Quantifying and sustaining biodiversity in tropical
agricultural landscapes
Chase D. Mendenhalla,b,c,1, Analisa Shields-Estradaa,b, Arjun J. Krishnaswamia,d, and Gretchen C. Dailya,b,e,f,1
a
Center for Conservation Biology, Stanford University, Stanford, CA 94305; bDepartment of Biology, Stanford University, Stanford, CA 94305; cThe Nature
Conservancy, Arlington, VA 22203; dDepartment of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305; eStanford Woods
Institute for the Environment, Stanford University, Stanford, CA 94305; and fThe Natural Capital Project, c/o Department of Biology and Stanford Woods
Institute, Stanford, CA 94305
Edited by Simon A. Levin, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, and approved September 27, 2016 (received
for review May 19, 2016)
Decision-makers increasingly seek scientific guidance on investing
in nature, but biodiversity remains difficult to estimate across diverse
landscapes. Here, we develop empirically based models for quanti-
fying biodiversity across space. We focus on agricultural lands in the
tropical forest biome, wherein lies the greatest potential to conserve
or lose biodiversity. We explore two questions, drawing from
empirical research oriented toward pioneering policies in Costa
Rica. First, can remotely sensed tree cover serve as a reliable basis
for improved estimation of biodiversity, from plots to regions?
Second, how does tropical biodiversity change across the land-use
gradient from native forest to deforested cropland and pasture?
We report on understory plants, nonflying mammals, bats, birds,
reptiles, and amphibians. Using data from 67,737 observations of
908 species, we test how tree cover influences biodiversity across
space. First, we find that fine-scale mapping of tree cover predicts
biodiversity within a taxon-specific radius (of 30–70 m) about a
point in the landscape. Second, nearly 50% of the tree cover in
our study region is embedded in countryside forest elements,
small (typically 0.05–100 ha) clusters or strips of trees on private
property. Third, most species use multiple habitat types, including
crop fields and pastures (to which 15% of species are restricted),
although some taxa depend on forest (57% of species are restricted
to forest elements). Our findings are supported by comparisons of 90
studies across Latin America. They provide a basis for a planning
tool that guides investments in tropical forest biodiversity similar
to those for securing ecosystem services.
|
conservation science countryside biogeography | ecosystem services |
|
extinctions species–area relationship
W hat is the potential of sustaining biodiversity and ecosystem
services in agricultural landscapes? The future of biodiversity
hinges on the answer, given the limited scope for expanding pro-
tected areas. Moreover, the generation and delivery of many vital
ecosystem services occurs on local to regional scales in social–
ecological systems where people make their livelihoods through
cropping, grazing, forestry, and other rural activities. The answer
is incomplete, but appears to be “high” (e.g., refs. 1–3). A further
question, however, is how can this potential for conservation into
the Anthropocene can be realized, with land use, other dimen-
sions of global change, and rates of extinction intensifying rapidly
worldwide (4–6) and weak institutions for protecting the global
commons (7)?
Efforts to secure biodiversity and ecosystem services in rural
landscapes are expanding and becoming more sophisticated (e.g.,
refs. 8 and 9). In the case of ecosystem services, both scientific and
policy support for targeting investments have advanced rapidly (10,
11). In China, for example, 200 million people presently are being
paid to engage in conservation and restoration activities; since
2000 these investments have resulted in many ecosystem service
improvements, although not in biodiversity, at a national scale (12,
13). By contrast, scientific support for targeting biodiversity in-
vestments remains limited by relatively coarse and underdeveloped
data, models, practical tools, and implementation efforts (14). This
14544–14551 | PNAS | December 20, 2016 | vol. 113 | no. 51
limitation is a bit ironic, because ecosystem services science was
opened originally as a pathway for understanding human dependence
on biodiversity and for motivating efforts to stem biodiversity
loss (15–17).
Here we address two key questions for guiding investments in
ecosystems services to benefit biodiversity. We seek answers to
our questions in the context of Costa Rica, a nation remarkable
for its rich biodiversity and for its innovative ecosystem services
policies, launched in 1996, that presently pay landowners for ser-
vices provided by forests ≥2.0 ha in size (18). The first question is
whether tree cover estimates from satellites can serve as a reliable
basis for improved estimation of biodiversity, on scales ranging
from plots to regions. The second question is how biodiversity
changes along the land-use gradient from native forest to defor-
ested crop and pasture lands, again on scales ranging from plots to
regions. We explore biodiversity at three levels: (i) the total
number of species across a region (γ-diversity), broadly comparing
forested and deforested areas; (ii) the total number of species at a
point or plot on a landscape (α-diversity); and (iii) changes in
species and abundances across different habitats (β-diversity). We
draw lessons from an intensively studied region of Costa Rica and
then generalize our findings through an intensive survey of studies
across Latin America. We focus on the tropical forest biome be-
cause it hosts most of the world’s terrestrial biodiversity.
Results
To guide investments in biodiversity across previously for-
ested agricultural landscapes, we first asked what character-
istics of a region can be remotely sensed using satellite images
to quantify biodiversity across space. We focused on remotely
sensing tree cover because it is a good predictor of biodiversity
in deforested tropical regions (3, 19). Moreover, we start our
approach by identifying tree cover at the finest spatial scales
feasible using satellite images, for two reasons. First, pre-
vious studies of bats and birds suggest that biodiversity re-
sponds to changes in small areas, such as the area inside a
circle with a 50- to 70-m radius (3, 19). Second, resampling or
aggregating tree cover from smaller to larger scales is simple
with spatial data. To estimate biodiversity for our regional
case study, we created a finely detailed tree cover map for Coto
This paper results from the Arthur M. Sackler Colloquium of the National Academy of
Sciences, “Coupled Human and Environmental Systems,” held March 14–15, 2016, at the
National Academy of Sciences in Washington, DC. The complete program and video
recordings of most presentations are available on the NAS website at www.nasonline.
org/Coupled_Human_and_Environmental_Systems.
Author contributions: C.D.M. and G.C.D. designed research; C.D.M., A.S.-E., and A.J.K.
performed research; C.D.M. analyzed data; and C.D.M. and G.C.D. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
1
To whom correspondence may be addressed. Email: cdm@stanford.edu or gdaily@
stanford.edu.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1604981113/-/DCSupplemental.
www.pnas.org/cgi/doi/10.1073/pnas.1604981113
 COLLOQUIUM
PAPER
SUSTAINABILITY
SCIENCE
Fig. 1. Using tree cover, we spatially modeled biodiversity across a diverse region of Costa Rica. (A) First, we remotely sensed tree cover at a fine spatial
resolution (0.61 m) across the canton of Coto Brus (934 km2). (B) Tree cover is concentrated in protected areas. (C) Nearly 50% of tree cover in Coto Brus is
embedded in smaller countryside forest elements (0.05–100 ha), clusters, or strips of trees. We created models that predict biodiversity at a point in space,
using the proportion of tree cover within a spatial scale specific to each taxonomic group.

Brus, Costa Rica (Fig. 1A) by measuring the surface area of When we used our remote sensing technique to estimate tree
land covered by large tree canopies (≥10 m in diameter). We cover, fully 100% of the 46 randomly selected sites across the
identified all the tree cover across the 934-km2 Costa Rican Coto Brus region agreed with ground observations of habitat
canton (Fig. 1B). classifications of forest and nonforest. Moreover, measurements

A Total number of plant and vertebrate B

1.0 Las Cruces
species from Coto Brus, Costa Rica
0.9 Forest Reserve &
0.8 smaller forest
Propportion of speciies

Las Cruces Forest Reserve &

countryside forest elements sites only elements only
0.7
Both
0.6 Both
0.5
0.4
00.33
0.2
Crop field &
0.1 pasture sites only
137 249 522 0.0
NF mammals (22)
Bats (40)

Reptiles (39)
Amphibians (28)
Plants (5516)

Birds (2263)

Crop field & pasture sites only

Fig. 2. (A) Of the 908 species recorded at all sites, 58% were observed only in forest sites, and 15% were observed only in crop field and pasture sites.
(B) Taxonomic groups varied in their response to deforestation and use of crop fields and pastures. Overall, the total number of species in each broad habitat
type of forest and nonforest, i.e., the γ-diversity of each habitat, was 771 species from all sites in forest elements (n = 101) and 386 species from all sites in crop
fields and pastures (n = 81). NF mammals, nonflying mammals.

Mendenhall et al. PNAS | December 20, 2016 | vol. 113 | no. 51 | 14545
of canopy cover taken inside each 0.05-ha site across the region
showed no differences in canopy cover between forest sites inside A 140 B 14 Las Cruces Forest Reserve
Countryside forest elements
Plants 12 Crop fields & pastures

Modeled species richness (mean ± SD )

a protected area (Las Cruces Forest Reserve) (Fig. 1B) and 120

Observed species richness

forest sites on private property (mean canopy cover ± SD, 84 ± 10
100
14% canopy cover, n = 23 sites). Sites in crop fields, mostly 8
coffee plantations, and pastures had significantly less tree canopy 80
* 6
cover than sites inside forests (mean canopy cover ± SD, 43 ± 60 Non-flying
34%; n = 23 sites), much of it in the form of banana plants and 4 mammals
40
trees used for agricultural purposes. 2
According to our remotely sensed tree cover map, nearly 50% 20
0
of the tree cover in Coto Brus is embedded in rural agricultural 0 0 0.2 0.4 0.6 0.8 1
land, much of it in small and complexly configured “countryside Crop fields & Countryside forest Las Cruces Forest
pastures (n = 9) elements (n = 27) Reserve (n = 8)
Proportion of tree cover within 70 m
forest elements” mostly on private property (Fig. 1C). These
elements comprise trees lining property boundaries, scattered C 40 Las Cruces Forest Reserve
Countryside forest elements
D 200
180
35
across pastures, and in winding, filamentous configurations over

± CI )

± )
Crop fields 160

Modeled species richness (estimate ±SE

Modeled species richness (estimate ±95
complex terrain in interconnected forms that typically cannot 30
140
be considered isolated forest patches. Collectively, countryside 25 120 Birds
forest elements cover ca. 264 km2, i.e., 40% of the 654 km2 of 20 100
the land outside the protected areas (Fig. 1B). 15 Bats
80
Taken together, tree cover estimates at a fine scale reveal two 10
60
40 Las Cruces Forest Reserve
broad habitat types in Coto Brus, where we conducted bio- 5 Countryside forest elements
20
diversity sampling: (i) forest elements, both inside legally pro- Crop fields
0 0
tected areas (public and private) and on legally unprotected 0 0.2 0.4 0.6 0.8 1 0 0.2 0.4 0.6 0.8 1
private property, and (ii) crop fields and pastures, virtually all Proportion of tree cover within 60 m Proportion tree cover within 30 m
on legally unprotected private property. To quantify the total
number of species in these two broad habitat types, we sampled E 10
9 Reptiles
F 10
9
Amphibians
forested sites (in both the Las Cruces Forest Reserve and in 2- to
Observed species richness (mean ± SD )

Observed species richness (mean ± SD )

100-ha countryside forest elements of various ages and shapes, 8 8

n = 101 sites) and deforested sites (crop fields and pastures, n = 7 7

81 sites). 6 6

We made 67,737 plant and animal observations, for a total of 5 5

908 species at all sites. We found 771 species in the forest sites 4 4

(including both the Las Cruces Forest Reserve and the coun- 3 3

tryside forest elements sites) and 386 species in crop fields and 2 2

pastures (Fig. 2A). Only 4% of the 516 plant species were exotic, 1 1

and all vertebrate species were native to the region. (We ex- 0
Crop fields & Countryside forest Las Cruces Forest
0
Crop fields & Countryside forest Las Cruces Forest
cluded humans, horses, cattle, cats, and dogs from all analyses). pastures (n = 24) elements (n=12) Reserve (n = 3) pastures (n = 24) elements (n=12) Reserve (n = 3)

Overall, 58% of all species were encountered only in forest sites,

15% of species were encountered only in crop field and pasture
sites, and 27% were observed in both (Fig. 2B). Plant species
showed the greatest differences between the two broad habitat
types in total number of species, with 407 species observed only in
forest sites, 87 species observed only in crop field and pasture sites,
and 22 species observed in both. Of the 392 vertebrate species, we
observed 115 species only in forest sites, 50 species only in crop
field and pasture sites, and 227 species in both (Fig. 2B).
In four of the six taxonomic groups sampled (i.e., plants,
nonflying mammals, bats, and birds) the number of species at a site
(α-diversity) increased significantly as the amount of tree cover at a
site increased. For example, the number of plant species was the
same among forest sites located in the Las Cruces Forest Reserve
and countryside forest elements, but sites located in crop fields and
pastures contained about half the number of plant species (R2 =
0.40, P < 0.001, n = 44) (Fig. 3A and Table S1). Medium- to large-
sized nonflying mammal species (>1 kg in size) were the verte-
brates most sensitive to deforestation, never venturing into open
areas (i.e. with <15% tree cover within 70 m) over nearly a year of
continuous camera trapping, even when bait was present (R2 =
0.70, P < 0.001, n = 21) (Fig. 3B and Table S2). The number of bat
species decreased by about a third in sites with no tree cover within
60 m (R2 = 0.32, P = 0.008, n = 18) (Fig. 3C and Table S3).
The number of bird species at a site responded differently to
the proportion of tree cover. The area of tree cover within a 30-m
radius correlated best with the number of small bird species at
a given point. However, because 24 bird species live exclusively
in agricultural land and many species thrive in that habitat, es-
pecially as tree canopies increase in size (19; Fig. 2), two distinct
species–area curves related to tree cover emerge (R2 = 0.67, P <
Fig. 3. Increasing the proportion of local tree cover generally increases the
total number of species at a point, i.e., the α-diversity. (A) The number of plant
species was the same in sites located in forest elements (light and dark green)
but was halved at sites in crop fields and pastures (yellow). (B–D) The number
of nonflying mammal species at a point responded strongly to the amount of
tree cover measured within 70 m of a site (B), whereas the numbers of bat
(C) and bird (D) species at a point on a landscape were explained best by the
amount of tree cover measured within 60 m and 30 m of the site, respectively.
(E and F) The numbers of reptile (E) and amphibian (F) species did not increase
significantly in sites with higher amounts of local tree cover, but a trend was
observed.
0.001, n = 21) (Fig. 3D and Table S4) for the two different,
overlapping bird communities, as described further in a
β-diversity analysis. The number of reptile and amphibian species
did not vary significantly across sites, but trends suggest more species
at sites with more tree cover (Fig. 3 E and F) and also show evidence
of overlapping biological communities in further β-diversity analyses.
Taken together, these results show that adding tree cover to a
tropical forest region generally increases the number of species at a
point or plot.
We tested for changes in species and abundances across dif-
ferent habitats, i.e., β-diversity between sites, in two ways, first by
comparing the relative abundances of each species from forest
and nonforest sites, and second, by comparing abundance-based
community similarity coefficients at forest and nonforest sites.
First, the relative abundances of each species were calculated for
sites in the Las Cruces Forest Reserve, forest sites in country-
side forest elements, and sites in crop fields and pastures. After
adjusting for sampling effort across multiple sites, a total of 30%

14546 | www.pnas.org/cgi/doi/10.1073/pnas.1604981113 Mendenhall et al.

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forest elements (Fig. 4 C–F). Note the decreasing order of sen-
A B sitivity to deforestation.
Next, to test statistically for changes in species and abundances
across different habitats, i.e., β-diversity, we compared abundance-
based community similarity coefficients at forest and nonforest sites.
All taxonomic groups differed significantly in their abundance-
based community similarity coefficients when categorized into forest
sites and nonforest sites. Permutational multivariate ANOVAs
(PERMANOVAs) detected the strongest differences in abundance-
based community composition between forest sites (including the
Las Cruces Forest Reserve and countryside forest elements) and
crop fields and pastures: plants, F1,42 = 9.60, P < 0.001 (Fig. 5A);
nonflying mammals, F1,19 = 3.57, P = 0.005 (Fig. 5B); bats, F1,249 =
C D 24.65, P < 0.001 (Fig. 5C); birds, F1,607 = 128.76, P < 0.001 (Fig. 5D);
reptiles, F1,36 = 6.67, P < 0.001 (Fig. 5E); and amphibians, F1,36 =
5.60, P = 0.01 (Fig. 5F). Essentially, shifts in abundance and
changes in species composition in all taxonomic groups from forest
to nonforest has resulted in the formation of two overlapping

A Las Cruces Forest Reserve

Countryside forest elements
Plants B Non-flying
mammals

SUSTAINABILITY
Crop fields & pastures

SCIENCE
E F Dimension 2

Dimension 2
Stress = 27.5; n = 44 sites Stress = 19.9; n = 20 sites
516 species; 16,257 individuals 22 species; 2,975 observations
Dimension 1 Dimension 1

C D
Birds
Bats
Dimension 2

Dimension 2
Fig. 4. Plots A–F show changes in abundances for each species across dif-
ferent habitats (i.e., a measure of β-diversity) for 908 species. A total of
67,737 individual plants and animals were recorded in sites distributed across
three broad categories: (i ) Las Cruces Forest Reserve (dark green);
(ii) countryside forest elements (light green); and (iii) crop fields and pastures
(yellow). Most species used multiple habitat types, including crop fields and
pastures. The forest-dependency rank ranges from forest avoidance (on the Stress = 34.8, n = 251 mist nets Stress = 28.1, n = 609 mist nets
40 species; 4,020 individuals 263 species; 40,008 individuals
left side of the x axis) to forest dependence (on the right side of the x axis)
and was determined by comparing relative abundance in the Las Cruces Dimension 1 Dimension 1
Forest Reserve (dark green) with that in crop fields and pastures (yellow). All
proportions of populations account for differences in sampling effort among E Reptiles F Amphibians

the three habitat types.

Dimension 2

Dimension 2

of the 67,737 plant and animal observations were recorded inside

the Las Cruces Forest Reserve, 38% in countryside forest ele-
ments, and 32% in crop fields and pastures (Fig. 4).
Species varied greatly in their dependence on forest, with 54%
of the 908 species found in multiple habitat types (Fig. 4). Of the
516 plant species, we classified 75% as forest dependent because
>50% of their population was observed in forest sites, inclusive
of the Las Cruces Forest Reserve (Fig. 4A). Of the 22 nonflying
mammal species, only three species (a rabbit, an opossum, and a
squirrel) preferred crop fields and pastures with >50% of their
observations occurring there; these data suggest that 86% of all
nonflying mammal species are dependent on forest elements
(Fig. 4B). Finally, assuming that a species is forest dependent if
>50% of the individuals are observed in forest sites, inclusive of
the Las Cruces Forest Reserve, we find that 88% of the 40 bat
species, 61% of the 263 bird species, 59% of the 39 reptile
species, and 54% of the 28 amphibian species are dependent on
Stress = 23.3, n = 38 sites Stress = 24.5, n = 38 sites
39 species; 685 observations 28 species; 981 observations
Dimension 1 Dimension 1
Fig. 5. Significant shifts in community composition across different habitats
(a measure of β-diversity) occur among all taxonomic groups. Shown in A–F
are nonmetric multidimensional scaling plots that depict abundance-based
community-similarity coefficients among all sites (or individual mist nets for
this analysis in C and D). Closer proximity represents greater similarity in
sites’ community composition. All taxonomic groups were significantly dis-
similar in community composition when split into two broad habitat types:
forest [including the Las Cruces Forest Reserve (dark green points) and
countryside forest elements (light green points)] and crop fields and pastures
(yellow points).

Mendenhall et al. PNAS | December 20, 2016 | vol. 113 | no. 51 | 14547
biological communities in our study region—a larger, more bio-
diverse community associated with forest and a smaller, less bio-
diverse community associated with agricultural land (Figs. 2 and 5).
A reporting of data (Table S5). We were able to extract data for 90
100
Countryside forest elements
Crop fields & pastures
Proportion of study comparisions
80
(33)
(25)
60
40 (15)
(11)
20
(3) (3)
0 with forest and a smaller, less biodiverse community associated
Decline Same Increase
Change in species richness compared to
minimally altered forest (> 100 ha in size)
B Total number of vertebrate species from
12 other studies across Latin America
Minimally altered forest (> 100 ha in size)
& countryside forest elements sites only
Both
100 235 397
Crop field & pasture sites only
Fig. 6. Across Latin America, the biodiversity of the tropical forest biome is
experiencing change and loss much in the same way as we report for Coto Brus,
Costa Rica. (A) A survey of comparisons of species richness representing 3,041
species of plants, nonflying mammals, bats, birds, reptiles, and amphibians
throughout Latin America revealed that sites located inside countryside forest
elements usually support the same number of species as sites located in minimally
altered forest. Comparisons of species richness in minimally altered forests and in
crop fields and pastures revealed greater losses in species richness, but 58% of the
comparisons between those habitat types were still statistically indistinguishable.
(B) Community shift statistics from 29 studies and data from 12 studies of species
occurrences throughout Latin America in three broad habitats for species of
nonflying mammals (47 species), bats (62 species), birds (460 species), reptiles (67
species), and amphibians (96 species) confirmed that deforestation is leading to
the formation of a novel, less biodiverse community that overlaps with a larger,
more diverse biological community associated with tropical forests.
14548 | www.pnas.org/cgi/doi/10.1073/pnas.1604981113
To generalize our findings beyond the study region in Costa Rica,
we conducted a literature survey of countryside biogeographic
studies of plants, nonflying mammals, bats, birds, reptiles, and
amphibians in the tropical forest biome across Latin America.
Of 857 reviewed articles, 19 (from Brazil, Costa Rica, Guate-
mala, Mexico, and Panama) met our criteria for study design and
study comparisons of biodiversity change across different habitats
representing the six taxonomic groups that we focused on in Costa
Rica (Dataset S1). The 90 study comparisons tested for differences
in the number of species (α-diversity) at sites in countryside forest
elements or at sites in crop fields and pastures compared with the
number of species at sites in minimally altered forest (>100 ha in
size). In total, 29% of the 90 study comparisons reported a signif-
icant loss of species in crop fields and pastures compared with
minimally altered forest, 68% reported no change, and 7% reported
a significant increase in the number of species (Fig. 6A).
Moreover, of the 29 study comparisons that tested for shifts in
abundances and/or changes in species composition between forested
and deforested areas, 25 reported significant changes in β-diversity
using various metrics. Finally, data published in 12 studies (20–31) of
five vertebrate taxa (i.e., nonflying mammals, bats, birds, reptiles, and
amphibians) supported the argument that two overlapping biological
communities form with deforestation—one community associated
with agricultural land (Fig. 6B). (Tests to determine general
trends between taxonomic groups were not permitted because of
data deficiency.)
Discussion
Protected areas span only 13% of the global land surface, and in
reality these areas are only partially protected (32), suggesting
that the future of terrestrial biodiversity depends in large part on
the effect of agricultural use of unprotected lands (33–36). We
developed an approach for quantifying the relationship between
local tree cover and biodiversity (Fig. 3). Nearly 50% of the rural
agricultural countryside of Coto Brus, our study region, is cov-
ered by trees, much of it in small forest elements of varied ages,
shapes, and sizes along rivers, steep terrain, and property bound-
aries (Fig. 1B). These forest elements, together with the agricultural
land in which they are embedded, support significant dimensions of
biodiversity, whereas the adjacent crop fields and pastures support
a different community (2, 3).
Despite the biodiversity found in deforested habitats, pro-
tected areas remain critical because most species at risk for ex-
tinction in the tropical forest biome require expansive forests.
For example, 9% of 908 species in our study were completely
dependent on the local protected area, occurring only in the Las
Cruces Forest Reserve. Moreover, several local extinctions have
occurred in the region because of habitat loss and poaching (37).
Our approach for modeling biodiversity across a tropical agri-
cultural region can inform conservation policies by quantifying
biodiversity using remotely sensed tree cover to scale from plots to
regions. By selecting specific spatial scales to measure the area of
tree cover for our α-diversity models that predict the number of
species at a site, our approach accounts for forest configuration
(38) and operationalizes the universal species–area relationship
(39). Finally, the region we use as a case study has >10% natural
habitat for most species; therefore large effects on biodiversity
resulting from habitat fragmentation are not expected (40). Of
course, our approach requires testing and adjustment based on the
ecological contexts in which it might be applied. Moreover, our
approach relies on high-quality inputs that will come from im-
provements in tree cover mapping and remote sensing. To repli-
cate our approach, global estimates of tree cover are needed to
guide investments in biodiversity and ecosystem services, especially
in the tropical forest biome where biodiversity is concentrated and
farms are small family businesses.
Mendenhall et al.

In practice, conservation applications of the predictive bio-
diversity models we present can be used to insulate protected areas
and to diversify farmland in once-forested landscapes. Specifically,
our models predicting the number of species at a site (α-diversity;
Tables S2–S4) coupled with results that describe the kinds of
species at a site (β-diversity) support arguments that increasing tree
cover around existing forest reserves will lead to small gains in the
number of species, but the species gained tend to be rare, unique,
and at risk for extinction because of deforestation (2, 3, 41, 42) Our
results also suggest that conservation efforts to diversify farmland
by increasing tree cover in and around crop fields and pastures
leads to large gains in the number of species, but the species gained
tend to be common. Our results provide a theoretical basis for
aligning conservation strategies to slow extinctions and for boosting
some ecosystem services by buffering remaining forests with wild-
life-friendly farmland and regenerating forests where politically
feasible, given demands to farm the planet (43).
Our work supports valuing farming systems in Costa Rica
and Latin America—including coffee plantations, pastures, and
remnants of forests— holistically for the provision of biodiversity
benefits as well as crops, forage, timber, carbon sequestration,
water quality, scenic beauty, and other ecosystem services. In our
study, remotely sensed tree cover serves as a reliable basis for
estimating biodiversity, on scales from plots to regions. Specifi-
cally, we find that increasing the amount of tree cover on private
property leads to increases in the richness of plant, nonflying
mammal, bat, and bird species at the plot level. Moreover, tree
cover on private property contributes to regional biodiversity by
supporting the larger, more biologically diverse communities
associated with tropical forests. Our survey of Latin American
biodiversity and similar work on other continents, e.g., in an
>2,000-y-old tropical agricultural system in the Western Ghats
of India (44), demonstrate that it is possible to sustain patterns
of relatively high biodiversity after deforestation when farming
ecosystems are heterogeneous, incorporate elements of naturally
occurring habitats, and grow perennial crops.
In grasslands and other biomes not dominated by forests or
situated in the tropics, sustaining the conservation values of ag-
ricultural lands will depend on successfully identifying the fea-
tures of agricultural lands linked with native biodiversity and
local ecosystem services. In the context of Costa Rica, with an
established program of payment for ecosystem services that has
incentivized forest conservation and restoration on private
property for 20 y, our approach of spatially linking tree cover at
taxon-specific spatial scales to biodiversity patterns can be used
as a basis for developing spatial planning tools to target invest-
ments in biodiversity and align values with goals to protect water,
store carbon, and provide scenic beauty. We share a replicable
approach for reducing extinctions caused by tropical de-
forestation and demonstrate it in the context of an existing policy
that pays farmers for ecosystem services and biodiversity on their
properties.
Methods
Study Area. This research is being conducted in the rugged, hilly countryside
of Coto Brus, a canton of Costa Rica, across agricultural landscapes spanning
700–1,350 m elevation. The region, originally tropical premontane wet
forest, was heavily deforested in the 1960s and early 1970s (45). Today, the
countryside comprises crop fields (mostly of coffee and diversified gardens),
pasture, and trees scattered through crop fields and pastures, in strips bor-
dering streams and property lines, and in forest elements of variable sizes
(typically 0.05–100 ha). The landscape and biogeography are described more
fully elsewhere (33, 37).
Tree Cover Estimates. We created a finely detailed tree cover map by hand
digitizing aerial photographs in Google Earth for the 934-km2 canton of Coto
Brus. We used photographs taken in 2014 by commercial QuickBird satellites
at a 0.61-m spatial resolution. We collected ground-truth data at 46 ran-
domly selected plots measuring 500 m2 in three major habitat types: (i) nine
Mendenhall et al.
COLLOQUIUM
PAPER
sites in the Las Cruces Forest Reserve, the last large forest tract at mid-
elevation and thus serving as a protected regional baseline; (ii) 14 sites in
forest elements of various ages and sizes; and (iii) 23 sites in crop fields and
pastures. In each site we surveyed vegetation to check whether the Google
Earth tree-cover map matched the tree cover observed in the field.
Biodiversity. To measure biodiversity, we identified and counted the abun-
dances of plants and all vertebrate taxa: nonflying mammals, bats, birds,
reptiles, and amphibians. We sampled plants and wildlife using standardized,
systematic techniques appropriate for each taxon over extensive time periods
(e.g., 1–5 y), with substantial trapping effort (i.e., ∼95,000 mist net hours and
∼15,000 trap nights), and at spatially independent sites across Coto Brus (i.e.,
18–44 sites per taxa). We used sampling in the protected Las Cruces Forest
Reserve as the regional baseline of minimally altered forest after sampling in
La Amistad International Park (25 km away) revealed no differences in the
total number of species recorded at that sampling site (i.e., in α-diversity)
compared with sites in the Las Cruces Forest Reserve. We also conducted
sampling in a suite of countryside forest elements of different ages and sizes
and in deforested crop fields, mostly coffee plantations, and in pastures used
for grazing. Biodiversity sampling of animals was conducted and approved
under Stanford University’s Institutional Animal Care and Use Committee
(IACUC), Assurance Number: A3213-01, Protocol: 26920.
Understory Plant Biodiversity. We used ground surveys to sample understory
plants, identifying and counting all plants that fell inside a 1-m2 frame, in-
cluding trees, shrubs, vines, forbs, grasses, and domestic plants. We selected
SUSTAINABILITY
sites randomly using Global Information System (GIS) software and repli-
SCIENCE
cated the 1-m2 sampling systematically 20 times in a total of 44 sites, each
measuring 500 m2. We surveyed plants in four major habitat types: cattle
pastures (three sites), coffee plantations (six sites), countryside forest ele-
ments (2- to 100-ha forest; 27 sites), and the Las Cruces Forest Reserve (eight
sites). Understory plant biodiversity was aggregated for each site by pooling
the 20 replicates of the 1-m2 frame inside each site. Plant species richness
values for each site were modeled using techniques that account for de-
tection biases (46).
Bird Biodiversity. We sampled birds through constant-effort mist netting,
using 20 12 × 2.6 m, 38-mm mesh ground-level mist nets in sites that covered
3–5 ha. We conducted sampling between January 25 and May 12 for 6 y
(2007–2012) at 21 sites in three major habitat types: coffee plantation (nine
sites), countryside forest elements (2- to 100-ha forest; nine sites), and in the
Las Cruces Forest Reserve (three sites). We primarily captured passerines and
other small birds, species that comprise the majority of the avifauna in the
area. We fitted each captured bird with a unique aluminum leg ring,
recorded the mist net location of capture, and released the bird at the
capture site. Bird species richness values for each site were modeled using
techniques that account for detection biases (46).
Bat Biodiversity. We used constant-effort mist netting to sample bats, placing
20 12 × 2.6 m 38-mm mesh ground-level mist nets in a site that covered 3–5 ha.
We conducted sampling between January 24 and March 28 for 4 y (2007–
2010) at 18 sites in three major habitat types: coffee plantations (six sites),
countryside forest elements (2- to 100-ha forest; nine sites), and the Las
Cruces Forest Reserve (three sites). We sampled birds at all sites where bats
were sampled. We primarily captured fruit bats; these species comprise the
majority of the bats in the area (3). We fitted all captured bats with a unique
collar, noted the net location of capture, and released bats at the capture
site. Bat species richness values for each site were modeled using a Bayesian
occupancy model that accounts for detection biases.
Nonflying Mammal Biodiversity. We sampled medium-sized nonflying mammals
(>1 kg in size) using both passive and baited camera traps. Camera trap pro-
tocols involved a motion-triggered camera trap fastened to a tree or post at 21
sites in four major habitat types of cattle pasture (three sites), coffee plantation
(six sites), countryside forest elements (2- to 100-ha forest; nine sites), and the
Las Cruces Forest Reserve (three sites). We operated camera traps without bait
for nearly 1 y (September 2014–July 2015) and operated camera traps with bait
(two bananas and three chicken gizzards, replenished daily) for a total of 14
d at each site. All cameras were at ground level. Species excluded from all
analyses were humans, horses, cattle, cats, and dogs. Observed species richness
of nonflying mammals at each site was used for analyses.
Reptile and Amphibian Biodiversity. We sampled reptiles and amphibians
using two complementary techniques: diurnal and nocturnal visual-encounter
PNAS | December 20, 2016 | vol. 113 | no. 51 | 14549
surveys and drift-fence trapping with pitfall and funnel traps. Six surveys for
reptiles and amphibians took place during the wet and dry seasons over 3 y
(2002–2004) at 39 sites in four major habitat types: cattle pasture (12 sites),
coffee plantation (12 sites), countryside forest element (2- to 100-ha forest;
12 sites), and the Las Cruces Forest Reserve (three sites). We identified cap-
tured individuals but did not mark them and released all animals at the
capture site. Observed reptile and amphibians species richness values for
each site were used for further analyses.
Statistical Analyses. To quantify how biodiversity changes along the land-use
gradient from protected native forests to deforested agricultural plots, we
explore biodiversity at three levels: (i) the total number of species in a region
of forest and nonforest (the γ-diversity of each habitat), (ii) the total number
of species at a point on a landscape (α-diversity), and (iii) similarity in species
and abundances across different habitats (β-diversity).
To quantify changes in the total number of species at a point on a
landscape, i.e., the α-diversity, we compared observed or modeled species
richness estimates for each site and tested for differences among sites with
different amounts of local tree cover. Plant and bird species richness was
modeled using Chao species richness estimates, and bat species richness was
estimated using a Bayesian occupancy model (46). We measured tree cover
at each site in two ways. In the first, we used three habitat categories of Las
Cruces Forest Reserve, countryside forest elements, and crop fields and
pastures. In the later, more refined approach, we used the proportion of
tree cover within a taxon-specific area, defined as the spatial scale at which
species respond most strongly to a habitat variable (47) and hypothesized to
be inclusive of configuration (38). We compared all linear models at differ-
ent spatial scales using corrected Akaike Information Criteria (AICc). Including
spatial structures in linear mixed effects models did not significantly influence
results and was not done in final analyses.
To quantify changes in abundances across different habitats, the
β-diversity, we calculated the relative abundance for each species in each habitat
type and adjusted by sampling effort in space and time. Additionally, we
tested statistically for changes in species and abundances across different
habitats (β-diversity) by testing for differences among sites using abundance-
based community similarity coefficients (46, 48). For each taxonomic group
we aggregated captures and counts of all species by site and, for finer res-
olution in this analysis, by specific mist net for birds and bats. Each site or
1. Rapidel B, DeClerck F, Le Coq JF, Beer J, eds (2011) Ecosystem Services from
Agriculture and Forestry: Measurement and Payment (Earthscan, London).
2. Frishkoff LO, et al. (2014) Loss of avian phylogenetic diversity in neotropical agri-
cultural systems. Science 345(6202):1343–1346.
3. Mendenhall CD, Karp DS, Meyer CFJ, Hadly EA, Daily GC (2014) Predicting biodiversity
change and averting collapse in agricultural landscapes. Nature 509(7499):213–217.
4. Tscharntke T, et al. (2012) Global food security, biodiversity conservation and the
future of agricultural intensification. Biol Conserv 151:53–59.
5. Ceballos G, et al. (2015) Accelerated modern human-induced species losses: Entering
the sixth mass extinction. Sci Adv 1(5):e1400253.
6. Steffen W, Broadgate W, Deutsch L, Gaffney O, Ludwig C (2015) The trajectory of the
Anthropocene: The Great Acceleration. The Anthropocene Review 2(1):81–98.
7. Levin SA (2000) Fragile Dominion: Complexity and the Commons (Perseus Publishing,
New York).
8. Lipper L, Sakuyama T, Stringer R, Silberman D, eds (2009) Payment for Environmental
Services in Agricultural Landscapes: Economic Policies and Poverty Reduction in
Developing Countries (Springer, New York).
9. Guerry AD, et al. (2015) Natural capital and ecosystem services informing decisions:
From promise to practice. Proc Natl Acad Sci USA 112(24):7348–7355.
10. Kareiva P, Tallis H, Ricketts TH, Daily GC, Polasky S, eds (2011) Natural Capital: Theory
and Practice of Mapping Ecosystem Services (Oxford Univ Press, Oxford, UK).
11. Sharp R, et al. InVEST +VERSION+ User’s Guide (2015) The Natural Capital Project.
Available at data.naturalcapitalproject.org/nightly-build/invest-users-guide/html/.
Accessed May 1, 2016.
12. Daily GC, et al. (2013) Securing natural capital and human well-being: Innovation and
impact in China. Acta Ecol Sin 33:669–676.
13. Ouyang Z, et al. (2016) Improvements in ecosystem services from investments in
natural capital. Science 352(6292):1455–1459.
14. Pereira HM, et al. (2010) Scenarios for global biodiversity in the 21st century. Science
330(6010):1496–1501.
15. Ehrlich PR, Mooney HA (1983) Extinction, substitution, and ecosystem services.
Bioscience 33:248–254.
16. Barbier EB, Burgess JC, Folke C (1994) Paradise Lost? The Ecological Economics of
Biodiversity (Earthscan, London).
17. Daily GC, ed (1997) Nature’s Services: Societal Dependence on Natural Ecosystems
(Island, Washington, DC).
18. Asamblea Legislativa de la República de Costa Rica (1996) Ley Forestal 7575. pp. 1–36.
19. Mendenhall CD, Sekercioglu CH, Brenes FO, Ehrlich PR, Daily GC (2011) Predictive
model for sustaining biodiversity in tropical countryside. Proc Natl Acad Sci USA
108(39):16313–16316.
14550 | www.pnas.org/cgi/doi/10.1073/pnas.1604981113
mist net was labeled by habitat type (i) Las Cruces Forest Reserve, (ii) countryside
forest elements, or (iii) crop fields and pastures (Fig. 5). Using PERMANOVA tests,
we tested for significant differences and clustering of abundance-based
community similarity coefficients by habitat types.
Survey of Latin American Countryside Biogeography Studies. To gather evi-
dence to generalize our approach for modeling biodiversity on agricultural
lands, we performed a survey of biogeographic studies in other agricultural
landscapes where contiguous tropical forest once existed. We created a
search term to target countryside biogeography studies in Latin America that
conducted richness sampling of plants, nonflying mammals, bats, birds,
reptiles, and/or amphibians (Table S5). All 857 studies returned by the search
term were evaluated for inclusion by two independent readers to extract
data (Dataset S1). We considered data only from studies with at least three
sites in countryside forest elements or three sites in crop fields and/or pas-
tures. Moreover, we required that studies consider at least three sites in
minimally altered forest. We defined sites as minimally altered forest if they
were located in continuous forest or in large forest fragments (>100 ha in
size). Countryside forest elements were defined as small clusters or strips of
trees (0.05–100 ha in size), secondary forests, riparian forest remnants, live
fences, and agricultural fields left to fallow at least 5 y ago. Sites in crop
fields and pastures were located on land that is currently being cultivated
for growing crops or rearing animals and included land that had been used
for agricultural purposes within 5 y.
ACKNOWLEDGMENTS. We thank Federico Oviedo Brenes, Jeisson Figueroa
Sandí, Paula Mesen Cabezas, and dozens of field assistants for help with
surveys of tree cover and biodiversity; Luke Frishkoff and Hannah Frank for
modeling bat species richness estimates; Ania Wrona and Leithen M’Gonigle
for help with tree cover calculations; the dozens of landowners in
Costa Rica who graciously allowed us to conduct field work on their prop-
erty; and Paul R. Ehrlich, Gerardo Ceballos, and Rakan A. Zahawi for pro-
ductive collaboration in the supportive environment of the Las Cruces
Biological Station of the Organization for Tropical Studies. This work was
supported by the Moore Family Foundation, the Winslow Foundation, the
Haberfeld family, and Peter and Helen Bing. C.D.M. was supported by the
Bing Fellowship in Honor of Paul Ehrlich, a National Science Foundation
Graduate Research Fellowship, and a NatureNet Science Fellowship through
The Nature Conservancy.
20. Almeida-Gomes M, Rocha CFD (2014) Landscape connectivity may explain anuran
species distribution in an Atlantic forest fragmented area. Landsc Ecol 29(1):29–40.
21. Avila-Cabadilla LD, Stoner KE, Henry M, Añorve MYA (2009) Composition, structure
and diversity of phyllostomid bat assemblages in different successional stages of a
tropical dry forest. For Ecol Manage 258(6):986–996.
22. Bael SA, Zambrano RV, Hall JS (2013) Bird communities in forested and human-modified
landscapes of Central Panama: A baseline survey for a native species reforestation treat-
ment. International Journal of Biodiversity Science, Ecosystem Services & Management
9(4):281–289.
23. Bohn JL, Diemont SAW, Gibbs JP, Stehman SV, Mendoza Vega J (2014) Implications of
Mayan agroforestry for biodiversity conservation in the Calakmul Biosphere Reserve,
Mexico. Agrofor Syst 88(2):269–285.
24. Cassano CR, Barlow J, Pardini R (2012) Large mammals in an agroforestry mosaic in
the Brazilian Atlantic forest. Biotropica 44(6):818–825.
25. Faria D, Baumgarten J (2007) Shade cacao plantations (Theobroma cacao) and bat
conservation in southern Bahia, Brazil. Biodivers Conserv 16(2):291–312.
26. Faria D (2006) Phyllostomid bats of a fragmented landscape in the north-eastern
Atlantic forest, Brazil. J Trop Ecol 22(05):531–542.
27. Garcia S, Finch DM, León GC (1998) Patterns of forest use and endemism in resident
bird communities of north-central Michoacán, Mexico. For Ecol Manage 110(1–3):
151–171.
28. Marsden SJ, Whiffin M, Galetti M (2001) Bird diversity and abundance in forest
fragments and Eucalyptus plantations around an Atlantic forest reserve, Brazil.
Biodiversity and Conservation 10(5):737–751.
29. Mendenhall CD, et al. (2014) Countryside biogeography of Neotropical reptiles and
amphibians. Ecology 95(4):856–870.
30. Santos-Filho M, Silva DJ, Sanaiotti TM (2008) Edge effects and landscape matrix use by
a small mammal community in fragments of semideciduous submontane forest in
Mato Grosso, Brazil. Braz J Biol 68(4):703–710.
31. Urbina-Cardona JN, Olivares-Pérez M, Reynoso VH (2006) Herpetofauna diversity and
microenvironment correlates across a pasture–edge–interior ecotone in tropical
rainforest fragments in the Los Tuxtlas Biosphere Reserve of Veracruz, Mexico. Biol
Conserv 132(1):61–75.
32. Ellis EC, Klein Goldewijk K, Siebert S, Lightman D, Ramankutty N (2010) Anthropo-
genic transformation of the biomes, 1700 to 2000. Glob Ecol Biogeogr 19:589–606.
33. Daily GC, Ehrlich PR, Sánchez-Azofeifa GA (2001) Countryside biogeography: Utili-
zation of human-dominated habitats by the avifauna of southern Costa Rica. Ecol
Appl 11:1–13.
34. Rosenzweig M (2003) Win-Win Ecology: How the Earth’s Species Can Survive in the
Midst of Human Enterprise (Oxford Univ Press, Oxford, UK).
Mendenhall et al.

35. Gardner TA, et al. (2009) Prospects for tropical forest biodiversity in a human-modi-
fied world. Ecol Lett 12(6):561–582.
36. Perfecto I, Vandermeer J, Wright A (2009) Nature’s Matrix: Linking Agriculture,
Conservation and Food Sovereignty (Earthscan, London).
37. Daily GC, Ceballos G, Pacheco J, Suzán G, Sánchez-Azofeifa A (2003) Countryside
biogeography of Neotropical mammals: Conservation opportunities in agricultural
landscapes of Costa Rica. Conserv Biol 17:1814–1826.
38. Fahrig L (2013) Rethinking patch size and isolation effects. J Biogeogr 40:1649–1663.
39. Harte J, Smith AB, Storch D (2009) Biodiversity scales from plots to biomes with a
universal species-area curve. Ecol Lett 12(8):789–797.
40. Rybicki J, Hanski I (2013) Species-area relationships and extinctions caused by habitat
loss and fragmentation. Ecol Lett 16(Suppl 1):27–38.
41. Balmford A, Green R, Phalan B (2015) Land for food and land for nature? Daedalus
144(4):57–75.
Mendenhall et al.
COLLOQUIUM
PAPER
42. Laurance WF, et al. (2012) Averting biodiversity collapse in tropical forest protected
areas. Nature 489(7415):290–294.
43. Kremen C (2015) Reframing the land-sparing/land-sharing debate for biodiversity
conservation. Ann N Y Acad Sci 1355:52–76.
44. Ranganathan J, Daniels RJ, Chandran MD, Ehrlich PR, Daily GC (2008) Sustaining
biodiversity in ancient tropical countryside. Proc Natl Acad Sci USA 105(46):17852–17854.
45. Zahawi RA, Duran G, Kormann U (2015) Sixty-seven years of land-use change in
southern Costa Rica. PLoS One 10(11):e0143554.
46. Chao A (1987) Estimating the population size for capture-recapture data with un-
equal catchability. Biometrics 43(4):783–791.
47. Holland JD, Bert DG, Fahrig L (2004) Determining the spatial scale of species’ response
to habitat. Bioscience 54(3):227–233.
48. Chao A, Chazdon R, Colwell R, Shen TA (2005) A new statistical approach for assessing
similarity of species composition with incidence and abundance data. Ecol Lett 8:148–159.
SUSTAINABILITY
SCIENCE
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