (B) IGS.

A B

Figure S15. Interpolated stem density for the Amazon. Stem density (no. of trees ≥10 cm dbh per ha) in

1,625 1-ha tree plots across Amazonia. The background color shows the LOESS interpolation of plot data for

one-degree grid cells (range 303–705 trees/ha).

Figure S16. Interpolated identification level of plots in the Amazon. LOESS interpolation of identification

level (percentage of individuals identified at plot level) of plots having ≥60% individuals identified to species

level. Red dots indicate the locations of the 1,480 plots.

Figure S17. Projected and observed deforestation in Amazonia from 2002 to 2013. A. Percentage of total

observed deforestation by 2002 per 1-degree grid cell (DGC) (1, 2). B. Percentage of total observed

deforestation by 2013 per DGC (1, 2, 15). C. Percentage of total deforestation projected by 2013 per DGC

according to the Improved Governance Scenario (IGS) (1, 2). D. Observed deforestation (=B-A) for the period

2002–2013 by DGC. E. Projected deforestation for the period 2002–2013 by DGC according to IGS (C-A) (1,

2). F. Frequency distribution of DGCs showing differences (in percentage DGC) between projected (IGS 2013)

and observed deforestation for the period 2002–2013. Negative differences correspond to pixels where observed

deforestation was higher than projected deforestation.

A B

C D

E F

Table S3. IUCN categories, designations, and conversion to SCRs (1) and SUIRs (2).

IUCN cat Designation N ATDNc

at

Ia Biological Reserve 13 1

Ia Ecological Station 14 1

Ia Forest Biological Reserve 1 1

Ia National Nature Reserve 1 1

Ia State Biological Reserve 3 1

Ia State Ecological Station 6 1

Ib Forest Biological Reserve 1 1

Ib Wildlife Reserve 1 1

II National Park 53 1

II National Park - Core Area 4 1

II Natural National Park 9 1

II Nature Park 1 1

II Nature Reserve 1 1

II State Forest 1 1

II State Park 25 1

III Historical Sanctuary 1 1

III National Sanctuary 3 1

III Natural Monument 22 1

IV Area of Outstanding Ecological Interest 25 1

IV Biotope Protection Order 3 1

IV Integrated Management Natural Area 5 1

IV Land acquired by Littoral and Lakeside Conservatory 5 1

IV National Nature Reserve 4 1

IV Nature Reserve 7 1

IV Wilderness Reserve/Managed Resource Use Area 3 1

IV Wildlife Refuge 7 1

Not Applicable Ramsar Site, Wetland of International Importance 6 1

Not Applicable UNESCO-MAB Biosphere Reserve 2 2

Not Applicable World Heritage Site 9 2

Not Reported Acquired Indigenous Area 4 2

Not Reported Area of Immobilization 4 2

Not Reported Biosphere Reserve 2 2

Not Reported Communal Reserve 3 2

Not Reported Dominial Indigenous Area 3 2

Not Reported Forest Plot 7 2

Not Reported Forest Reserve 10 2

Not Reported Indigenous Area 444 2

Not Reported Indigenous Reserve 76 2

Not Reported Indigenous Territory 2 2

Not Reported Multiple Use Management Area 2 2

Not Reported National Park 1 2

Not Reported National Sanctuary 1 2

Not Reported Natural Monument 3 2

Not Reported Natural National Park 2 2

Not Reported Natural Regional Park 3 2

Not Reported Natural Reserve 2 2

Not Reported Natural Reserve of Immobilization 1 2

Not Reported Nature Reserve 2 2

Not Reported Other Area 1 2

Not Reported Park 1 2

Not Reported Particular Reserve of Natural Heritage 4 2

Not Reported Private Regional Administration 71 2

Not Reported Regional Natural Park 2 2

Not Reported Regional Park 2 2

Not Reported Reserved Zone 5 2

Not Reported Scientific, Ecological and Archaeological Reserve 1 1

V Environmental Protection Area 214 2

V National Park - Buffer zone 17 2

V Protective Zone 6 2

V Regional Nature Park 2 2

V State Environmental Protection Area 309 2

V Sustainable Development Reserve 2 2

VI Amazonian National Wildlife Reserve 1 2

VI Biosphere Reserve 3 2

VI Communal Reserve 7 2

VI Community Owned Conservation Area 1 2

VI Ecological Reserve 1 2

VI Extractive Reserve 44 2

VI Faunal Production Reserve 1 2

VI Forest Reserve 5 2

VI Marine Extractive Reserve 6 2

VI Multiple Use Management Area 2 2

VI National Forest 37 2

VI National Protective Forests Reserves 5 2

VI National Reserve 5 2

VI Protection Forest 3 2

VI State Extractive Reserve 24 2

VI State Forest 93 2

VI State Park 1 2

VI State Sustainable Development Reserve 11 2

VI Sustainable Development Reserve 3 2

Legends of Excel Appendices

Appendix S1 Data by 1 degree grid cell

Longitude: Longitude of grid cell

Latitude: Latitude of grid cell

Region: Region in Amazon (see Fig. S1)

Treesha: Estimated number of trees per ha for grid cell

area (ha): Land area in grid cell with Amazonian forest

protected1: Fraction of original forest in strict conservation reserves

protected2: Fraction of original forest in sustainable utilization and

indigenous reserves

protected12: Overlap between protect1 and protected2

deforestation

defor13: Fraction of original forest deforested by 2013

defor50BAU: Fraction of original forest predicted to be lost by 2050 under business as usual

scenario

defor50IGS: Fraction of original forest predicted to be lost by 2050 under an improved

governance scenario

deforestation in PA’s

defor13: Fraction of original forest deforested in protected areas by 2013

defor50BAU: Fraction of original forest predicted to be lost protected areas by 2050 under

business as usual scenario

defor50IGS: Fraction of original forest predicted to be lost protected areas by 2050 under

an improved governance scenario

Area (km2)

AreaP1: Area (km2) of original forest land in strict conservation reserves

AreaP2: Area (km2) of original forest in sustainable utilization and

Indigenous reserves

P12: Overlap between protect1 and protected2

deforestation

defor13: Area (km2) of original forest deforested by 2013

defor50BAU: Area (km2) of original forest predicted to be lost by 2050 under

business as usual scenario

defor50IGS: Area (km2) of original forest predicted to be lost by 2050 under an

improved governance scenario

deforestation in PA’s

defor13: Area (km2) of original forest deforested in protected areas by 2013

defor50BAU: Area (km2) of original forest predicted to be lost in protected areas in

2050 under business as usual scenario

defor50IGS: Area (km2) of original forest predicted to be lost in protected areas in

2050 under an improved governance scenario

Appendix S2 Data by species

Species: Species names as verified by TNRS (62)

Estimated population: total number of estimated individuals in the Amazon forest

Fraction Population in PA1: Fraction of total number of individuals in strict conservation

reserves

Fraction Population in PA2: Fraction of total number of individuals in sustainable use and

indigenous reserves

Fraction Population lost 2013: Fraction of individuals estimated to be lost by 2013

Fraction Population lost 2050 BAU: Fraction of individuals estimated to be lost by 2050

under business as usual scenario (BAU)

Fraction Population lost 2050 IGS: Fraction of individuals estimated to be lost by 2050 under

improved governance scenario (IGS)

Fraction Population lost PA 2013: Fraction of individuals estimated to be lost within

protected areas by 2013

Fraction Population lost PA 2050 BAU: Fraction of individuals estimated to be lost within

protected areas under business as usual scenario (BAU)

Fraction Population lost PA 2050 IGS: Fraction of individuals estimated to be lost within

protected areas under improved governance scenario (IGS)

IUCN2013: IUCN threat classification for 2013

IUCN2050BAU: IUCN threat classification for 2050 business as usual scenario (BAU)

IUCN2050IGS: IUCN threat classification for 2050 improved governance scenario (IGS)

Appendix S3. Data of individuals by region.

Original number of individuals (regional checklists): total number of estimated individuals in

the Amazon forest by region. Regions as in Fig. S1

Individuals lost by deforestation 2013: Number of individuals estimated to be lost by 2013

Individuals lost by deforestation 2050 BAU: Number of individuals estimated to be lost by

2050 under business as usual scenario (BAU)

Individuals lost by deforestation 2050 Gov Scen: Number of individuals estimated to be lost

by 2050 under improved governance scenario (IGS)

Individuals protected by PA1: Number of total number of individuals in strict conservation

reserves

Individuals protected by PA2: Number of total number of individuals in sustainable use and

indigenous reserves

Individuals lost in PA 2013: Number of individuals estimated to be lost within protected

areas by 2013

Individuals lost in PA 2050 BAU: Number of individuals estimated to be lost within

protected areas under business as usual scenario (BAU)

Individuals lost in PA 2050 IGS: Number of individuals estimated to be lost within protected

areas under improved governance scenario (IGS)

Appendix S3. Tree species estimated to occur in Cristalino State Park, Brazil, but not yet

recorded there fide Zappi et al. (2011), and their estimated threat status according to historical

and projected deforestation. See text for explanation.

Species: species name according to TNRS (62)

Estimated IUCN threat status based on 1900–2013 forest loss (IUCN A2)

Estimated IUCN threat status based on 1900–2050 BAU forest loss (IUCN A4)

Estimated IUCN threat status based on 1900–2050 IGS forest loss (IUCN A4)

Appendix S5. Plot metadata

ATDNNR: nr in ATDN database

Country: country in which plot is located

Subdivision: mostly province

Site: site name

PlotCode: Unique ATDN plot code

Latitude, Longitude

PlotSize: plot size in ha.

PlotType: single: 1 single contiguous area; combi; few plots very close added together; pcq:

plots built from point center quarter data. Plot size equivalent calculated from tree density

estimate.

DBHmin: min dbh cut off

Year_est: Year in which the plot was established (not necessarily the census year)

Owner/contact: Owner of plot data

Source: literature reference of plot data. This source does not always contain the full data set.

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