Cyberinfrastructure Deployments on Public Research Clouds Enable Accessible Environmental Data Science Education

Modern science depends on computers, but not all scientists have access to the scale of computation they need. A digital divide separates scientists who accelerate their science using large cyberinfrastructure from those who do not, or who do not have access to the compute resources or learning opportunities to develop the skills needed. The exclusionary nature of the digital divide threatens equity and the future of innovation by leaving people out of the scientific process while over-amplifying the voices of a small group who have resources. However, there are potential solutions: recent advancements in public research cyberinfrastructure and resources developed during the open science revolution are providing tools that can help bridge this divide. These tools can enable access to fast and powerful computation with modest internet connections and personal computers. Here we contribute another resource for narrowing the digital divide: scalable virtual machines running on public cloud infrastructure. We describe the tools, infrastructure, and methods that enabled successful deployment of a reproducible and scalable cyberinfrastructure architecture for a collaborative data synthesis working group in February 2023. This platform enabled 45 scientists with varying data and compute skills to leverage 40,000 hours of compute time over a 4-day workshop. Our approach provides an open framework that can be replicated for educational and collaborative data synthesis experiences in any data- and compute-intensive discipline

ESIIL Strategic Plan

The 5 year plan (2022-2027) for the Environmental Data Science Innovation &amp; Inclusion Lab (ESIIL). ESIIL is a next-generation NSF synthesis center led by the University of Colorado Boulder in collaboration with NSF&rsquo;s CyVerse at the University of Arizona, and the University of Oslo. ESIIL enables a global community of environmental data scientists to leverage the wealth of environmental data and emerging analytics to develop science-based solutions to solve pressing challenges in the environmental sciences. This plan highlights ESIIL's mission, vision, and objectives, outlining a roadmap that will guide our efforts towards fulfilling the mission of accelerating innovation and driving just and equitable solutions through the power of data and technology. </p

Relative motion as an ecological mechanism

Relative motion is an ecological mechanism with the power to change the stability and longevity of populations and predict large scale movement patterns in highly mobile species. This dissertation introduces relative motion as an ecological mechanism using simulations and experiments at varying levels of spatial complexity. Chapters 2 and 3 describe the interactions between population movement and one-dimensional habitat movement, while Chapters 4 and 5 focus on the interactions between individual movement and three-dimensional habitat movement. Chapters 2 and 4 lay out my model justification, model development, and simulation results, while the remaining two chapters describe case studies competing those models with data. In Chapter 2, I simulate populations chasing moving habitat using stochastic spatial spread models. Results from these simulations show that populations lose symmetry when the habitat begins to move and suggest that loss of symmetry increases extinction risk. Results also show that assisted migration can restore some of that lost symmetry, but the success of assisted migration is sensitive to the transplant location and habitat speed. In Chapter 3, I build on the simulations presented in Chapter 2 by investigating assisted migration as a method of restoring symmetry using Tribolium microcosm experiments. Experimental results show that assisted migration both restored symmetry to the moving populations under fast-moving habitat conditions and significantly reduced extinction risk compared to the controls. Chapter 4 describes a 3-dimensional Geographic Information System (GIS) to track multiple sources of relative motion in the environment at once, using rigid body mathematics to move individual components in their own direction. In Chapter 5, I apply this GIS to deconstruct the migratory paths of 22 Greater shearwater (Puffinus gravis) migrants and rank the relative contributions of solar, wind, temperature, humidity, and surface cues to the figure-8 shaped migratory paths observed in this species

Phenology and brown-headed cowbird parasitism

The brown-headed cowbird (Molothrus ater) is an obligate, generalist brood parasite that reduces the reproductive success of its many host species, but the magnitude of that reduction remains unknown. To address this question, I used a combination of field and laboratory experimentation, along with quantitative modeling, to evaluate the impact of parasitism on two local hosts in the Colorado Front Range: the primary host, the Plumbeous Vireo (Vireo plumbeus) and the least-parasitized host, the Western Wood-pewee (Contopus sordidulus). Results suggest that phenology is the main driver of cowbird host preference and parasitism impact. Temporal asynchrony in host breeding initially partitions hosts, which is then reinforced by host behavior. Paradoxically, Vireos, the negatively impacted primary cowbird host, are able to circumvent some of those impacts through phenology; predated vireos are forced to renest later in the season when parasitism has subsided, ultimately resulting in a higher success rate

Data from: The roles of demography and genetics in the early stages of colonization

Colonization success increases with the size of the founding group. Both demographic and genetic factors underlie this relationship, yet because genetic diversity normally increases with numbers of individuals, their relative importance remains unclear. Furthermore, their influence may depend on the environment and may change as colonization progresses from establishment through population growth and then dispersal. We tested the roles of genetics, demography and environment in the founding of Tribolium castaneum populations. Using three genetic backgrounds (inbred to outbred), we released individuals of four founding sizes (2–32) into two environments (natal and novel), and measured establishment success, initial population growth and dispersal. Establishment increased with founding size, whereas population growth was shaped by founding size, genetic background and environment. Population growth was depressed by inbreeding at small founding sizes, but growth rates were similar across genetic backgrounds at large founding size, an interaction indicating that the magnitude of the genetic effects depends upon founding population size. Dispersal rates increased with genetic diversity. These results suggest that numbers of individuals may drive initial establishment, but that subsequent population growth and spread, even in the first generation of colonization, can be driven by genetic processes, including both reduced growth owing to inbreeding depression, and increased dispersal with increased genetic diversity

Data from: Genetic and demographic founder effects have long-term fitness consequences for colonising populations

Colonisation is a fundamental ecological and evolutionary process that drives the distribution and abundance of organisms. The initial ability of colonists to establish is determined largely by the number of founders and their genetic background. We explore the importance of these demographic and genetic properties for longer term persistence and adaptation of populations colonising a novel habitat using experimental populations of Tribolium castaneum. We introduced individuals from three genetic backgrounds (inbred – outbred) into a novel environment at three founding sizes (2–32), and tracked populations for seven generations. Inbreeding had negative effects, whereas outbreeding generally had positive effects on establishment, population growth and long-term persistence. Severe bottlenecks due to small founding sizes reduced genetic variation and fitness but did not prevent adaptation if the founders originated from genetically diverse populations. Thus, we find important and largely independent roles for both demographic and genetic processes in driving colonisation success

Szucs et al 2014_Data_for_Dryad

The three sheets in the file contain all the data used to assess establishment success, population growth, and dispersal rates of the populations described in the methods section of the manuscript

Szucs et al Ecol Lett DATA

Before each data tab and there is a tab with metadata explaining what each column means

Data from: Three types of rescue can avert extinction in a changing environment

Setting aside high-quality large areas of habitat to protect threatened populations is becoming increasingly difficult as humans fragment and degrade the environment. Biologists and managers therefore must determine the best way to shepherd small populations through the dual challenges of reductions in both the number of individuals and genetic variability. By bringing in additional individuals, threatened populations can be increased in size (demographic rescue) or provided with variation to facilitate adaptation and reduce inbreeding (genetic rescue). The relative strengths of demographic and genetic rescue for reducing extinction and increasing growth of threatened populations are untested, and which type of rescue is effective may vary with population size. Using the flour beetle (Tribolium castaneum) in a microcosm experiment, we disentangled the genetic and demographic components of rescue, and compared them with adaptation from standing genetic variation (evolutionary rescue in the strictest sense) using 244 experimental populations founded at either a smaller (50 individuals) or larger (150 individuals) size. Both types of rescue reduced extinction, and those effects were additive. Over the course of six generations, genetic rescue increased population sizes and intrinsic fitness substantially. Both large and small populations showed evidence of being able to adapt from standing genetic variation. Our results support the practice of genetic rescue in facilitating adaptation and reducing inbreeding depression, and suggest that demographic rescue alone may suffice in larger populations even if only moderately inbred individuals are available for addition