International Institute of Tropical Forestry

ABSTRACT We explore the issues relevant to those types of ecosystems containing new combinations of species that arise through human action, environmental change, and the impacts of the deliberate and inadvertent introduction of species from other regions. Novel ecosystems (also termed ‘emerging ecosystems’) result when species occur in combinations and relative abundances that have not occurred previously within a given biome. Key characteristics are novelty, in the form of new species combinations and the potential for changes in ecosystem functioning, and human agency, in that these ecosystems are the result of deliberate or inadvertent human action. As more of the Earth becomes transformed by human actions, novel ecosystems increase in importance, but are relatively little studied. Either the degradation or invasion of native or ‘wild’ ecosystems or the abandonment of intensively managed systems can result in the formation of these novel systems. Important considerations are whether these new systems are persistent and what values they may have. It is likely that it may be very difficult or costly to return such systems to their previous state, and hence consideration needs to be given to developing appropriate management goals and approaches.

Abstract. Question: What are the major vegetation units in the Arctic, what is their composition, and how are they distributed among major bioclimate subzones and countries? Location: The Arctic tundra region, north of the tree line. Methods: A photo‐interpretive approach was used to delineate the vegetation onto an Advanced Very High Resolution Radiometer (AVHRR) base image. Mapping experts within nine Arctic regions prepared draft maps using geographic information technology (ArcInfo) of their portion of the Arctic, and these were later synthesized to make the final map. Area analysis of the map was done according to bioclimate subzones, and country. The integrated mapping procedures resulted in other maps of vegetation, topography, soils, landscapes, lake cover, substrate pH, and above‐ground biomass. Results: The final map was published at 1:7 500 000 scale map. Within the Arctic (total area = 7.11 × 106 km 2 ), about 5.05 × 10 6 km 2 is vegetated. The remainder is ice covered. The map legend generally portrays the zonal vegetation within each map polygon. About 26% of the vegetated area is erect shrublands, 18% peaty graminoid tundras, 13% mountain complexes, 12% barrens, 11% mineral graminoid tundras, 11% prostrate‐shrub tundras, and 7% wetlands. Canada has by far the most terrain in the High Arctic mostly associated with abundant barren types and prostrate dwarf‐shrub tundra, whereas Russia has the largest area in the Low Arctic, predominantly low‐shrub tundra. Conclusions: The CAVM is the first vegetation map of an entire global biome at a comparable resolution. The consistent treatment of the vegetation across the circumpolar Arctic, abundant ancillary material, and digital database should promote the application to numerous land‐use, and climate‐change applications and will make updating the map relatively easy.

Amazon deforestation has been measured by remote sensing for three decades. In comparison, selective logging has been mostly invisible to satellites. We developed a large-scale, high-resolution, automated remote-sensing analysis of selective logging in the top five timber-producing states of the Brazilian Amazon. Logged areas ranged from 12,075 to 19,823 square kilometers per year (+/-14%) between 1999 and 2002, equivalent to 60 to 123% of previously reported deforestation area. Up to 1200 square kilometers per year of logging were observed on conservation lands. Each year, 27 million to 50 million cubic meters of wood were extracted, and a gross flux of approximately 0.1 billion metric tons of carbon was destined for release to the atmosphere by logging.

Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.

In the wake of widespread loss of old-growth forests throughout the tropics, secondary forests will likely play a growing role in the conservation of forest biodiversity. We considered a complex hierarchy of factors that interact in space and time to determine the conservation potential of tropical secondary forests. Beyond the characteristics of local forest patches, spatial and temporal landscape dynamics influence the establishment, species composition, and persistence of secondary forests. Prospects for conservation of old-growth species in secondary forests are maximized in regions where the ratio of secondary to old-growth forest area is relatively low, older secondary forests have persisted, anthropogenic disturbance after abandonment is relatively low, seed-dispersing fauna are present, and old-growth forests are close to abandoned sites. The conservation value of a secondary forest is expected to increase over time, as species arriving from remaining old-growth forest patches accumulate. Many studies are poorly replicated, which limits robust assessments of the number and abundance of old-growth species present in secondary forests. Older secondary forests are not often studied and few long-term studies are conducted in secondary forests. Available data indicate that both old-growth and second-growth forests are important to the persistence of forest species in tropical, human-modified landscapes.

Exchange of carbon between forests and the atmosphere is a vital component of the global carbon cycle. Satellite laser altimetry has a unique capability for estimating forest canopy height, which has a direct and increasingly well understood relationship to aboveground carbon storage. While the Geoscience Laser Altimeter System (GLAS) onboard the Ice, Cloud and land Elevation Satellite (ICESat) has collected an unparalleled dataset of lidar waveforms over terrestrial targets, processing of ICESat data to estimate forest height is complicated by the pulse broadening associated with large‐footprint, waveform‐sampling lidar. We combined ICESat waveforms and ancillary topography from the Shuttle Radar Topography Mission to estimate maximum forest height in three ecosystems; tropical broadleaf forests in Brazil, temperate broadleaf forests in Tennessee, and temperate needleleaf forests in Oregon. Final models for each site explained between 59% and 68% of variance in field‐measured forest canopy height (RMSE between 4.85 and 12.66 m). In addition, ICESat‐derived heights for the Brazilian plots were correlated with field‐estimates of aboveground biomass (r 2 = 73%, RMSE = 58.3 Mgha −1 ).

Invasive species, disease vectors, and pathogens affect biodiversity, ecosystem function and services, and human health. Climate change, land use, and transport vectors interact in complex ways to determine the spread of native and non-native invasive species, pathogens, and their effects on ecosystem dynamics. Early detection and in-depth understanding of invasive species and infectious diseases will require an integrated network of research platforms and information exchange to identify hotspots of invasion or disease emergence. Partnerships with state and federal agencies that monitor the spread and impacts of invasive species and pathogens will be critical in developing a national data and research network that can facilitate a full understanding of the resulting effects on ecosystems and society. Citizen science can also play a role; individuals can report new invasions, record phenological changes associated with invasions or disease outbreaks, and can participate in efforts such as the Breeding Bird Survey, which may reveal long-term biotic change following species invasions and disease spread. The ecological and societal impacts of invasive species and pathogens differ across gradients of climate and land use, and in the presence of global climate change may exacerbate both their propagation and impacts. Understanding the interactions of invasive species, disease vectors, and pathogens with other drivers of ecosystem change is critical to human health and economic well-being.

Abstract Approximately half of the tropical biome is in some stage of recovery from past human disturbance, most of which is in secondary forests growing on abandoned agricultural lands and pastures. Reforestation of these abandoned lands, both natural and managed, has been proposed as a means to help offset increasing carbon emissions to the atmosphere. In this paper we discuss the potential of these forests to serve as sinks for atmospheric carbon dioxide in aboveground biomass and soils. A review of literature data shows that aboveground biomass increases at a rate of 6.2 Mg ha − 1 yr − 1 during the first 20 years of succession, and at a rate of 2.9 Mg ha − 1 yr − 1 over the first 80 years of regrowth. During the first 20 years of regrowth, forests in wet life zones have the fastest rate of aboveground carbon accumulation with reforestation, followed by dry and moist forests. Soil carbon accumulated at a rate of 0.41 Mg ha − 1 yr − 1 over a 100‐year period, and at faster rates during the first 20 years (1.30 Mg carbon ha − 1 yr − 1 ). Past land use affects the rate of both above‐ and belowground carbon sequestration. Forests growing on abandoned agricultural land accumulate biomass faster than other past land uses, while soil carbon accumulates faster on sites that were cleared but not developed, and on pasture sites. Our results indicate that tropical reforestation has the potential to serve as a carbon offset mechanism both above‐ and belowground for at least 40 to 80 years, and possibly much longer. More research is needed to determine the potential for longer‐term carbon sequestration for mitigation of atmospheric CO 2 emissions.

Summary Tree mortality rates appear to be increasing in moist tropical forests ( MTF s) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and identify the next steps for improved understanding and reduced prediction. Increasing mortality rates are associated with rising temperature and vapor pressure deficit, liana abundance, drought, wind events, fire and, possibly, CO 2 fertilization‐induced increases in stand thinning or acceleration of trees reaching larger, more vulnerable heights. The majority of these mortality drivers may kill trees in part through carbon starvation and hydraulic failure. The relative importance of each driver is unknown. High species diversity may buffer MTF s against large‐scale mortality events, but recent and expected trends in mortality drivers give reason for concern regarding increasing mortality within MTF s. Models of tropical tree mortality are advancing the representation of hydraulics, carbon and demography, but require more empirical knowledge regarding the most common drivers and their subsequent mechanisms. We outline critical datasets and model developments required to test hypotheses regarding the underlying causes of increasing MTF mortality rates, and improve prediction of future mortality under climate change. Contents Summary 852 I. Introduction 852 II. Increasing mortality rates in the Amazon Basin 854 III. Global and regional mortality drivers and mechanisms 855 IV. On the coupling of mortality drivers and mechanisms 859 V. Mitigating factors that may promote future survival 859 VI. The state of ESM simulations of moist tropical tree mortality 859 VII. Next steps 860 VIII. Conclusions 863 Acknowledgements 863 ORCID 863 References 863

NASA's Black Marble nighttime lights product suite (VNP46) is available at 500 m resolution since January 2012 with data from the Visible Infrared Imaging Radiometer Suite (VIIRS) Day/Night Band (DNB) onboard the Suomi National Polar-orbiting Platform (SNPP). The retrieval algorithm, developed and implemented for routine global processing at NASA's Land Science Investigator-led Processing System (SIPS), utilizes all high-quality, cloud-free, atmospheric-, terrain-, vegetation-, snow-, lunar-, and stray light-corrected radiances to estimate daily nighttime lights (NTL) and other intrinsic surface optical properties. Key algorithm enhancements include: (1) lunar irradiance modeling to resolve non-linear changes in phase and libration; (2) vector radiative transfer and lunar bidirectional surface anisotropic reflectance modeling to correct for atmospheric and BRDF effects; (3) geometric-optical and canopy radiative transfer modeling to account for seasonal variations in NTL; and (4) temporal gap-filling to reduce persistent data gaps. Extensive benchmark tests at representative spatial and temporal scales were conducted on the VNP46 time series record to characterize the uncertainties stemming from upstream data sources. Initial validation results are presented together with example case studies illustrating the scientific utility of the products. This includes an evaluation of temporal patterns of NTL dynamics associated with urbanization, socioeconomic variability, cultural characteristics, and displaced populations affected by conflict. Current and planned activities under the Group on Earth Observations (GEO) Human Planet Initiative are aimed at evaluating the products at different geographic locations and time periods representing the full range of retrieval conditions.

Ecologists need data on animal–habitat associations in terrestrial and aquatic environments to design and implement effective conservation strategies. Habitat characteristics used in models typically incorporate (1) field data of limited spatial extent and/or (2) remote sensing data that do not characterize the vertical habitat structure. Remote sensing tools that directly characterize three-dimensional (3-D) habitat structure and that provide data relevant to organism–habitat interactions across a hierarchy of scales promise to improve our understanding of animal–habitat relationships. Laser altimetry, commonly called light detection and ranging (lidar), is a source of geospatial data that can provide fine-grained information about the 3-D structure of ecosystems across broad spatial extents. In this review, we present a brief overview of lidar technology, discuss recent applications of lidar data in investigations of animal–habitat relationships, and propose future applications of this technology to issues of broad species-management and conservation interest.

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.

The reality confronting ecosystem managers today is one of heterogeneous, rapidly transforming landscapes, particularly in the areas more affected by urban and agricultural development. A landscape management framework that incorporates all systems, across the spectrum of degrees of alteration, provides a fuller set of options for how and when to intervene, uses limited resources more effectively, and increases the chances of achieving management goals. That many ecosystems have departed so substantially from their historical trajectory that they defy conventional restoration is not in dispute. Acknowledging novel ecosystems need not constitute a threat to existing policy and management approaches. Rather, the development of an integrated approach to management interventions can provide options that are in tune with the current reality of rapid ecosystem change.

Recent assessments of areas of different tropical forest types and their corresponding stand volumes were used to calculate the biomass densities and total biomass of tropical forests. Total biomass was estimated at 205 x 10(9) tons, and weighted biomass densities for undisturbed closed and open broadleaf forests were 176 and 61 tons per hectare, respectively. These values are considerably lower than those previously reported and raise questions about the role of the terrestrial biota in the global carbon budget.

MOTIVATION: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. MAIN TYPES OF VARIABLES INCLUDED: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. SPATIAL LOCATION AND GRAIN: ). TIME PERIOD AND GRAIN: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. MAJOR TAXA AND LEVEL OF MEASUREMENT: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. SOFTWARE FORMAT: .csv and .SQL.

Studies have documented biodiversity losses due to intensification of coffee management (reduction in canopy richness and complexity). Nevertheless, questions remain regarding relative sensitivity of different taxa, habitat specialists, and functional groups, and whether implications for biodiversity conservation vary across regions.We quantitatively reviewed data from ant, bird, and tree biodiversity studies in coffee agroecosystems to address the following questions: Does species richness decline with intensification or with individual vegetation characteristics? Are there significant losses of species richness in coffee-management systems compared with forests? Is species loss greater for forest species or for particular functional groups?and Are ants or birds more strongly affected by intensification? Across studies, ant and bird richness declined with management intensification and with changes in vegetation. Species richness of all ants and birds and of forest ant and bird species was lower in most coffee agroecosystems than in forests, but rustic coffee (grown under native forest canopies) had equal or greater ant and bird richness than nearby forests. Sun coffee(grown without canopy trees) sustained the highest species losses, and species loss of forest ant, bird, and tree species increased with management intensity. Losses of ant and bird species were similar, although losses of forest ants were more drastic in rustic coffee. Richness of migratory birds and of birds that forage across vegetation strata was less affected by intensification than richness of resident, canopy, and understory bird species. Rustic farms protected more species than other coffee systems, and loss of species depended greatly on habitat specialization and functional traits. We recommend that forest be protected, rustic coffee be promoted,and intensive coffee farms be restored by augmenting native tree density and richness and allowing growth of epiphytes. We also recommend that future research focus on potential trade-offs between biodiversity conservation and farmer livelihoods stemming from coffee production.

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Each clade is discussed in terms of key morphological and ecological traits. At least 11 origins of the ectomycorrhizal habit appear to have evolved in the Agaricales, with possibly as many as nine origins in the Agaricoid plus Tricholomatoid clade alone. A family-based phylogenetic classification is sketched for the Agaricales, in which 30 families, four unplaced tribes and two informally named clades are recognized.

When characterizing the processes that shape ecosystems, ecologists increasingly use the unique perspective offered by repeat observations of remotely sensed imagery. However, the concept of change embodied in much of the traditional remote‐sensing literature was primarily limited to capturing large or extreme changes occurring in natural systems, omitting many more subtle processes of interest to ecologists. Recent technical advances have led to a fundamental shift toward an ecological view of change. Although this conceptual shift began with coarser‐scale global imagery, it has now reached users of Landsat imagery, since these datasets have temporal and spatial characteristics appropriate to many ecological questions. We argue that this ecologically relevant perspective of change allows the novel characterization of important dynamic processes, including disturbances, long‐term trends, cyclical functions, and feedbacks, and that these improvements are already facilitating our understanding of critical driving forces, such as climate change, ecological interactions, and economic pressures.

The long-term viability of a forest industry in the Amazon region of Brazil depends on the maintenance of adequate timber volume and growth in healthy forests. Using extensive high-resolution satellite analyses, we studied the forest damage caused by recent logging operations and the likelihood that logged forests would be cleared within 4 years after timber harvest. Across 2,030,637 km2 of the Brazilian Amazon from 1999 to 2004, at least 76% of all harvest practices resulted in high levels of canopy damage sufficient to leave forests susceptible to drought and fire. We found that 16+/-1% of selectively logged areas were deforested within 1 year of logging, with a subsequent annual deforestation rate of 5.4% for 4 years after timber harvests. Nearly all logging occurred within 25 km of main roads, and within that area, the probability of deforestation for a logged forest was up to four times greater than for unlogged forests. In combination, our results show that logging in the Brazilian Amazon is dominated by highly damaging operations, often followed rapidly by deforestation decades before forests can recover sufficiently to produce timber for a second harvest. Under the management regimes in effect at the time of our study in the Brazilian Amazon, selective logging would not be sustained.

Live woody vegetation is the largest reservoir of biomass carbon, with its restoration considered one of the most effective natural climate solutions. However, terrestrial carbon fluxes remain the largest uncertainty in the global carbon cycle. Here, we develop spatially explicit estimates of carbon stock changes of live woody biomass from 2000 to 2019 using measurements from ground, air, and space. We show that live biomass has removed 4.9 to 5.5 PgC year −1 from the atmosphere, offsetting 4.6 ± 0.1 PgC year −1 of gross emissions from disturbances and adding substantially (0.23 to 0.88 PgC year −1 ) to the global carbon stocks. Gross emissions and removals in the tropics were four times larger than temperate and boreal ecosystems combined. Although live biomass is responsible for more than 80% of gross terrestrial fluxes, soil, dead organic matter, and lateral transport may play important roles in terrestrial carbon sink.