Mapping forest types over large areas with Landsat data partially affected by clouds and SLC gaps

The ecosystem services that forests provide depend on tree species composition. Therefore, it is important to map not only forest extent and its dynamics, but also composition. Open access to Landsat has resulted in considerable improvements in remote sensing methods for mapping tree species, but most approaches fail to perform when there is a shortage of clear observations. Our main goal was to map forest composition with Landsat imagery in various data availability conditions, and to investigate how the missing data, either due to clouds or scan line problems affect classification accuracy. We tested a data driven approach that is based on multi-temporal analysis of the tree species’ spectral characteristics making it applicable to regional-scale mapping even when the gap-free imagery is not available. Our study area consisted of one Landsat footprint (26/28) located in Northern Wisconsin, USA. We selected this area because of numerous tree species (23), heterogenic composition of forests where the majority of stands are mixed, and availability of high-quality reference data. We quantified how classification accuracy at the species level was affected by a) the amount of missing data due to cloud cover and Scanning Line Corrector (SLC) gaps, b) the number of acquisitions, and c) the seasonal availability of images. We applied a decision tree classifier, capable of handling missing data to both single- and a three-year Landsat-7 and Landsat-8 observations. We classified the dominant tree species in each pixel and grouped results to forest stands to match our reference data. Our results show four major findings. First, producer’s and user’s accuracies range from 46.2% to 96.2% and from 59.9% to 93.7%, respectively for the most abundant forest types in the study area (all types covering greater than 2% of the forest area). Second, all tree species were mapped with overall accuracy above 70% even in when we restricted our data set to images having gaps larger than 30% of the study area. Third, the classification accuracy improved with more acquisitions, especially when images were available for the fall, spring, and summer. Finally, producer’s accuracies for pure-stands were higher than those for mixed stands by 10 to 30 percentage points. We conclude that inclusion of Landsat imagery with missing data allows to map forest types with accuracies that previously could be achieved only for those rare years for which several gap-free images were available. The approach presented here is directly applicable to Landsat-like observations and derived products such as seasonal composites and temporal statistics that miss 30% or more of the data for any single date to develop forest composition maps that are important for both forest management and ecology.

File: 1-s2.0-S0303243422000150-main.pdf

Statistical tests for non-independent partitions of large autocorrelated datasets

Large sets of autocorrelated data are common in fields such as remote sensing and genomics. For example, remote sensing can produce maps of information for millions of pixels, and the information from nearby pixels will likely be spatially autocorrelated. Although there are well-established statistical methods for testing hypotheses using autocorrelated data, these methods become computationally impractical for large datasets.
•The method developed here makes it feasible to perform F -tests, likelihood ratio tests, and t -tests for large autocorrelated datasets. The method involves subsetting the dataset into partitions, analyzing each partition separately, and then combining the separate tests to give an overall test.
•The separate statistical tests on partitions are non-independent, because the points in different partitions are not independent. Therefore, combining separate analyses of partitions requires accounting for the non- independence of the test statistics among partitions.
•The methods can be applied to a wide range of data, including not only purely spatial data but also spatiotemporal data. For spatiotemporal data, it is possible to estimate coefficients from time-series models at different spatial locations and then analyze the spatial distribution of the estimates. The spatial analysis can be simplified by estimating spatial autocorrelation directly from the spatial autocorrelation among time series.

File: 1-s2.0-S2215016122000449-main.pdf

Satellite image texture captures vegetation heterogeneity and explains patterns of bird richness

Addressing global declines in biodiversity requires accurate assessments of key environmental attributes determining patterns of species diversity. Spatial heterogeneity of vegetation strongly affects species diversity patterns, and measures of vegetation structure derived from lidar and satellite image texture analysis correlate well with species richness. Our goal here was to gain a better understanding of why image texture explains bird richness, by linking field-based measures of vegetation structure directly with both image texture and bird richness. In addition, we asked how image texture compares with lidar-based canopy height variability, and how sensor resolution affects the explanatory power of image texture. We generated texture metrics from 30 m (Landsat 8) and 10 m (Sentinel-2) resolution Enhanced Vegetation Index (EVI) imagery from 2017 to 2019. We compared textures with vegetation metrics and bird richness data from 27 National Ecological Observatory Network (NEON) terrestrial field sites across the continental US. Both 30 and 10 m resolution texture metrics were strongly correlated with lidar-based canopy height variability (|r| = 0.64 and 0.80, respectively). Texture was moderately correlated with field-based metrics, including variability of vegetation height and tree stem diameter, and foliage height diversity (range |r| = 0.31–0.52). Generally, 10 m resolution texture had stronger correlations with lidar and field-based metrics than 30 m resolution texture. In univariate linear models of total bird richness, 10 m resolution texture metrics also had higher explanatory power (up to R2adj = 0.45), than 30 m texture metrics (up to R2adj = 0.31). Among all metrics evaluated, the 10 m homogeneity texture was the best univariate predictor of total bird richness. In multivariate bird richness models that combined texture with lidarbased canopy height variability and field-based metrics, both 30 m and 10 m resolution texture metrics were selected in top-ranked models and independently contributed explanatory power (up to R2adj = 46%). Lidarbased canopy height variability was also selected in a top-ranked model of total bird richness, but independently contributed only 15% of the variance explained. Our results show satellite image texture characterized multiple features of structural and compositional vegetation heterogeneity, complemented more commonly used metrics in models of bird richness and for some guilds outperformed both lidar-based canopy height variability and field-based vegetation measurements. Ours is the first study to directly link image texture both to specific components of vegetation heterogeneity and to bird richness across multiple ecoregions and spatial resolutions, thereby shedding light on habitat features underlying the strong correlation between image texture and biodiversity.

File: 1-s2.0-S0034425720305484-main.pdf

Forest phenoclusters for Argentina based on vegetation phenology and climate

Forest biodiversity conservation and species distribution modeling greatly benefit from broad-scale forest maps depicting tree species or forest types rather than just presence and absence of forest, or coarse classifications. Ideally, such maps would stem from satellite image classification based on abundant field data for both model training and accuracy assessments, but such field data do not exist in many parts of the globe. However, different forest types and tree species differ in their vegetation phenology, offering an opportunity to map and characterize forests based on the seasonal dynamic of vegetation indices and auxiliary data. Our goal was to map and characterize forests based on both land surface phenology and climate patterns, defined here as forest phenoclusters. We applied our methodology in Argentina (2.8 million km2), which has a wide variety of forests, from rainforests to cold-temperate forests. We calculated phenology measures after fitting a harmonic curve of the enhanced vegetation index (EVI) time series derived from 30-m Sentinel 2 and Landsat 8 data from 2018–2019. For climate, we calculated land surface temperature (LST) from Band 10 of the thermal infrared sensor (TIRS) of Landsat 8, and precipitation from Worldclim (BIO12). We performed stratified X-means cluster classifications followed by hierarchical clustering. The resulting clusters separated well into 54 forest phenoclusters with unique combinations of vegetation phenology and climate characteristics. The EVI 90th percentile was more important than our climate and other phenology measures in providing separability among different forest phenoclusters. Our results highlight the potential of combining remotely sensed phenology measures and climate data to improve broad-scale forest mapping for different management and conservation goals, capturing functional rather than structural or compositional characteristics between and within tree species. Our approach results in classifications that go beyond simple forest–nonforest in areas where the lack of detailed ecological field data precludes tree species–level classifications, yet conservation needs are high. Our map of forest phenoclusters is a valuable tool for the assessment of natural resources, and the management of the environment at scales relevant for conservation actions.

File: Ecological-Applications-2022-Silveira-Forest-phenoclusters-for-Argentina-based-on-vegetation-phenology-and-climate.pdf

Changes in the grasslands of the Caucasus based on Cumulative Endmember Fractions from the full 1987–2019 Landsat record

Grasslands are important for global biodiversity, food security, and climate change analyses, which makes mapping and monitoring of vegetation changes in grasslands necessary to better understand, sustainably manage, and protect these ecosystems. However, grassland vegetation monitoring at spatial and temporal resolution relevant to land management (e.g., ca. 30-m, and at least annually over long time periods) is challenging due to complex spatio-temporal pattern of changes and often limited data availability. Here we assess both shortand long-term changes in grassland vegetation cover from 1987 to 2019 across the Caucasus ecoregion at 30-m resolution based on Cumulative Endmember Fractions (i.e., annual sums of monthly ground cover fractions) derived from the full Landsat record, and temporal segmentation with LandTrendr. Our approach combines the benefits of physically-based analyses, missing data prediction, annual aggregations, and adaptive identification of changes in the time-series. We analyzed changes in vegetation fraction cover to infer the location, timing, and magnitude of vegetation change episodes of any length, quantified shifts among all ground cover fractions (i.e., green vegetation, non-photosynthetic vegetation, soil, and shade), and identified change pathways (i.e., green vegetation loss, desiccation, dry vegetation loss, revegetation green fraction, greening, or revegetation dry fraction). We found widespread long-term positive changes in grassland vegetation (32.7% of grasslands), especially in the early 2000s, but negative changes pathways were most common before the year 2000. We found little association between changes in green vegetation and meteorological conditions, and varied relationships with livestock populations. However, we also found strong spatial heterogeneity in vegetation dynamics among neighboring fields and pastures, demonstrating capability of our approach for grassland management at local levels. Our results provide a detailed assessment of grassland vegetation change in the Caucasus Ecoregion, and present an approach to map changes in grasslands even where availability of Landsat data is limited.

File: 1-s2.0-S2666017221000225-main.pdf

Statistical inference for trends in spatiotemporal data

Global change analyses are facilitated by the growing number of remote-sensing datasets that have both broad spatial extent and repeated observations over decades. These datasets provide unprecedented power to detect patterns of time trends involving information from all pixels on a map. However, rigorously testing for time trends requires a solid statistical foundation to identify underlying patterns and test hypotheses. Appropriate statistical analyses are challenging because environmental data often have temporal and spatial autocorrelation, which can either obscure underlying patterns in the data or suggest false associations between patterns in the data and independent values used to explain them. Existing statistical methods that account for temporal and spatial autocorrelation are not practical for remote-sensing datasets that often contain millions of pixels. Here, we first analyze simulated data to show the need to account for both spatial and temporal autocorrelation in time-trend analyses. Second, we present a new statistical approach, PARTS (Partitioned Autoregressive Time Series), to identify underlying patterns and test hypotheses about time trends using all pixels in large remote sensing datasets. PARTS is flexible and can include, for example, the effects of multiple independent variables, such as land-cover or latitude, on time trends. Third, we use PARTS to analyze global trends in NDVI, focusing on trends in pixels that have not experienced land-cover change. We found that despite the appearance of overall increases in NDVI in all continents, there is little statistical support for these trends except for Asia and Europe, and only in some land-cover classes. Furthermore, we found no overall latitudinal trend in greening for any continent, but some latitude by land-cover class interactions, implying that latitudinal patterns differed among land-cover classes. PARTS makes it possible to identify patterns and test hypotheses that involve the aggregate information from many pixels on a map, thereby increasing the value of existing remote-sensing datasets.

File: 1-s2.0-S0034425721003989-main.pdf

Patterns of bird species richness explained by annual variation in remotely sensed Dynamic Habitat Indices

Bird species richness is highly dependent on the amount of energy available in an ecosystem, with more available
energy supporting higher species richness. A good indicator for available energy is Gross Primary Productivity
(GPP), which can be estimated from satellite data.
Our question was how temporal dynamics in GPP affect bird species richness. Specifically, we evaluated the
potential of the Dynamic Habitat Indices (DHIs) derived from MODIS GPP data together with environmental and
climatic variables to explain annual patterns in bird richness across the conterminous United States. By focusing
on annual DHIs, we expand on previous applications of multi-year composite DHIs, and could evaluate lag-effects
between changes in GPP and species richness.
We used 8-day GPP data from 2003 to 2013 to calculate annual DHIs, which capture three aspects of vegetation
productivity: (1) annual cumulative productivity, (2) annual minimum productivity, and (3) annual
seasonality expressed as the coefficient of variation in productivity. For each year from 2003 to 2013, we
calculated total bird species richness and richness within six functional guilds, based on North American
Breeding Bird Survey data.
The DHIs alone explained up to 53% of the variation in annual bird richness within the different guilds
(adjusted deviance-squared D2adj = 0.20–0.52), and up to 75% of the variation (D2adj = 0.28–0.75) when
combined with other environmental and climatic variables. Annual DHIs had the highest explanatory power for
habitat-based guilds, such as grassland (D2adj = 0.67) and woodland breeding species (D2adj = 0.75). We found
some inter-annual variability in the explanatory power of annual DHIs, with a difference of 5–7 percentage
points in explained variation among years in DHI-only models, and 3–7 points for models combining DHI,
environmental and climatic variables. Our results using lagged year models did not deviate substantially from
same-year annual models.
We demonstrate the relevance of annual DHIs for biodiversity science, as effective predictors of temporal
variation in species richness patterns. We suggest that the use of annual DHIs can improve conservation planning,
by conveying the range of patterns of biodiversity response to global changes, over time.

File: Hobi-et-al-2021_BirdSpeciesRichness_DynamicHabIndices_EcolIndicators.pdf

Land cover and land abandonment maps of the Eurasian Steppe for biological research

Maps are a key instrument and important data source for a wide range of research from global modeling to detailed ecological studies of a specific species. However different scales of tasks require proper instruments including a suitable maps detalization. For instance, a scientist who is interested in the general trends of agriculture abandonment may not have to pay too much attention to which specific fields are not in use anymore. However, for a conservation biologist studying a rare species, detailed maps of habitats, such as abandoned crops, is critical. However, it is difficult to make such detailed maps for large areas. Global maps are many, but they lack necessary details, while fine-scale maps only cover small areas if they exist at all. Unfortunately, using inappropriate scale of the input information either makes the results too general to be sensible or leads to incorrect conclusions.

In practical terms, precise mapping is a matter of balance of time and efforts versus the desired quality of results. The more accurate is a map the more resources are required to make it. But the amount of the resources necessary for creating a good map for a large area may be beyond what project managers can afford.

Coming back to the abandonment and land cover mapping, the maps are important for a variety of tasks including economic (re)development, nature conservation, and agriculture improvements. Thus, the absence of proper maps could make ecological and economic problems even worse.

Part of my research is about the level of accuracy we could (or should) achieve when mapping large areas. I have chosen the Eurasian Steppe as a test site because it is vast, large areas of abandonment, as well as permanently used field,) and rich diversity of natural vegetation. At the same time, it is one of the most transformed landscapes in Eurasia where biodiversity conservation and preserving intact steppes as the source of both rare and dominant native species to re-habit the man-made vacuum is a top priority. What makes the mapping of these areas challenging though is that the natural vegetation, mainly grasses and herbs, is spectrally very similarly to agriculture in satellite images.

I am planning to test several mapping techniques taking into account the advantages of each and adjust them to specific conditions of the steppe. The random forest algorithm is easy and fast enough to make initial maps. These maps show general land cover of an area and allow to reveal sources of mismapping. The segmentation algorithm is helpful in drawing more clear borders but fails to distinguish objects that have similar reflection while belonging to different classes. The understanding of general structure gained from the initial maps gives better reasons to divide a large heterogeneous area into smaller and more solid parts where differences between the mapping classes are higher than in-class variability. Ultimately, I hope to achieve two results. The first is understanding of how to combine existing methods to improve the whole map quality. The second is to create maps suitable for ecological research, preserving biodiversity and the establishment of new protected areas.

Spatio-temporal remotely sensed indices identify hotspots of biodiversity conservation concern

Over the course of a year, vegetation and temperature have strong phenological and seasonal patterns, respectively, and many species have adapted to these patterns. High inter-annual variability in the phenology of vegetation and in the seasonality of temperature pose a threat for biodiversity. However, areas with high spatial variability likely have higher ecological resilience where inter-annual variability is high, because spatial variability indicates presence of a range of resources, microclimatic refugia, and habitat conditions. The integration of inter-annual and spatial variability is thus important for biodiversity conservation. Areas where spatial variability is low and inter-annual variability is high are likely to limit resilience to disturbance. In contrast, areas of high spatial variability may be high priority candidates for protection. Our goal was to develop spatiotemporal remotely sensed indices to identify hotspots of biodiversity conservation concern. We generated indices that capture the inter-annual and spatial variability of vegetation greenness and land surface temperature and integrated them to identify areas of high, medium, and low biodiversity conservation concern. We applied our method in Argentina (2.8 million km2), a country with a wide range of climates and biomes. To generate the inter-annual variability indices, we analyzed MODIS Enhanced Vegetation Index (EVI) and Land Surface Temperature (LST) time series from 2001 to 2018, fitted curves to obtain annual phenological and seasonal metrics, and calculated their inter-annual variability. To generate the spatial variability indices, we calculated standard deviation image texture of Landsat 8 EVI and LST. When we integrated our inter-annual and spatial variability indices, areas in the northeast and parts of southern Argentina were the hotspots of highest conservation concern. High inter-annual variability poses a threat in these areas, because spatial variability is low. These are areas where management efforts could be valuable. In contrast, areas in the northwest and central-west are where protection should be strongly considered because the high spatial variability may confer resilience to disturbance, due to the variety of conditions and resources within close proximity. We developed remotely sensed indices to identify hotspots of high and low conservation concern at scales relevant to biodiversity conservation, = which can be used to target management actions in order to minimize biodiversity loss.

File: RSE_Silveira_2021.pdf

Contrasting seasonal patterns of relative temperature and thermal heterogeneity and their influence on breeding and winter bird richness patterns across the conterminous United States

Environmental heterogeneity enhances species richness by creating niches and providing refugia. Spatial variation in climate has a particularly strong positive correlation with richness, but is often indirectly inferred from proxy variables, such as elevation and related topographic heterogeneity indices, or derived from interpolated coarsegrain weather station data. Our aim was to develop new remotely sensed metrics of relative temperature and thermal heterogeneity, compare them with proxy measures, and evaluate their performance in predicting species richness patterns. We analyzed Landsat 8’s Thermal Infrared Sensor data, calculated two thermal metrics during summer and winter, and compared their seasonal spatial patterns with those of elevation and topographic heterogeneity. We fit generalized least squares models to evaluate each variable’s effect in predicting seasonal bird richness using data from the North American Breeding Bird Survey. Generally speaking, neither elevation nor topographic heterogeneity were good proxies for temperature or thermal heterogeneity, respectively. Relative temperature had a non-linear relationship with elevation that was negatively quadratic in summer, but slightly positively quadratic in winter. Topographic heterogeneity had a stronger positive relationship with thermal heterogeneity in winter than in summer. The magnitude and direction of elevation–temperature and topographic heterogeneity–thermal heterogeneity relationships in each season also varied substantially across ecoregions. Remotely sensed metrics of relative temperature and thermal heterogeneity improved the predictive performance of species richness models, and both thermal variables had significant effects on bird richness that were independent of elevation and topographic heterogeneity. Thermal heterogeneity was positively related to total breeding bird richness, migrant breeding bird richness and resident bird richness, whereas topographic heterogeneity was negatively related to total breeding richness and unrelated to migrant or resident bird richness. Because thermal and topographic heterogeneity had contrasting seasonal patterns and effects on richness, they must be carefully contextualized when guiding conservation priorities.

File: ecog.05520.pdf