Ecological filtering shapes the impacts of agricultural deforestation on biodiversity.

The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability-proxied by drier and more seasonal climates under a greater disturbance regime-and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation.

Understanding different dominance patterns in western Amazonian forests.

Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥2.5 cm diameter, 2609 species) to explore the relationships between local abundance, regional frequency and spatial aggregation of dominant species in four main habitat types in western Amazonia. Although the abundance-occupancy relationship is positive for the full dataset, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unravelling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests.

Pollinator-mediated plant coexistence requires high levels of pollinator specialization.

In pollen-limited plant communities, the foraging behavior of pollinators might mediate coexistence and competitive exclusion of plant species by determining which plants receive conspecific pollen. A key question is whether realistic pollinator foraging behavior promotes coexistence or exclusion of plant species. We use a simulation model to understand how pollinator foraging behavior impacts the coexistence dynamics of pollen-limited plants. To determine whether pollinators are likely to provide a biologically important coexistence mechanism, we compare our results to bee foraging data from the literature and from a novel experimental analysis. Model results indicate that strong specialization at the level of individual foraging paths is required to promote coexistence. However, few empirical studies have robustly quantified within-bout specialization. Species-level data suggest that foraging behavior is sufficient to permit pollinator-mediated coexistence in species-poor plant communities and possibly in diverse communities where congeneric plants co-occur. Our experiments using bumblebees show that individual-level specialization does exist, but not at levels sufficient to substantially impact coexistence dynamics. The literature on specialization within natural foraging paths suffers from key limitations, but overall suggests that pollinator-mediated coexistence should be rare in diverse plant communities.

The structure and organisation of an Amazonian bird community remains little changed after nearly four decades in Manu National Park.

Documenting patterns of spatiotemporal change in hyper-diverse communities remains a challenge for tropical ecology yet is increasingly urgent as some long-term studies have shown major declines in bird communities in undisturbed sites. In 1982, Terborgh et al. quantified the structure and organisation of the bird community in a 97-ha. plot in southeastern Peru. We revisited the same plot in 2018 using the same methodologies as the original study to evaluate community-wide changes. Contrary to longitudinal studies of other neotropical bird communities (Tiputini, Manaus, and Panama), we found little change in community structure and organisation, with increases in 5, decreases in 2 and no change in 7 foraging guilds. This apparent stability suggests that large forest reserves such as the Manu National Park, possibly due to regional topographical influences on precipitation, still provide the conditions for establishing refugia from at least some of the effects of global change on bird communities.

High sensitivity of tropical forest birds to deforestation at lower altitudes.

Habitat conversion is a major driver of tropical biodiversity loss, but its effects are poorly understood in montane environments. While community-level responses to habitat loss display strong elevational dependencies, it is unclear whether these arise via elevational turnover in community composition and interspecific differences in sensitivity or elevational variation in environmental conditions and proximity to thermal thresholds. Here we assess the relative importance of inter- and intraspecific variation across the elevational gradient by quantifying how 243 forest-dependent bird species vary in sensitivity to landscape-scale forest loss across a 3000-m elevational gradient in the Colombian Andes. We find that species that live at lower elevations are strongly affected by loss of forest in the nearby landscape, while those at higher elevations appear relatively unperturbed, an effect that is independent of phylogeny. Conversely, we find limited evidence of intraspecific elevational gradients in sensitivity, with populations displaying similar sensitivities to forest loss, regardless of where they exist in a species' elevational range. Gradients in biodiversity response to habitat loss thus appear to arise via interspecific gradients in sensitivity rather than proximity to climatically limiting conditions.

Biogeographic multi-species occupancy models for large-scale survey data.

Ecologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously. We show how this challenge can be overcome by incorporating preexisting range information into MSOMs, yielding a "biogeographic multi-species occupancy model" (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey and entire avian communities in forests and pastures of Colombia's West Andes. Compared with traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species. Incorporating preexisting range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false absences are modeled in an occupancy framework.

Amazon tree dominance across forest strata.

The forests of Amazonia are among the most biodiverse plant communities on Earth. Given the immediate threats posed by climate and land-use change, an improved understanding of how this extraordinary biodiversity is spatially organized is urgently required to develop effective conservation strategies. Most Amazonian tree species are extremely rare but a few are common across the region. Indeed, just 227 'hyperdominant' species account for >50% of all individuals >10 cm diameter at 1.3 m in height. Yet, the degree to which the phenomenon of hyperdominance is sensitive to tree size, the extent to which the composition of dominant species changes with size class and how evolutionary history constrains tree hyperdominance, all remain unknown. Here, we use a large floristic dataset to show that, while hyperdominance is a universal phenomenon across forest strata, different species dominate the forest understory, midstory and canopy. We further find that, although species belonging to a range of phylogenetically dispersed lineages have become hyperdominant in small size classes, hyperdominants in large size classes are restricted to a few lineages. Our results demonstrate that it is essential to consider all forest strata to understand regional patterns of dominance and composition in Amazonia. More generally, through the lens of 654 hyperdominant species, we outline a tractable pathway for understanding the functioning of half of Amazonian forests across vertical strata and geographical locations.

First record of the gray-legged tinamou, Crypturellus duidae, and other poor-soil specialist birds from peatlands in the Putumayo River basin, Loreto, Peru

Crypturellus duidae (Tinamidae) is a poor-soil specialist with isolated populations in Amazonia, and is considered restricted to white-sand forest habitats. We report the first record of C. duidae in a peatland forest in northern Peru, in the Putumayo River basin. Our record extends the known distribution of C. duidae between two disjoint areas of occurrence in Peru and Colombia, and shows its presence in peatland forest, another forest type on nutrient-poor soils. Additionally, we report the presence of other poor-soil specialist bird species that were previously registered in peatlands. Together with the new record of C. duidae, these bird records provide evidence of the diversity of poor-soil specialists in peatland forests. (AU)

Forest-type specialization strongly predicts avian responses to tropical agriculture.

Species' traits influence how populations respond to land-use change. However, even in well-characterized groups such as birds, widely studied traits explain only a modest proportion of the variance in response across species. Here, we show that associations with particular forest types strongly predict the sensitivity of forest-dwelling Amazonian birds to agriculture. Incorporating these fine-scale habitat associations into models of population response dramatically improves predictive performance and markedly outperforms the functional traits that commonly appear in similar analyses. Moreover, by identifying habitat features that support assemblages of unusually sensitive habitat-specialist species, our model furnishes straightforward conservation recommendations. In Amazonia, species that specialize on forests along a soil-nutrient gradient (i.e. both rich-soil specialists and poor-soil specialists) are exceptionally sensitive to agriculture, whereas species that specialize on floodplain forests are unusually insensitive. Thus, habitat specialization per se does not predict disturbance sensitivity, but particular habitat associations do. A focus on conserving specific habitats that harbour highly sensitive avifaunas (e.g. poor-soil forest) would protect a critically threatened component of regional biodiversity. We present a conceptual model to explain the divergent responses of habitat specialists in the different habitats, and we suggest that similar patterns and conservation opportunities probably exist for other taxa and regions.

Conservation of Tropical Forests in the Anthropocene.

If current trends continue, the tropical forests of the Anthropocene will be much smaller, simpler, steeper and emptier than they are today. They will be more diminished in size and heavily fragmented (especially in lowland wet forests), have reduced structural and species complexity, be increasingly restricted to steeper, less accessible areas, and be missing many heavily hunted species. These changes, in turn, will greatly reduce the quality and quantity of ecosystem services that tropical forests can provide. Driving these changes will be continued clearance for farming and monoculture forest plantations, unsustainable selective logging, overhunting, and, increasingly, climate change. Concerted action by local and indigenous communities, environmental groups, governments, and corporations can reverse these trends and, if successful, provide future generations with a tropical forest estate that includes a network of primary forest reserves robustly defended from threats, recovering logged and secondary forests, and resilient community forests managed for the needs of local people. Realizing this better future for tropical forests and people will require formalisation of land tenure for local and indigenous communities, better-enforced environmental laws, the widescale roll-out of payments for ecosystem service schemes, and sustainable intensification of under-yielding farmland, as well as global-scale societal changes, including reduced consumerism, meat consumption, fossil fuel reliance, and population growth. But the time to act is now, while the opportunity remains to protect a semblance of intact, hyperdiverse tropical forests.

Overlooked biodiversity loss in tropical smallholder agriculture.

Smallholder agriculture is the main driver of deforestation in the western Amazon, where terrestrial biodiversity reaches its global maximum. Understanding the biodiversity value of the resulting mosaics of cultivated and secondary forest is therefore crucial for conservation planning. However, Amazonian communities are organized across multiple forest types that support distinct species assemblages, and little is known about smallholder impacts across the range of forest types that are essential for sustaining biodiversity. We addressed this issue with a large-scale field inventory of birds (point counts) and trees (transects) in primary forest and smallholder agriculture in northern Peru across 3 forest types that are key for Amazonian biodiversity. For birds smallholder agriculture supported species richness comparable to primary forest within each forest type, but biotic homogenization across forest types resulted in substantial losses of biodiversity overall. These overall losses are invisible to studies that focus solely on upland (terra firma) forest. For trees biodiversity losses in upland forests dominated the signal across all habitats combined and homogenization across habitats did not exacerbate biodiversity loss. Proximity to forest strongly predicted the persistence of forest-associated bird and tree species in the smallholder mosaic, and because intact forest is ubiquitous in our study area, our results probably represent a best-case scenario for biodiversity in Amazonian agriculture. Land-use planning inside and outside protected areas should recognize that tropical smallholder agriculture has pervasive biodiversity impacts that are not apparent in typical studies that cover a single forest type. The full range of forest types must be surveyed to accurately assess biodiversity losses, and primary forests must be protected to prevent landscape-scale biodiversity loss.

Pérdida de Biodiversidad Pasada por Alto en la Agricultura de Pequeños Propietarios Resumen La agricultura de pequeños propietarios es la principal causa de la deforestación en la Amazonía occidental, donde la biodiversidad terrestre alcanza su máximo global. Por lo tanto, comprender el valor de la biodiversidad de los mosaicos resultantes de bosques cultivados y secundarios es crucial para para la planificación de la conservación. Sin embargo, las comunidades amazónicas están organizadas a través de múltiples tipos de bosques que soportan ensambles de especies distintas, y poco se sabe sobre los impactos de los pequeños agricultores en toda la gama de tipos de bosques que son esenciales para mantener la biodiversidad. Abordamos este problema con un inventario de campo a gran escala de aves (puntos de conteo) y árboles (transectos) en bosques primarios y agricultura de pequeños productores en el norte de Perú en 3 tipos de bosques que son clave para la biodiversidad amazónica. Para aves, la agricultura de pequeños productores soportó una riqueza de especies comparable a la de los bosques primarios dentro de cada tipo de bosque, pero la homogeneización biótica entre los tipos de bosques dio lugar a pérdidas sustanciales de biodiversidad en general. Estas pérdidas globales son invisibles para los estudios que se centran únicamente en los bosques de tierra firme. En el caso de árboles, las pérdidas de biodiversidad en bosques de tierra firme fueron dominantes en todos los hábitats combinados y la homogeneización en todos los hábitats no agravó la pérdida de biodiversidad. La proximidad a los bosques predijo robustamente la persistencia de especies de aves y árboles asociadas a bosques en el mosaico de pequeños productores, y debido a la omnipresencia de bosque intacto en el área de estudio, nuestros resultados probablemente representan el mejor escenario para la biodiversidad en la agricultura amazónica. La planificación del uso de suelo dentro y fuera de las áreas protegidas debe reconocer que la agricultura tiene impactos generalizados sobre la biodiversidad que no son evidentes en estudios que solo abarcan un solo tipo de bosque. Se debe examinar toda la gama de tipos de bosque para evaluar con precisión las pérdidas de biodiversidad, y los bosques primarios deben ser protegidos para prevenir la pérdida de biodiversidad a escala de paisaje.

Phenological shifts conserve thermal niches in North American birds and reshape expectations for climate-driven range shifts.

Species respond to climate change in two dominant ways: range shifts in latitude or elevation and phenological shifts of life-history events. Range shifts are widely viewed as the principal mechanism for thermal niche tracking, and phenological shifts in birds and other consumers are widely understood as the principal mechanism for tracking temporal peaks in biotic resources. However, phenological and range shifts each present simultaneous opportunities for temperature and resource tracking, although the possible role for phenological shifts in thermal niche tracking has been widely overlooked. Using a canonical dataset of Californian bird surveys and a detectability-based approach for quantifying phenological signal, we show that Californian bird communities advanced their breeding phenology by 5-12 d over the last century. This phenological shift might track shifting resource peaks, but it also reduces average temperatures during nesting by over 1 °C, approximately the same magnitude that average temperatures have warmed over the same period. We further show that early-summer temperature anomalies are correlated with nest success in a continental-scale database of bird nests, suggesting avian thermal niches might be broadly limited by temperatures during nesting. These findings outline an adaptation surface where geographic range and breeding phenology respond jointly to constraints imposed by temperature and resource phenology. By stabilizing temperatures during nesting, phenological shifts might mitigate the need for range shifts. Global change ecology will benefit from further exploring phenological adjustment as a potential mechanism for thermal niche tracking and vice versa.

Trade-offs between savanna woody plant diversity and carbon storage in the Brazilian Cerrado.

Incentivizing carbon storage can be a win-win pathway to conserving biodiversity and mitigating climate change. In savannas, however, the situation is more complex. Promoting carbon storage through woody encroachment may reduce plant diversity of savanna endemics, even as the diversity of encroaching forest species increases. This trade-off has important implications for the management of biodiversity and carbon in savanna habitats, but has rarely been evaluated empirically. We quantified the nature of carbon-diversity relationships in the Brazilian Cerrado by analyzing how woody plant species richness changed with carbon storage in 206 sites across the 2.2 million km(2) region at two spatial scales. We show that total woody plant species diversity increases with carbon storage, as expected, but that the richness of endemic savanna woody plant species declines with carbon storage both at the local scale, as woody biomass accumulates within plots, and at the landscape scale, as forest replaces savanna. The sharpest trade-offs between carbon storage and savanna diversity occurred at the early stages of carbon accumulation at the local scale but the final stages of forest encroachment at the landscape scale. Furthermore, the loss of savanna species quickens in the final stages of forest encroachment, and beyond a point, savanna species losses outpace forest species gains with increasing carbon accumulation. Our results suggest that although woody encroachment in savanna ecosystems may provide substantial carbon benefits, it comes at the rapidly accruing cost of woody plant species adapted to the open savanna environment. Moreover, the dependence of carbon-diversity trade-offs on the amount of savanna area remaining requires land managers to carefully consider local conditions. Widespread woody encroachment in both Australian and African savannas and grasslands may present similar threats to biodiversity.

How Should Beta-Diversity Inform Biodiversity Conservation?

To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning.