The migration of vegetation under the influence of climate change is of great interest to ecologists, but can be difficult to quantify—especially in less accessible landscapes. Monitoring land cover change through remote sensing has become the best solution, especially with the use of unmanned aerial systems (UASs; drones) as low-cost remote sensing platforms are able to collect data at high spatial and spectral resolutions. Unfortunately, in the context of climate change studies, the lack of comparative UAS data sets over decadal timescales has been limiting. Here, we describe a technique for the integration of historical, low spatial resolution satellite-based Normalized Difference Vegetation Index (NDVI) data with short-term high-resolution multispectral UAS data to track the vegetation changes in a Costa Rican rainforest over a 33-year time frame. The study reveals the transition of a mixed forest from strongly deciduous to weakly deciduous phenology in the Hacienda Barú National Wildlife Refuge (HBNWR), southwestern Costa Rica. This case study presents an approach for researchers and forest managers to study and track vegetation changes over time in locations that lack detailed historical vegetation data. Vegetation migration due to climate change is not well documented and difficult to monitor, especially in remote or inaccessible locations. This case study presents researchers, students, and forest managers an approach for leveraging freely available satellite imagery and UASs to track these changes over time.
It is widely recognized that climate change is causing significant shifts in temperature and precipitation which alter the regional ecology and distribution of species . Although there is a high potential for vegetation migration in ecosystems, this has not been well documented in inaccessible areas [2–5]. Many tree species may have a capacity for climate-induced migration, but individual species migrate at markedly different rates  leading to changes in tree community composition. Some trees also have the ability to transition their phenological cycles in response to climate change, although a continuing change to climate will favor certain species .
Remote sensing has become an essential tool to monitor land cover change in large inaccessible areas [8–10]. The Normalized Difference Vegetation Index (NDVI) has been shown to be effective in monitoring vegetation’s vigor by measuring the amount of active chlorophyll (red light absorbance) to vegetation cell structure near-infrared reflectance (NIR) as shown in Equation (1) .
This monitoring of vegetation’s vigor has also been linked to responses to a change in climate [8, 12, 13]. Monitoring changes in forest also plays a significant role when trying to mitigate climate change . An increasing number of studies have employed the use of time series analysis of all available observations using individual pixels to characterize land cover types  and to quantify abrupt changes such as forest clearing [9, 14–15]. More recently, by analyzing every Landsat image collected from a study area, interannual and intraannual trajectories and harmonics can be derived from the natural ecosystem to detect very small changes in the environment  with the goal of providing a more continuous view of ecosystem dynamics.
In addition to traditionally collected satellite imagery, unmanned aerial systems (UASs) are emerging as a remote sensing platform in ecological applications collecting data at high spatial and spectral resolutions . Terrestrial collection of ground reference data, such as the locations of specific tree species, is challenging tropical locations due to both their inaccessibility and the degradation of the global positioning system (GPS) signal for handheld GPS units under jungle canopy. In response, researchers have demonstrated the ability of UAS to quickly and accurately collect land cover samples in tropical areas for environmental research . These UASs are often equipped with multispectral sensors such as the moderately priced (~$3,500 in 2017) MicaSense Sequoia (micasense.com/sequoia) which collects on the red edge (735 nm) and near-infrared (790 nm) wavelengths, as well as traditional green (550 nm) and red (660 nm) channels to improve vegetation characterization and classification. UASs are especially well suited for very fine spatial mapping of tropical dry vegetation because imagery can be collected throughout the year enabling the monitoring of seasonal changes in the vegetation. More generally, the accessibility of drone-based imagery has become increasingly important in promoting low-cost, community-based remote sensing project in the tropics [19, 20]
In response to the importance and challenges of monitoring the composition and biodiversity of tropical ecosystems, we present an approach utilizing dense Landsat time series analysis to reveal patterns of phenological change to deciduous trees in a selected forest in southwestern Costa Rica: the Hacienda Barú National Wildlife Refuge (HBNWR). The HBNWR straddles an ecozone between the Lowland Evergreen Moist Forest of Corcovado National Park with less than 35 days of water deficit per annum  and the Northern Pacific Lowland Seasonal Forest of Guanacaste and Santa Rosa National Park, which experiences a pronounced dry season of 3 months or more . A 37-year record of rainfall for the HBNWR (http://costarica.jsd.claremont.edu/weather.shtml) suggests that the area may be experiencing a long-term decrease in annual precipitation, presumed to correlate with regional patterns of climate change.
A common component of the HBNWR forest is the Guanacaste tree (Enterolobium cyclocarpum), a semi-deciduous, conspicuous canopy species widely distributed from northern South America through Central America. E. cyclocarpum tolerates significant seasonal drought, as is typical of northwestern Costa Rica, by shedding its leaves. In areas with a less pronounced dry season, E. cyclocarpum may retain some or all of its foliage. The tree becomes progressively rarer in less drought-stressed biomes and is essentially absent in extreme southwestern Costa Rica, except where associated with human disturbance and introduction . Long-term changes in dry season length and severity along a north-south transect of Costa Rica’s Pacific coast can thus be expected to influence E. cyclocarpum success. Moreover, because the tree can respond to drought severity with varying degrees of deciduosity, it has potential as a remotely sensed environmental monitor.
By analyzing individual pixels across all available Landsat images taken from 1984 to 2017 and leveraging fixed-wing UAS platforms equipped with multispectral sensors designed for high taxonomic precision of vegetation species, the temporal pattern of phenological change to deciduous trees in Costa Rica’s mixed forests can be resolved.
Site Selection and Source Data
In the 1980s, Costa Rica was one of the countries with highest deforestation rates due to the changes for farmland and pasture. According to a study done by the University of Costa Rica’s Center for Tropical Studies and the World Resources Institute, the deforestation rate went from about 46,500 ha/year from 1950 to 1962 to 31,830 ha/year from 1974 to 1989 . A species-rich country, Costa Rica, contains approximately 5% of the Earth’s species making it the most species-dense country in the world, a feat made possible impart because it contains 12 life zones and six climatic transitions .
Within Costa Rica, three areas were chosen as the sites of research: 1), a forest on Costa Rica’s central Pacific coast typically subject to an annual drought of approximately 3 months and currently undergoing potential phenological change—the HBNWR; 2) an exemplar of a monsoonal (tropical dry) forest in northwestern Pacific Costa Rica forest, subject to a severe annual drought of 5+ months and hosting a largely deciduous tree community—Santa Rosa National Park; and 3) an exemplar of a tropical wet Costa Rican forest experiencing 12 rainfall months a year and a fully evergreen tree community—Corcovado National Park (Figure 1). These forests are distributed along a north-south transect of Pacific coastal, lowland Costa Rica, and have benefited from being protected areas since before the study period began in 1984.
Hacienda Barú Refuge
The Hacienda Barú Refuge is a national wildlife refuge and private reserve located in Puntarenas province, Southwestern Costa Rica (9°15′N 84°14′W) (Hacienda Barú 2017). The HBNWR has a drier climate than Corcovado National Park, notably experiencing 3–4 months of marked drought between December and April (http://costarica.jsd.claremont.edu/weather.shtml, Climate Change Knowledge Bank ). The Refuge consists of 330 ha having different habitats including primary rainforest, secondary forest, and wetland. Its mission is to preserve and educate others on the natural resources and biodiversity of the area forming one component of the regionally important 82,000 ha Path of the Tapir project . Within this refuge, two regions of interest (ROIs) were selected to monitor changes in vegetation over time. Consisting of 516 Landsat pixels, or an area of 464,029 m2, this area is a mix of tropical and deciduous trees in a fully canopied forest (Figure 2).
Santa Rosa National Park
Santa Rosa National Park (Santa Rosa) is located in Guanacaste province, northwestern Costa Rica (10°84′N, 85°62′W) . Santa Rosa became the first national park in Costa Rica, created in 1971. Santa Rosa has an area of 856.05 km2 and is recognized as a World Heritage Site by UNESCO conserving one of the only areas of tropical dry forest (Holdridge life Zone df-T) in Mesoamerica. Santa Rosa is now one of the few parks which has maintained its land cover with a deforestation rate of 0% . Within this park, two ROIs were selected as exemplars of a protected deciduous forest in western Costa Rica. ROI #1 covered 56,081 m2 or 70 pixels (Figure 3a), and ROI #2 consisted of 38 pixels or an area of 27,188 m2 (Figure 3b).
Corcovado National Park
Corcovado National Park (Corcovado) is located in the Osa Peninsula in Puntarenas province, Southwestern Costa Rica (8°33′N 83°35′W). It was created as a National Park in 1975 to help preserve the wet tropical forest in the area. Corcovado has a mean annual temperature of 26.9°C and a mean annual precipitation of 3,500 mm in the coast near the study area . Corcovado lies within the tropical wet forest Holdridge life zone, but without a marked dry season. Corcovado is one of the most affected areas by deforestation compared with other national parks or biological reserves , although some locations, such as those chosen for this study, have remained as persistent tropical forest.
In Corcovado, two ROIs were identified as tropical wet forest exemplars totaling 154,362.62 m2 or 185 pixels in the satellite imagery (Figure 4). These areas consist of fully canopied tropical wet, evergreen forest, protected, and preserved since 1975.
The analysis of the migration of tropical forests was conducted using data sourced from level 1 terrain-corrected (L1T) images, Landsat images. L1T images are georeferenced, terrain corrected, and calibrated across the Landsat constellation of sensors allowing for a direct comparison of pixels over time. The images are prepared and stored by the US Geological Survey Earth Resources Observation and Science (EROS) Science Processing Architecture (ESPA). Processing options selected included generating surface reflectance, producing NDVI, and using nearest neighbor to preserve individual pixel values. The imagery processing options also included the pixel quality assessment (QA) band containing integers representing atmospheric, instrumental, or cloud contamination factors easily allowing the removal of contaminated pixels. A total of 1,777 Landsat images were analyzed for this study from 1984 to 2017. To automatize data processing, we utilized Python coding to unzip the imagery, composite the bands by date, screen pixels by QA band, and then extract individual pixel values within our delineated study sites. A notional guide to this process is provided in Appendix A.
Two missions of an eBee SenseFly UAS (www.sensefly.com/ebee) were flown on May 31, 2017, at 120 m above ground level (AGL) and third mission flown on June 1 at 600 m AGL (Figure 5). Only the Hacienda Barú Refuge was flown because of the need for higher spatial resolution imagery to differentiate deciduous versus tropical wet tree stands. In Santa Rosa and Corcovado, the tree species is homogeneous, so UAS flights were not necessary. After processing the first mission, the results showed a large section of the study area without images in the processed orthomosaic. This lack of imagery was attributed to the low elevation used in the flight plan and the homogeneous land cover preventing the creation of tie points to mosaic the images. A second flight was needed in order to solve this issue. The eBee specifications suggest that the maximum flight time is 40 min. Taking this into account, the flight plans were designed to have a maximum flight time of 32 min. Identifying a suitable landing and starting point was difficult, with a narrow beach approximately 2.5 km from the center of the study area finally selected. Line of sight was not able to be maintained with the UAS due to the long distance to the study area and thick forest canopy adjacent to the beach. In both missions, a MicaSense Sequoia camera (www.micssense.com/sequoia) was used to provide multispectral images as well as 16 megapixel RGB camera. The flights were planned using eMotion 2, and the data were then processed in Pix4Dmapper.
Analyzing these phenological changes overtime has been shown to be useful to identify climatic variations. Our approach built on this research by creating phenological profiles of deciduous and tropical wet tree stands over the course of the year (intraanual; Figures 6 and 7), shown to be useful in classifying forest composition . To do this, we averaged all NDVI values for each ROI in Santa Rosa (deciduous) and Corcovado (tropical). Individual pixels in the Hacienda Barú Reserve were then selected using UAS imagery and compared with modeled intraanual curves of deciduous exemplars.
Deciduous Phenological Curve (Santa Rosa)
Intraannual NDVI curves in deciduous forest tend to clearly represent a period of senescence, occurring during the first 100 days of the year in the Santa Rosa region . Following this period, rains bring new leaf growth and sustained vigor through the remainder of the calendar year. In Santa Rosa, we averaged 429 images from ROI #1 (Figure 3, top) and 482 from ROI #2 (Figure 3, bottom) to create an intraannual graph to model this phenological cycle (Figure 6). The graphs were created using 10-year temporal brackets to compare the phenological changes over time. Although the intraannual NDVI curve is clear, there is also an interannual (across the years) trend of increased vigor, represented by higher NDVI values over the past 12 years (shown in green) resulting in increasing NDVI values per bracket and showing the past 12 years with even higher NDVI values.
Tropical Evergreen Phenological Curve (Corcovado)
The tropical Corcovado study area exhibits a consistently high level of NDVI across the season (Figure 7). This is in contrast to the Santa Rosa deciduous study area, which displays a significant reduction in NDVI for the first 100 days followed by a large increase when the rains return to the area. In Corcovado, we averaged 294 images from ROI #1 (Figure 4, top) and 289 from ROI #2 (Figure 4, bottom). This represents a smaller number of total images than Santa Rosa’s 429 images due to the increased cloud cover over the tropical area. ROI #2 contains less imagery than ROI #1 because on several dates the entire ROI was cloud covered.
Although Santa Rosa has a long, severe annual drought and is just south of the Premonte wet forest, Basal Transition HLZ, Corcovado, is tropical evergreen. In between is the Hacienda Barú’s forest containing mixed deciduous and tropical vegetation. In our analysis, we were interested in how parts or all of the Hacienda Barú’s forest has been changing over time in response to changes in climate. To examine this, we looked at the UAS imagery identifying individual pixels in Hacienda Barú, classifying them as deciduous or tropical evergreen and then comparing them to what we are seeing in Santa Rosa and Corcovado. The analysis of the resulted data mining included averaging the NDVI values per date of image acquisition.
Mixed Phenological Curve (Hacienda Barú Refuge)
Although the Santa Rosa and Corcovado study sites represent exemplars of deciduous and tropical forests in western, costal Costa Rica, respectively, the Hacienda Barú Refuge is a mixed forest containing both tropical and deciduous vegetation. To analyze how the vegetation is changing over time, we leveraged UAS multispectral imagery to identify individual pixels within the Hacienda Barú Refuge which were at least 75% contained by either all tropical evergreen or deciduous vegetation for that 30 m2 pixel (Figure 8). From this, we visually identified a sampling of 20 deciduous forest pixels and 20 tropical forest pixels spread over the study area (Figure 9). We then created individual intraannual graphs of these 40 pixels over the 417 Landsat images that were available over this region from 1984 to 2017.
When examining the time series NDVI of pixels identified as containing all tropical evergreen vegetation (Figure 10), we see consistently high NDVI values similar to those of a tropical forest (Figure 7). In contrast, when analyzing the pixels identified as deciduous vegetation by approximately 10-year brackets, the transition from a deciduous phenological curve such as in Santa Rosa (Figure 6) to a tropical wet phenological curve becomes evident (Figure 11).
To quantify the transition of Hacienda Barú Refuge from a semi-deciduous or mixed forest to one of the tropical wet characteristics, we calculated the average vegetation vigor and standard deviation: 20 deciduous and 20 tropical wet pixels from the Hacienda Barú Refuge at roughly decadal periods (Table 1). Our results show that from 1984 to 1994, deciduous pixels more closely matched the deciduous phenological curve from Santa Rosa with lower average NDVI (0.74) and a higher standard deviation (0.079). But by the last decadal period, the pixels more closely resembled the tropical exemplar with an NDVI (0.873) very similar to those pixels in Corcovado or those identified as tropical in the Refuge (0.874). Their annual deviation also reduced showing a significant reduction in dry season senescence, more closely the tropical wet phenological curve exemplar of Corcovado by the end of the study period.
|ID .||Type .||1984–1994 .||1995–2004 .||2005–2017 .|
|.||.||Average .||Standard deviation .||Average .||Standard deviation .||Average .||Standard deviation .|
|ID .||Type .||1984–1994 .||1995–2004 .||2005–2017 .|
|.||.||Average .||Standard deviation .||Average .||Standard deviation .||Average .||Standard deviation .|
This study presents a unique analytical approach for measuring the phenological changes to individual trees in mixed tropical forests. By combining UAS multispectral data from a single set of flights (high spatial resolution, low temporal resolution) with Landsat satellite imagery since 1984 (low spatial resolution, high temporal resolution), we are able to identify and document the transition of Guanacaste trees in a mixed forest from strongly deciduous to weakly deciduous behavior more closely resembling the phenological cycle of tropical evergreen vegetation in the country. These trends were identified by comparing deciduous pixels in the study area with exemplars developed from the deciduous forest of Santa Rosa and the tropical wet forest of Corcovado.
Furthermore, this analysis identifies how this transition of the deciduous trees in the Hacienda Barú Refuge correlates with the wetter conditions mid-latitude Costa Rica has experienced over the years. If the trend of wetter climate continues in mid-latitude Costa Rica, conditions will increasingly favor tropical evergreen vegetation threatening the existence of deciduous trees in these mixed forests. These heterogeneous forests provide a habitat for some of the world’s richest biodiversity and are under threat from changing climate conditions. In response, this manuscript demonstrates a functional approach for the continued monitoring of the phenological processes of vegetation in mixed tropical forests and serves as a warning that the rich biodiversity of Costa Rica’s mixed, mid-latitude forests is under threat from climate change.
CASE STUDY QUESTIONS
What is the connection between global climate change and vegetation migration? Why does geography make it especially hard to examine this connection?
How does publicly available, historical satellite imagery serve as a resource for all of us in tracking global climate change? How can this resource be used to project future threats to biodiversity?
How can UAS be used in your local community to track and describe changes to the natural environment?
Notional guide to download and processing temporal stack of Landsat imagery.
Log onto EarthExplorer.usgs.gov and select the area and date period you are interested in
Under the “Data Sets” tab, Select Landsat Analysis Ready Data (ARD) under Landsat
Under “Additional Criteria,” select Cloud Cover “Less than 10%”
Select desired images for “Bulk Download” (see attached)
Use the Bulk Download Application to download images (https://earthexplorer.usgs.gov/bulk)
In Esri ArcMap or ArcGIS Pro, use the tool “Extract by Points” to extract the raster cell values over the coordinated you are interested in. Use Modelbuilder to iterate through a folder where all the Landsat images are.
In this manuscript, we extracted red and near Infrared, and in excel calculated Normalized Difference Vegetation Index (NDVI).
AM contributed to research design, analysis, and manuscript creation. DM assisted in the analysis and manuscript creation.
We would like to thank Clayton Sayre and Warren Roberts for their contributions to field data collection. We would also like to thank the Claremont Graduate University for their support for this research.
The BLAIS Foundation scholarship titled “Connecting Imagery-Based Data Science with Environmental Analysis: Collaborative Fieldwork in Costa Rica and Analysis in Claremont” (Grant number: 221-2170058) supported Andrew Marx.
The authors have declared that no competing interests exist.