CyVerse: Cyberinfrastructure for open science.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

Bugs scaring bugs: enemy-risk effects in biological control systems.

Enemy-risk effects, often referred to as non-consumptive effects (NCEs), are an important feature of predator-prey ecology, but their significance has had little impact on the conceptual underpinning or practice of biological control. We provide an overview of enemy-risk effects in predator-prey interactions, discuss ways in which risk effects may impact biocontrol programs and suggest avenues for further integration of natural enemy ecology and integrated pest management. Enemy-risk effects can have important influences on different stages of biological control programs, including natural enemy selection, efficacy testing and quantification of non-target impacts. Enemy-risk effects can also shape the interactions of biological control with other pest management practices. Biocontrol systems also provide community ecologists with some of the richest examples of behaviourally mediated trophic cascades and demonstrations of how enemy-risk effects play out among species with no shared evolutionary history, important topics for invasion biology and conservation. We conclude that the longstanding use of ecological theory by biocontrol practitioners should be expanded to incorporate enemy-risk effects, and that community ecologists will find many opportunities to study enemy-risk effects in biocontrol settings.

Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry.

Locusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band's collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.

Disease, contagious cannibalism, and associated population crash in an omnivorous bug, Geocoris pallens.

Disease and cannibalism are two strongly density-dependent processes that can suppress predator populations. Here we show that California populations of the omnivorous predatory bug Geocoris pallens are subject to infection by a pathogen, as yet unidentified, that elicits elevated expression of cannibalism. Laboratory experiments showed that the pathogen is moderately virulent, causing flattened abdomens, elevated nymphal mortality, delayed development, and reduced body size of adult females. Infection furthermore increases the expression of cannibalism. Field populations of Geocoris spp. declined strongly in association with sharp increases in the expression of egg cannibalism by adult G. pallens. Increased cannibalism was accompanied by a strongly bimodal distribution of cannibalism expression, with some females (putatively uninfected) expressing little cannibalism and others (putatively infected) consuming most or all of the eggs present. Highly cannibalistic females did not increase their consumption of Ephestia cautella moth eggs, suggesting that the high cannibalism phenotype reflected a specific loss of restraint against eating conspecifics. Highly cannibalistic females also often exhibited reduced egg laying, consistent with a virulent pathogen; less frequently, more cannibalistic females exhibited elevated egg laying, suggesting that cannibalism might also facilitate recycling of nutrients in eggs. Elevated cannibalism was not correlated with reduced prey availability or elevated field densities of G. pallens. Geocoris pallens population crashes appear to reflect the combined consequences of direct virulence-adverse pathogen effects on the infected host's physiology-and indirect virulence-mortality of both infected and uninfected individuals due to elevated cannibalism expression by infected individuals.