Fluctuating asymmetry and feather growth bars as biomarkers to assess the habitat quality of shade coffee farming for avian diversity conservation

Interactive effects of multiscale diversification practices on farmland bird stress

Farmland diversification practices (i.e., methods used to produce food sustainably by enhancing biodiversity in cropping systems) are sometimes considered beneficial to both agriculture and biodiversity, but most studies of these practices rely on species richness, diversity, or abundance as a proxy for habitat quality. Biodiversity assessments may miss early clues that populations are imperiled when species presence does not imply persistence. Physiological stress indicators may help identify low-quality habitats before population declines occur. We explored how avian stress indicators respond to on-farm management practices and surrounding seminatural area (1-km radius) across 21 California strawberry farms. We examined whether commonly used biodiversity metrics correlate with stress responses in wild birds. We used ∼1000 blood and feather samples and body mass and wing chord measurements, mostly from passerines, to test the effects of diversification practices on four physiological stress indicators: heterophil to lymphocyte ratios (H:L), body condition, hematocrit values, and feather growth rates of individual birds. We then tested the relationship between physiological stress indicators and species richness, abundance, occurrence, and diversity derived from 285 bird point count surveys. After accounting for other biological drivers, landscape context mediated the effect of local farm management on H:L and body condition. Local diversification practices were associated with reduced individual stress in intensive agricultural landscapes but increased it in landscapes surrounded by relatively more seminatural area. Feathers grew more slowly in landscapes dominated by strawberry production, suggesting that nutritional condition was lower here than in landscapes with more crop types and seminatural areas. We found scant evidence that species richness, abundance, occurrence, or diversity metrics were correlated with the individual's physiological stress, suggesting that reliance on these metrics may obscure the impacts of management on species persistence. Our findings underscore the importance of considering landscape context when designing local management strategies to promote wildlife conservation.

The Dark Side of Shade: How Microclimates Drive the Epidemiological Mechanisms of Coffee Berry Disease

Coffee berry disease (CBD) can cause significant coffee yield losses along with major income losses for African smallholders. Although these farmers cannot afford to purchase pesticides to control the disease, agroecological solutions have rarely been investigated, and how epidemiological mechanisms are linked to the environment of the coffee tree and the plot remains unclear. Agroforestry systems are a promising agroecological option, but the effect of shade on CBD regulation is the subject of debate, and the use of plant species diversity remains uncertain. Here, we address how shade affects epidemiological mechanisms by modifying the microclimate. For this purpose, we developed a mechanistic susceptible-exposed-infectious-removed model and used a Bayesian framework to infer the epidemiological parameters against microclimatic covariates. We show that shade has opposing effects on different epidemiological mechanisms. Specifically, shade can limit disease dynamics by reducing disease transmission while simultaneously promoting disease dynamics by reducing the latent period of the pathogen. However, in full sun, efficient disease transmission compensates for long latent periods. As a result, the balances between microclimatic variables can counterbalance the epidemiological rates, which can dramatically alter the fate of epidemics in shade versus full sun conditions. We propose research avenues to help design cost- and environmentally effective management strategies for CBD that are notably based on the functional traits of shade trees that could hamper CBD dispersal.