Harnessing open science practices to teach ecology and evolutionary biology using interactive tutorials.

Open science skills are increasingly important for a career in ecology and evolutionary biology (EEB) as efforts to make data and analyses publicly available continue to become more commonplace. While learning core concepts in EEB, students are also expected to gain skills in conducting open science to prepare for future careers. Core open science skills like programming, data sharing, and practices that promote reproducibility can be taught to undergraduate students alongside core concepts in EEB. Yet, these skills are not always taught in biology undergraduate programs, and a major challenge in developing open science skills and learning EEB concepts simultaneously is the high cognitive load associated with learning multiple disparate concepts at the same time. One solution is to provide students with easily digestible, scaffolded, pre-formatted code in the form of vignettes and interactive tutorials. Here, we present six open source teaching tutorials for undergraduate students in EEB. These tutorials teach fundamental ecological concepts, data literacy, programming (using R software), and analysis skills using publicly available datasets while introducing students to open science concepts and tools. Spanning a variety of EEB topics and skill levels, these tutorials serve as examples and resources for educators to integrate open science tools, programming, and data literacy into teaching EEB at the undergraduate level.

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.

Algunas veces se considera a las prácticas de diversificación agrícola (es decir, los métodos usados para producir alimentos de manera sustentable mediante el enriquecimiento de la biodiversidad en los sistemas de cultivo) como benéficas para la agricultura y la biodiversidad, pero la mayoría de los estudios sobre estas prácticas dependen de la riqueza, abundancia o diversidad de especies como indicadores de la calidad del hábitat. Las valoraciones de la biodiversidad pueden ignorar las señales tempranas de una población en peligro cuando la presencia de la especie no implica persistencia. Los indicadores de estrés fisiológico pueden auxiliar en la identificación de hábitats de baja calidad antes de que ocurra la declinación poblacional. Analizamos las respuestas de los indicadores de estrés en aves al manejo en las granjas y áreas seminaturales circundantes (1 km de radio) de 21 cultivos de fresas en California. Evaluamos si las medidas comunes de biodiversidad se correlacionan con las respuestas al estrés de las aves silvestres. Usamos aproximadamente mil muestras de sangre y plumas y medidas de masa corporal y cuerda alar, la mayoría de paseriformes, para analizar los efectos de las prácticas de diversificación sobre cuatro indicadores de estrés fisiológico: la relación heterófilos/linfocitos (H:L), condición corporal; valores hematocritos; y la tasa de crecimiento de las plumas en aves individuales. Después probamos la relación entre los indicadores de estrés fisiológicos y la riqueza, abundancia, presencia y diversidad de especies tomadas de 285 conteos por puntos de aves. Después de considerar otros factores biológicos, el contexto del paisaje medió el efecto de la gestión de las granjas locales sobre la H:L y la condición corporal. Las prácticas locales de diversificación estuvieron asociadas con una reducción en el estrés individual en los paisajes con agricultura intensiva; sin embargo, el estrés aumentó en los paisajes rodeados por áreas relativamente más seminaturales. Encontramos poca evidencia que respalde que las medidas de riqueza, abundancia, presencia y diversidad de especies estuvieran correlacionadas con el estrés fisiológico de los individuos, lo que sugiere que depender de estas medidas puede nublar el impacto de la gestión sobre la persistencia de las especies. Nuestros descubrimientos apuntalan lo importante que es considerar el contexto del paisaje cuando se diseñan las estrategias de gestión local para promover la conservación de la fauna.

Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host.

Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits-thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.IMPORTANCE The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications. Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications.