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ContextThe landscape heterogeneity hypothesis states that increased heterogeneity in agricultural landscapes will promote biodiversity. However, this hypothesis does not detail which components of landscape heterogeneity (compositional or configurational) most affect biodiversity and how these compare to the effects of surrounding agricultural land-use.ObjectivesOur objectives were to: (1) assess the influence of the components of structural landscape heterogeneity on taxonomic diversity; and (2) compare the effects of landscape heterogeneity to those of different types of agricultural land-use in the same landscape across different taxonomic groups.MethodsWe identified a priori independent gradients of compositional and configurational landscape heterogeneity within an agricultural mosaic of north-eastern Swaziland. We tested how bird, dung beetle, ant and meso-carnivore richness and diversity responded to compositional and configurational heterogeneity and agricultural land-use across five different spatial scales.ResultsCompositional heterogeneity best explained species richness in each taxonomic group. Bird and ant richness were both positively correlated with compositional heterogeneity, whilst dung beetle richness was negatively correlated. Commercial agriculture positively influenced bird species richness and ant diversity, but had a negative influence on dung beetle richness. There was no effect of either component of heterogeneity on the combined taxonomic diversity or richness at any spatial scale.ConclusionsOur results suggest that increasing landscape compositional heterogeneity and limiting the negative effects of intensive commercial agriculture will foster diversity across a greater number of taxonomic groups in agricultural mosaics. This will require the implementation of different strategies across landscapes to balance the contrasting influences of compositional heterogeneity and land-use. Strategies that couple large patches of core habitat across broader scales with landscape structural heterogeneity at finer scales could best benefit biodiversity.

Parkinson’s disease (PD) is a serious neurodegenerative disorder marked by significant clinical and progression heterogeneity. This study aimed at addressing heterogeneity of PD through integrative analysis of various data modalities. We analyzed clinical progression data (≥5 years) of individuals with de novo PD using machine learning and deep learning, to characterize individuals’ phenotypic progression trajectories for PD subtyping. We discovered three pace subtypes of PD exhibiting distinct progression patterns: the Inching Pace subtype (PD-I) with mild baseline severity and mild progression speed; the Moderate Pace subtype (PD-M) with mild baseline severity but advancing at a moderate progression rate; and the Rapid Pace subtype (PD-R) with the most rapid symptom progression rate. We found cerebrospinal fluid P-tau/α-synuclein ratio and atrophy in certain brain regions as potential markers of these subtypes. Analyses of genetic and transcriptomic profiles with network-based approaches identified molecular modules associated with each subtype. For instance, the PD-R-specific module suggested STAT3 , FYN , BECN1 , APOA1 , NEDD4 , and GATA2 as potential driver genes of PD-R. It also suggested neuroinflammation, oxidative stress, metabolism, PI3K/AKT, and angiogenesis pathways as potential drivers for rapid PD progression (i.e., PD-R). Moreover, we identified repurposable drug candidates by targeting these subtype-specific molecular modules using network-based approach and cell line drug-gene signature data. We further estimated their treatment effects using two large-scale real-world patient databases; the real-world evidence we gained highlighted the potential of metformin in ameliorating PD progression. In conclusion, this work helps better understand clinical and pathophysiological complexity of PD progression and accelerate precision medicine.

Monitoring species ranges and suitable and occupied habitat are core components of biogeography, ecology and conservation biology, but it is difficult to do for rare, cryptic, wide-ranging, migratory or nomadic species. We present a transparent and objective process to combine multiple types of locality data (peer-reviewed and grey literature, museum collections, camera-trap inventories, and citizen science reports). We illustrate the advantages of this pooled approach by assessing change in range and patch occupancy for a data-poor and threatened nomadic keystone species, the bearded pig Sus barbatus, in Borneo, Sumatra and Peninsular Malaysia. We used a collated set of all occurrence observations (n = 240) to create minimum convex polygons for forested habitats for two time periods. We evaluated confidence that a patch was truly occupied by the overlap among data types. We found that 62% of the forest habitat of the Sumatran bearded pig S. barbatus oi was lost during 1990–2010 and that its range contracted by 76%; the Bornean bearded pig S. barbatus barbatus lost 23 and 24% of its forest habitat and range, respectively, and in Peninsular Malaysia the 93% range collapse of this subspecies during 1985–2010 is more severe than the 33% habitat loss alone would suggest. We conclude that integrating data types can improve mapping of the ranges of many data-poor species.

Land-use change currently constitutes the primary driver of modern biodiversity loss. One way that land conversion to agriculture can lead to biodiversity loss is through biotic homogenization where agriculture consistently favors the same species, causing communities to converge in species composition over space or time. Biotic homogenization could also occur phylogenetically, where species from the similar phylogenetic lineages are consistently favored by agriculture. However, whether phylogenetic homogenization occurs across multiple scales and in tropical regions is rarely investigated. In Chapter 1, I leveraged species’ phylogeny and traits to understand how land-use change affects tropical bird communities within Costa Rica and Colombia. We conducted bird surveys across Costa Rica and Colombia in 294 sites that varied in levels of local forest cover and annual precipitation. We then analyzed sites in Costa Rica and Colombia together to find that land conversion from forest to agriculture consistently favors the same types of species at a large scale. While most trait-based studies measure effects of global changes on species occurrences or abundances, changes in species abundance or occurrence provide little information about how species actually use the habitats where they occur. For example, a species detected in agriculture could simply be passing through (and not actually resilient to land-use change) or it could be using agriculture to forage, reproduce, or otherwise complete its lifecycle (meaning the species is resilient to land-use change). In Chapter 2, I developed and then validated a statistical model to analyze how species’ behavior differs between habitat types using observational data. To our knowledge, this is the first model to measure how animals use different environments while accounting for behavior-specific imperfect detection probability. We compared the model to an alternative model that did not account for imperfect detection probability and found that our new model produced more accurate estimates of the mean and uncertainty of the effects of environmental covariates on behaviors. Thus, this model allows researchers and managers to more accurately assess how species use the environments they are in using observational behavior data. In Chapter 3, I applied this model to over 14,000 behavioral observations across 55 bird species in Northwest Costa Rica to understand how local forest cover and forest protection level affect bird behaviors. We found that birds were more likely to perform reproductive behaviors in protected forest than private forest and agriculture, meaning that protected areas are likely important for bird reproduction and conservation. This chapter also demonstrates the importance of behavioral analyses in conservation planning, as species’ behavioral responses were not always consistent with their differences in abundance. Beyond measuring changes in occurrence and behavior, it is also critical to understand if habitats can support sufficient reproductive rates to allow for population persistence. Tropical cavity-nesting birds may be particularly threatened by agricultural land-use change, which removes the tree they rely on for nesting and roosting. In Chapter 4, I aimed to understand how land-use change affects tropical cavity-nesting bird reproduction by measuring nest site availability and conducting a nest-box addition experiment in forest and agriculture Northwest Ecuador. I found that land-use change likely limits the reproduction of cavity-nesting birds in agriculture, as nest boxes in agriculture had much higher levels of avian activity than nest boxes in forest. Nest boxes also had a relatively high rate of chicks fledged, meaning that nest boxes could be a successful conservation strategy for certain species. Overall, my dissertation explores the different effects of agricultural land-use change on tropical bird occurrence, behavior, and reproduction. I found that these effects can differ from each other and across scales. The results highlight the importance of forest conservation, especially in wet regions, and support investigating species’ responses beyond occurrence when comparing the conservation value of habitat types.

Understanding how and why animals use the environments where they occur is both foundational to behavioral ecology and essential to identify critical habitats for species conservation. However, some behaviors are more difficult to observe than others, which can bias analyses of raw observational data. To our knowledge, no method currently exists to model how animals use different environments while accounting for imperfect behavior-specific detection probability. We developed an extension of a binomial N-mixture model (hereafter the behavior N-mixture model) to estimate the probability of a given behavior occurring in a particular environment while accounting for imperfect detection. We then conducted a simulation to validate the model's ability to estimate the effects of environmental covariates on the probabilities of individuals performing different behaviors. We compared our model to a naïve model that does not account for imperfect detection, as well as a traditional N-mixture model. Finally, we applied the model to a bird observation data set in northwest Costa Rica to quantify how three species behave in forests and farms. Simulations and sensitivity analyses demonstrated that the behavior N-mixture model produced unbiased estimates of behaviors and their relationships with predictor variables (e.g., forest cover, habitat type). Importantly, the behavior N-mixture model accurately characterized uncertainty, unlike the naïve model, which often suggested erroneous effects of covariates on behaviors. When applied to field data, the behavior N-mixture model suggested that Hoffmann's woodpecker (Melanerpes hoffmanii) and Inca dove (Columbina inca) behaved differently in forested versus agricultural habitats, while turquoise-browed motmot (Eumomota superciliosa) did not. Thus, the behavior N-mixture model can help identify habitats that are essential to a species' life cycle (e.g., where individuals nest, forage) that nonbehavioral models would miss. Our model can greatly improve the appropriate use of behavioral survey data and conclusions drawn from them. In doing so, it provides a valuable path forward for assessing the conservation value of alternative habitat types.

The associations of habitat area and fragmentation with species richness long have been major topics within community ecology. Recent discussion has focused on properly assessing fragmentation independent of habitat area (fragmentation per se), and on whether fragmentation has significant negative or positive associations with species richness. We created a novel, multipleregion, N-mixture community model (MNCM) to examine the relations of riparian area and fragmentation with species richness of breeding birds in mountain ranges within the Great Basin, Nevada, USA. Our MNCM accounts for imperfect detection in count data at the survey-point level while allowing comparisons of species richness among regions in which those points are embedded. We used individual canyons within mountain ranges as regions in our model and measured riparian area and the Normalized Landscape Shape Index, a metric of fragmentation that is independent of total riparian area. We found that riparian area, but not its fragmentation, was a primary predictor of canyon-level species richness of both riparian obligates and all species. The relationship between riparian area and riparian obligate species richness was nonlinear: canyons with ≥25 ha woody riparian vegetation had relatively high species richness, whereas species richness was considerably lower in canyons with <25 ha. Our MNCM can be used to calculate other metrics of diversity that require abundance estimates. For example, Simpson’s evenness of riparian obligate species had a weak negative association with riparian area and was not associated with fragmentation. Projections of future riparian contraction suggested that decreases in species richness are likely to be greatest in canyons that currently have moderate (∼10–25 ha) amounts of riparian vegetation. Our results suggest that if a goal of management is to maximize the species richness of breeding birds in montane riparian areas in the Great Basin, it may be more effective to focus on total habitat area than on fragmentation of patches within canyons, and that canyons with at least moderate amounts of riparian vegetation should be prioritized.

Context Conservation in working landscapes is critical for halting biodiversity declines and ensuring farming system sustainability. However, concerns that wildlife may carry foodborne pathogens has created pressure on farmers to remove habitat and reduce biodiversity, undermining farmland conservation. Nonetheless, simplified farming landscapes may host bird communities that carry higher foodborne disease risks. Objectives We analyzed the effects of local farming practices and surrounding landscapes on bird communities and food-safety risks across 30 California lettuce farms. Specifically, we sought to determine how farmland diversification affects bird diversity, fecal contamination, and foodborne pathogen incidences, thereby identifying potential tradeoffs between managing farms for bird conservation versus food safety. Methods We surveyed birds at 227 point-count locations, quantified fecal contamination along 120 transects, and assayed 601 bird feces for pathogenic E. coli , Campylobacter spp . , and Salmonella spp. We then used hierarchical models to quantify effects of farm management and landscape context on bird communities and food-safety risks. Results Surrounding ungrazed seminatural areas were associated with higher bird diversity, more species of conservation concern, and fewer flocks that may increase risks from foodborne pathogens. In contrast, on-farm diversification practices and surrounding grazing lands offered weaker bird conservation benefits. Surrounding grazed lands were associated with more potentially pathogenic bird feces in crop fields. Conclusions Our results suggest that habitat conservation around produce farms could support bird conservation without increasing foodborne pathogens, especially on farms further from grazing lands. Thus, interventions that diversify farming systems offer potential to simultaneously conserve biodiversity and provide safe food for human consumption.

The outcome of the ongoing biodiversity crisis depends on the capacity of the Earth’s wildlife to persist in working landscapes. Yet, the species that occupy working landscapes are often distinct from those in protected areas, with a large group of “sensitive species” thought to rarely venture into human‐dominated landscapes. As governments have committed to restoring degraded lands world‐wide, determining whether and how working landscapes can be restored to benefit sensitive species remains a major challenge. We surveyed Neotropical birds across Northwestern Costa Rica in protected areas, farms and forests embedded within working landscapes. We analysed community composition to understand how gradients of forest cover, fragmentation and regional precipitation determine how conserving (or restoring) tropical forests in working landscapes could safeguard entire communities, especially sensitive species with limited ranges. We found agricultural sites maintained relatively high bird diversity but hosted very distinct communities from those found in protected areas. The average range size of species found in agricultural communities was double the size of species in protected areas. However, high forest cover sites in working landscapes housed bird communities with small range sizes that were equivalent to those in nearby protected areas, despite being twice as fragmented and significantly more disturbed. The effect of local forest cover on bird composition was contingent on both landscape context and regional climate. When local forest cover increased in wetter regions and more forested landscapes, bird communities in working landscapes exhibited a stronger shift towards the assemblages found in protected areas. Specifically, we found that reforesting the wettest sites would increase similarity to protected areas fourfold compared to only a twofold increase in the driest sites. Synthesis and applications. Despite experiencing much more fragmentation and degradation than protected areas, forests in Costa Rican working landscapes can maintain bird communities that strongly resemble those found in protected areas. This suggests that conserving or restoring forests in working landscapes, particularly within wetter regions and already forested landscapes, may safeguard bird communities when creating protected areas is infeasible. RESUMEN La capacidad que tiene la vida silvestre terrestre para persistir en paisajes modificados es crucial para combatir el resultado de la crisis que actualmente sufre la biodiversidad. Sin embargo, las especies que ocupan dichos paisajes son a menudo distintas de las que se encuentran en las áreas protegidas, ya que se cree que varias \"especies sensibles\" pocas veces se hallan en los paisajes modificados. Varios gobiernos se han comprometido a restaurar las tierras degradadas en sus territorios, por lo tanto, es un gran desafío determinar si los paisajes modificados se pueden restaurar con el fin de beneficiar a las especies sensibles. Muestreamos aves Neotropicales en el noroeste de Costa Rica en áreas protegidas, fincas y bosques integrados en paisajes modificados. También, analizamos la composición de la comunidad de aves para comprender cómo los gradientes de cobertura boscosa, la fragmentación de los bosques y la precipitación regional determinan si la conservación (o la restauración) de los bosques tropicales puede salvaguardar las comunidades de aves, y las especies sensibles que tienen rangos de distribución reducidos. Encontramos que las zonas agrícolas mantuvieron una diversidad de aves relativamente alta, pero albergaron comunidades de aves muy distintas a las que se encuentraron en las áreas protegidas. De hecho, las especies de las comunidades de aves de las zonas agrícolas tuvieron rangos de distribución el doble de grandes en comparación con los rangos de las especies que se encuentran únicamente en las áreas protegidas. Sin embargo, los sitios con alta cobertura boscosa albergaron comunidades de aves con rangos de distribución reducidos, semejando las especies de las comunidades de aves que se encuentran en las áreas protegidas aledañas. Esto ocurrió, a pesar de que dichas áreas boscosas son dos veces más fragmentadas y significativamente más perturbadas que las áreas protegidas El efecto de la cobertura boscosa local sobre la composición de las aves dependió tanto de la matriz del paisaje, cómo del clima regional. Cuando la cobertura boscosa local aumentó en regiones más húmedas y en matrices dominadas por bosques, las comunidades de aves en los paisajes modificados se parecieron más a los ensamblajes de comunidades de aves de las áreas protegidas. Específicamente, encontramos que reforestar áreas en los sitios más húmedos aumenta cuatro veces la similitud de las comunidades de las zonas protegidas versus las no protegidas, mientras reforestar zonas en los sitios más secos aumenta la similitud dos veces. Síntesis y aplicaciones: A pesar de que los bosques en zonas no protegidas están mucho más fragmentados y degradados en comparación con los bosques de las áreas protegidas, demostramos que, en Costa Rica, dichos bosques pueden albergar comunidades de aves que se parecen a las de las áreas protegidas. Nuestros resultados sugieren que conservar o reforestar bosques en paisajes modificados, especialmente en las regiones más húmedas y en paisajes ya boscosos, puede ayudar a salvaguardar las comunidades de aves Neotropicales cuando la creación de nuevas áreas protegidas sea inviable. Despite experiencing much more fragmentation and degradation than protected areas, forests in Costa Rican working landscapes can maintain bird communities that strongly resemble those found in protected areas. This suggests that conserving or restoring forests in working landscapes, particularly within wetter regions and already forested landscapes, may safeguard bird communities when creating protected areas is infeasible.

There is an ongoing need to integrate agricultural production with wildlife conservation to maintain biodiversity, especially in developing countries. The landscape heterogeneity hypothesis identifies a potential means for promoting biodiversity in agricultural landscapes by emphasizing that increasing heterogeneity can increase biodiversity. However, the importance of landscape heterogeneity relative to habitat amount and vegetation structure is poorly understood, particularly regarding the relative importance of different components of landscape heterogeneity. We investigated how taxonomic, functional, and phylogenetic diversity of non-breeding birds responded to two components of landscape heterogeneity, compositional and configurational heterogeneity, and compared the importance of the landscape heterogeneity hypothesis relative to the habitat amount hypothesis and vegetation structural heterogeneity hypothesis. To do so, we conducted point counts at 80 plots across 16 landscapes during June–July 2016 in northeastern Swaziland, a sub-tropical savanna. We found a positive effect of landscape heterogeneity on taxonomic diversity, but no effect of habitat amount or vegetation structure. In contrast to taxonomic diversity, we found a positive trend between the amount of savanna habitat and phylogenetic diversity. In agricultural mosaics in subtropical savannas, conservation value may be created if landscape compositional heterogeneity, landscape configurational heterogeneity, and large areas of habitat are incorporated into land planning. Our findings show that it is important to use multiple measures of diversity in conjunction with various landscape and habitat measures when designing conservation management strategies.

Purpose of Review Countryside biogeography seeks to explain the distribution of wildlife in human-dominated landscapes. We review the theoretical and empirical progress towards this goal, assessing what forces control the presence, abundance, and richness of species in anthropogenic and natural habitats, based on characteristics of the landscape and the species themselves. Recent Findings Recent modifications of species-area relationships that incorporate multiple habitat types have improved understanding of species diversity in countryside landscapes. Attempts to understand why species affiliate with human-modified habitats have been met with only partial success. Though traits frequently explain associations with human-modified habitats within studies, explanatory traits are only rarely shared between studies, regions, or taxa. Nonetheless, greater attention to the regional and climatological context of countryside landscapes has uncovered that (i) species that associate with human-modified habitats within landscapes tend to occur primarily in warm and/or dry biomes at regional scales and (ii) species that rely exclusively on human-modified habitats in cool or wet regions may be restricted to natural habitats in warm or dry regions. Summary There remains a pressing need to determine how biodiversity can best be supported within landscapes to preserve nature and maximize ecosystem service benefits for humans. Future work in countryside biogeography must identify how land-use change interacts with other global stressors (e.g., climate change), determine how extinction debt and population sinks influence diversity, quantify the cascading effects of community changes on ecosystem services, and elucidate the evolutionary history and origins of species that today dwell in the countryside.