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  1. Free, publicly-accessible full text available August 1, 2024
  2. Abstract In restoration ecology, the Field of Dreams hypothesis posits that restoration efforts that create a suitable environment could lead to the eventual recovery of the remaining aspects of the ecosystem through natural processes. Natural processes following partial restoration has led to ecosystem recovery in both terrestrial and aquatic systems. However, understanding the efficacy of a “Field of Dreams” approach requires a comparison of different approaches to partial restoration in terms of spatial, temporal, and ecological scale with what would happen given more comprehensive restoration efforts. We explore the relative effect of partial restoration and ongoing recovery on restoration efficacy with a dynamical model based on temperate rocky reefs in Northern California. We analyze our model for both the ability and rate of bull kelp forest recovery under different restoration strategies. We compare the efficacy of a partial restoration approach with a more comprehensive restoration effort by exploring how kelp recovery likelihood and rate change with varying intensities of urchin removal and kelp outplanting over different time periods and spatial scales. We find that, in the case of bull kelp forests, setting more favorable initial conditions for kelp recovery by implementing both urchin harvesting and kelp outplanting at the start of the restoration project has a bigger impact on the kelp recovery rate than applying restoration efforts through a longer period of time. Therefore, partial restoration efforts, in terms of spatial and temporal scale, can be significantly more effective when applied across multiple ecological scales in terms of both the capacity and rate for achieving the target outcomes. 
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    Free, publicly-accessible full text available June 1, 2024
  3. Abstract

    Ecologists have put forward many explanations for coexistence, but these are onlypartial explanations; nature is complex, so it is reasonable to assume that in any given ecological community, multiple mechanisms of coexistence are operating at the same time. Here, we present a methodology for quantifying the relative importance of different explanations for coexistence, based on an extension of theModern Coexistence Theory. Current versions of Modern Coexistence Theory only allow for the analysis of communities that are affected by spatialortemporal environmental variation, but not both. We show how to analyze communities with spatiotemporal fluctuations, how to parse the importance of spatial variation and temporal variation, and how to measure everything with either mathematical expressions or simulation experiments. Our extension of Modern Coexistence Theory shows that many more species can coexist than originally thought. More importantly, it allows empiricists to use realistic models and more data to better infer the mechanisms of coexistence in real communities.

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  4. Abstract Entender las respuestas de la población a perturbaciones ambientales, específicamente a pulsadas individuales, es esencial para la conservación y la gestión adaptativa. Las poblaciones de interés pueden reducirse a niveles bajas debido a la perturbación, y es necesario entender las diferencias interespecíficas en las trayectorias de recuperación para evaluar las opciones de gestión. Analizamos modelos para especies individuales para investigar los factores demográficos y de gestión que determinan los dos componentes de la ‘resiliencia’ de la población: la magnitud del impacto inicial sobre la abundancia de la población y la duración del tiempo de recuperación. Simulamos poblaciones estructuradas por edad con reclutamiento que depende de la densidad, las sometimos a una perturbación pulsada que consiste en un período de mayor mortalidad del grupo etário juvenil o de todos los grupos etários, y calculamos tanto el impacto como el tiempo de retorno. A modo de ilustración, utilizamos parámetros demográficos de un conjunto de 16 especies de peces. Formulamos el modelo como una ecuación de renovación, lo que nos permite describir matemáticamente los impactos de las perturbaciones como una convolución. También incluimos dinámicas no lineales que representan poblaciones que se recuperan hacia un estado estable; esto es más realista (en la mayoría de los casos) que los análisis previos de resiliencia en modelos lineales sin la dependencia de la densidad. Cuando la perturbación ha afectado a uno o a algunos pocos grupos etários jóvenes, la longevidad fue el principal determinante de la historia de vida del impacto y el tiempo de recuperación. Las especies de vida más corta sufrieron mayores impactos cuando fueron perturbadas porque cada grupo etáreo representa una mayor proporción de la población. Sin embargo, las especies con vidas más cortas también tuvieron tiempos de recuperación más rápidos, por la misma razón. Cuando la perturbación afectó a los grupos etários adultos, el impacto fue más inmediato y ya no se vio afectado por la longevidad de las especies, aunque se mantuvo el efecto de la longevidad sobre el tiempo de recuperación. Estos resultados mejoran nuestra comprensión de las diferencias interespecíficas de la resiliencia y aumentan nuestra capacidad para hacer predicciones con fin a la gestión adaptativa. Además, formular el problema como una ecuación de renovación y usar convoluciones matemáticas nos permite cuantificar cómo las perturbaciones con distintos lapsos de tiempo (no solo un nivel de perturbación constante e inmediato, sino niveles de perturbación que aumentan o disminuyen gradualmente) tendrían diferentes efectos sobre la resiliencia de la población: respuestas tardías para especies en las que la biomasa se concentra en grupos etários de mayor edad y para perturbaciones que se vuelven progresivamente más severas. 
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  5. Abstract New graduate students in biology programs may lack the quantitative skills necessary for their research and professional careers. The acquisition of these skills may be impeded by teaching and mentoring experiences that decrease rather than increase students’ beliefs in their ability to learn and apply quantitative approaches. In this opinion piece, we argue that revising instructional experiences to ensure that both student confidence and quantitative skills are enhanced may improve both educational outcomes and professional success. A few studies suggest that explicitly addressing productive failure in an instructional setting and ensuring effective mentoring may be the most effective routes to simultaneously increasing both quantitative self-efficacy and quantitative skills. However, there is little work that specifically addresses graduate student needs, and more research is required to reach evidence-backed conclusions. 
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    Free, publicly-accessible full text available April 29, 2024
  6. Twombly, Saran, Alan Hastings, Tom Miller, Michael Cortez, Karen Abbott, Tanjona Ramiadantsoa, Julie Blackwood, and Olivia Prosper. “New Theory for Increasingly Tangled Banks.” Issues in Science and Technology 38, no. 4 (Summer 2022): 39–44. Theory has fallen out of fashion in the sciences, in favor of data collection and number crunching. But the conceptual frameworks provided by theory are essential for addressing society’s most complex and urgent problems. 
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  7. Abstract

    During their lifetimes, individuals in populations pass through different states, and the notion of an occupancy time describes the amount of time an individual spends in a given set of states. Questions related to this idea were studied in a recent paper by Roth and Caswell for cases where the environmental conditions are constant. However, it is truly important to consider the case where environments are changing randomly or in directional way through time, so the transition probabilities between different states change over time, motivating the use of time-dependent stage-structured models. Using absorbing inhomogenous Markov chains and the discrete-time McKendrick–von Foerster equation, we derive explicit formulas for the occupancy time, its expectation, and its higher-order moments for stage-structured models with time-dependent transition rates. The results provide insights into the dynamics of long lived plant or animal populations where individuals transition in both directions between reproductive and non reproductive stages. We apply our approach to study a specific time-dependent model of the Southern Fulmar, and obtain insights into how the number of breeding attempts depends on external conditions that vary through time.

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  8. Abstract One of the main factors that determines habitat suitability for sessile and territorial organisms is the presence or absence of another competing individual in that habitat. This type of competition arises in populations occupying patches in a metacommunity. Previous studies have looked at this process using a continuous-time modeling framework, where colonizations and extinctions occur simultaneously. However, different colonization processes may be performed by different species, which may affect the metacommunity dynamics. We address this issue by developing a discrete-time framework that describes these kinds of metacommunity interactions, and we consider different colonization dynamics. To understand potential dynamics, we consider specific functional forms that characterize the colonization and extinction processes of metapopulations competing for space as their limiting factor. We then provide a mathematical analysis of the models generated by this framework, and we compare these results to what is seen in nature and in previous models. 
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