Leaf phenology amplitude derived from MODIS NDVI and EVI: maps of leaf phenology synchrony for Meso‐ and South America

The leaf phenology (i.e. the seasonality of leaf amount and leaf demography) of ecosystems can be characterized through the use of Earth observation data using a variety of different approaches. The most common approach is to derive time series of vegetation indices (VIs) which are related to the temporal evolution of FPAR, LAI and GPP or alternatively used to derive phenology metrics that quantify the growing season. The product presented here shows a map of average ‘amplitude’ (i.e. maximum minus minimum) of annual cycles observed in MODIS‐derived NDVI and EVI from 2000 to 2013 for Meso‐ and South America. It is a robust determination of the amplitude of annual cycles of vegetation greenness derived from a Lomb–Scargle spectral analysis of unevenly spaced data. VI time series pre‐processing was used to eliminate measurement outliers, and the outputs of the spectral analysis were screened for statistically significant annual signals. Amplitude maps provide an indication of net ecosystem phenology since the satellite observations integrate the greenness variations across the plant individuals within each pixel. The average amplitude values can be interpreted as indicating the degree to which the leaf life cycles of individual plants and species are synchronized. Areas without statistically significant annual variations in greenness may still consist of individuals that show a well‐defined annual leaf phenology. In such cases, the timing of the phenology events will vary strongly within the year between individuals. Alternatively, such areas may consist mainly of plants with leaf turnover strategies that maintain a constant canopy of leaves of different ages. Comparison with in situ observations confirms our interpretation of the average amplitude measure. VI amplitude interpreted as leaf life cycle synchrony can support model evaluation by informing on the likely leaf turn over rates and seasonal variation in ecosystem leaf age distribution

Intra-annual taxonomic and phenological drivers of spectral variance in grasslands

According to the Spectral Variation Hypothesis (SVH), spectral variance has the potential to predict taxonomic composition in grasslands over time. However, in previous studies the relationship has been found to be unstable. We hypothesise that the diversity of phenological stages is also a driver of spectral variance and could act to confound the species signal. To test this concept, intra-annual repeat spectral and botanical sampling was performed at the quadrat scale at two grassland sites, one displaying high species diversity and the other low species diversity. Six botanical metrics were used, three taxonomy based and three phenology based. Using uni-temporal linear permutation models, we found that the SVH only held at the high diversity site and only for certain metrics and at particular time points. We also tested the seasonal influence of phenological stage dominance, alongside the taxonomic and phenological diversity metrics on spectral variance using linear mixed models. A term of percentage mature leaves, alongside an interaction term of percentage mature leaves and species diversity, explained 15-25% of the model variances, depending on the spectral region used. These results indicate that the dominant canopy phenology stage is a confounding variable when examining the spectral variance-species diversity relationship. We emphasise the challenges that exist in tracking species or phenology-based metrics in grasslands using spectral variance but encourage further research that contextualises spectral variance data within seasonal plant development alongside other canopy structural and leaf traits

Leaf age effects on the spectral predictability of leaf traits in Amazonian canopy trees

Recent work has shown that leaf traits and spectral properties change through time and/or seasonally as leaves age. Current field and hyperspectral methods used to estimate canopy leaf traits could, therefore, be significantly biased by variation in leaf age. To explore the magnitude of this effect, we used a phenological dataset comprised of leaves of different leaf age groups -developmental, mature, senescent and mixed-age- from canopy and emergent tropical trees in southern Peru. We tested the performance of partial least squares regression models developed from these different age groups when predicting traits for leaves of different ages on both a mass and area basis. Overall, area-based models outperformed mass-based models with a striking improvement in prediction observed for area-based leaf carbon (Carea) estimates. We observed trait-specific age effects in all mass-based models while area-based models displayed age effects in mixed-age leaf groups for Parea and Narea. Spectral coefficients and variable importance in projection (VIPs) also reflected age effects. Both mass- and area-based models for all five leaf traits displayed age/temporal sensitivity when we tested their ability to predict the traits of leaves of other age groups. Importantly, mass based mature models displayed the worst overall performance when predicting the traits of leaves from other age groups. These results indicate that the widely adopted approach of using fully expanded mature leaves to calibrate models that estimate remotely-sensed tree canopy traits introduces error that can bias results depending on the phenological stage of canopy leaves. To achieve temporally stable models, spectroscopic studies should consider producing area-based estimates as well as calibrating models with leaves of different age groups as they present themselves through the growing season. We discuss the implications of this for surveys of canopies with synchronised and unsynchronised leaf phenology

The feasibility of leaf reflectance-based taxonomic inventories and diversity assessments of species-rich grasslands: a cross-seasonal evaluation using waveband selection

Hyperspectral leaf-level reflectance data may enable the creation of taxonomic inventories and diversity assessments of grasslands, but little is known about the stability of species-specific spectral classes and discrimination models over the course of a growing season. Here, we present a cross-seasonal dataset of seventeen species that are common to a temperate, dry and nutrient-poor calcareous grassland, which spans thirteen sampling dates, a week apart, during the spring and summer months. By using a classification model that incorporated waveband selection (a sparse partial least squares discriminant analysis), most species could be classified, irrespective of the sampling date. However, between 42 and 95% of the available spectral information was required to obtain these results, depending on the date and model run. Feature selection was consistent across time for 70 out of 720 wavebands and reflectance around 1410 nm, representing water features, contributed the most to the discrimination. Model transferability was higher between neighbouring sampling dates and improved after the “green-up” period. Some species were consistently easy to classify, irrespective of time point, when using up to six latent variables, which represented about 99% of the total spectral variance, whereas other species required many latent variables, which represented very small spectral differences. We concluded that it did seem possible to create reliable taxonomic inventories for combinations of certain grassland species, irrespective of sampling date, and that the reason for this could lie in their distinctive morphological and/or biochemical leaf traits. Model transferability, however, was limited across dates and cross-seasonal sampling that captures leaf development would probably be necessary to create a predictive framework for the taxonomic monitoring of grasslands. In addition, most variance in the leaf reflectance within this system was driven by a subset of species and this finding implies challenges for the application of spectral variance in the estimation of biodiversity

Prediction of grassland biodiversity using measures of spectral variance: a meta-analytical review

Over the last 20 years, there has been a surge of interest in the use of reflectance data collected using satellites and aerial vehicles to monitor vegetation diversity. One methodological option to monitor these systems involves developing empirical relationships between spectral heterogeneity in space (spectral variation) and plant or habitat diversity. This approach is commonly termed the ‘Spectral Variation Hypothesis’. Although increasingly used, it is controversial and can be unreliable in some contexts. Here, we review the literature and apply three-level meta-analytical models to assess test results of the hypothesis across studies using several moderating variables, relating to the botanical and spectral sampling strategies, and the types of sites evaluated. We focus on the literature relating to grasslands, which are less well studied compared to forests and are likely to require separate treatment due to their dynamic phenology and the taxonomic complexity of their canopies over small scales. Across studies, results suggest an overall positive relationship between spectral variation and species diversity (mean correlation co-efficient = 0.36). However, high levels of both within study and between study heterogeneity was found. Whether data was collected at the leaf or canopy level had the most impact on the mean effect size, with leaf level studies displaying a stronger relationship compared to canopy level studies. We highlight the challenges facing synthesis of these kinds of experiments, the lack of studies carried out in arid or tropical systems and the need for scalable, multi-temporal assessments to resolve controversy in the field

A framework for improved predictions of the climate impacts on potential yields of UK winter wheat and its applicability to other UK crops

•Changes in the frequency of extreme weather events related to climate change potentially pose significant challenges to UK agricultural production. There is a need for improved climate change risk assessments to support adaptation strategies and to ensure security of food production in future. •We describe an innovative and practical framework for spatially explicit modelling of climate change impacts on crop yields, based on the UKCP18 climate projections. Our approach allows the integration of relatively simple crop growth models with high spatial and temporal resolution Earth Observation datasets, describing changes in crop growth parameters within year and over the longer term. We focus on modelling winter wheat, a commercially important crop. We evaluate the results of the model against precision yield data collected from 719 fields. We show that the assimilation of leaf area index data from Sentinel-2 satellite observations improves the agreement of the modelled yields with those observed. Our national-scale results indicate that wheat production initially becomes more favourable under climate change across much of the UK with the projected increase in temperature. From 2050 onwards, yields increase northwards, whilst they decline in South East England as the decrease in precipitation offsets the benefits of rising temperature. •Our framework can readily accommodate growth models for other crops and LAI retrievals from other satellite sensors. The ability to explore impacts of crop yields at fine spatial resolutions is an important part of assessing the potential risks of climate change to UK agriculture and of designing more climate resilient agricultural systems

Slow development of woodland vegetation and bird communities during 33 years of passive rewilding in open farmland

Passive rewilding is a potential tool for expanding woodland cover and restoring biodiversity by abandoning land management and allowing natural vegetation succession to occur. Land can be abandoned to passive rewilding deliberately or due to socio-economic change. Despite abandonment being a major driver of land use change, few have studied the long-term outcomes for vegetation and biodiversity in Western Europe. Studies are also biased towards sites that are close to seed sources and favourable to woodland colonisation. In this case-study, we reconstruct a time series of passive rewilding over 33 years on 25 ha of former farmland that had been subject to soil tipping, far from woodland seed sources. Natural colonisation by shrubs and trees was surveyed at three points during the time series, using field mapping and lidar. Breeding birds were surveyed at three time points, and compared with surveys from nearby farmland. Results showed that natural colonisation of woody vegetation was slow, with open grassland dominating the old fields for two decades, and small wetlands developing spontaneously. After 33 years, thorny shrub thickets covered 53% of the site and former hedgerows became subsumed or degraded, but trees remained scarce. However, the resulting habitat mosaic of shrubland, grassland and wetland supported a locally distinctive bird community. Farmland bird species declined as passive rewilding progressed, but this was countered by relatively more wetland birds and an increase in woodland birds, particularly songbirds, compared to nearby farmland. Alongside biodiversity benefits, shrubland establishment by passive rewilding could potentially provide ecosystem services via abundant blossom resources for pollinators, and recreation and berry-gathering opportunities for people. Although closed-canopy woodland remained a distant prospect even after 33 years, the habitat mosaic arising from passive rewilding could be considered a valuable outcome, which could contribute to nature recovery and provision of ecosystem services

Intra-annual taxonomic and phenological drivers of spectral variance in grasslands

According to the Spectral Variation Hypothesis (SVH), spectral variance has the potential to predict taxonomic composition in grasslands over time. However, in previous studies the relationship has been found to be unstable. We hypothesise that the diversity of phenological stages is also a driver of spectral variance and could act to confound the species signal. To test this concept, intra-annual repeat spectral and botanical sampling was performed at the quadrat scale at two grassland sites, one displaying high species diversity and the other low species diversity. Six botanical metrics were used, three taxonomy based and three phenology based. Using uni-temporal linear permutation models, we found that the SVH only held at the high diversity site and only for certain metrics and at particular time points. We tested the seasonal influence of the taxonomic and phenological metrics on spectral variance using linear mixed models. A significant interaction term of percent mature leaves and species diversity was found, with the most parsimonious model explaining 43% of the intra-annual change. These results indicate that the dominant canopy phenology stage is a confounding variable when examining the spectral variance -species diversity relationship. We emphasise the challenges that exist in tracking species or phenology-based metrics in grasslands using spectral variance but encourage further research that contextualises spectral variance data within seasonal plant development alongside other canopy structural and leaf traits

Determination of freedom-from-rabies for small Indian mongoose populations in the United States Virgin Islands, 2019–2020

Mongooses, a nonnative species, are a known reservoir of rabies virus in the Caribbean region. A cross-sectional study of mongooses at 41 field sites on the US Virgin Islands of St. Croix, St. John, and St. Thomas captured 312 mongooses (32% capture rate). We determined the absence of rabies virus by antigen testing and rabies virus exposure by antibody testing in mongoose populations on all three islands. USVI is the first Caribbean state to determine freedom-from-rabies for its mongoose populations with a scientifically-led robust cross-sectional study. Ongoing surveillance activities will determine if other domestic and wildlife populations in USVI are rabies-free

Mongooses (\u3ci\u3eUrva auropunctata\u3c/i\u3e) as reservoir hosts of leptospira species in the United States Virgin Islands, 2019–2020

During 2019–2020, the Virgin Islands Department of Health investigated potential animal reservoirs of Leptospira spp., the bacteria that cause leptospirosis. In this cross-sectional study, we investigated Leptospira spp. exposure and carriage in the small Indian mongoose (Urva auropunctata, syn: Herpestes auropunctatus), an invasive animal species. This study was conducted across the three main islands of the U.S. Virgin Islands (USVI), which are St. Croix, St. Thomas, and St. John. We used the microscopic agglutination test (MAT), fluorescent antibody test (FAT), real-time polymerase chain reaction (lipl32 rt-PCR), and bacterial culture to evaluate serum and kidney specimens and compared the sensitivity, specificity, positive predictive value, and negative predictive value of these laboratory meth-ods. Mongooses (n = 274) were live-trapped at 31 field sites in ten regions across USVI and humanely euthanized for Leptospira spp. testing. Bacterial isolates were sequenced and evaluated for species and phylogenetic analysis using the ppk gene. Anti-Leptospira spp. antibodies were detected in 34% (87/256) of mongooses. Reactions were observed with the following serogroups: Sejroe, Icterohaemorrhagiae, Pyrogenes, Mini, Cynopteri, Australis, Hebdomadis, Autumnalis, Mankarso, Pomona, and Ballum. Of the kidney specimens exam-ined, 5.8% (16/270) were FAT-positive, 10% (27/274) were culture-positive, and 12.4% (34/ 274) were positive by rt-PCR. Of the Leptospira spp. isolated from mongooses, 25 were L. borgpetersenii, one was L. interrogans, and one was L. kirschneri. Positive predictive values of FAT and rt-PCR testing for predicting successful isolation of Leptospira by culture were 88% and 65%, respectively. The isolation and identification of Leptospira spp. in mongooses highlights the potential role of mongooses as a wildlife reservoir of leptospirosis; mongooses could be a source of Leptospira spp. infections for other wildlife, domestic animals, and humans