Biology subjects

Chism, G.

Publications and source records attributed to Chism, G..

4 recordsLinked to original sources

bioRxiv2023

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 110,000 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 two 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.

scientific communication and education↗

bioRxiv2022

Temnothorax rugatulus ants do not change their nest walls in response to environmental humidity

Animal architectures are interesting biological phenomena that can greatly increase the fitness of the builder and exist in a variety of forms and functions across taxa. Among the most intricate architectures are social insect nests, which may have several functions, one of which is the control of internal microclimate. In social insects, the regulation particularly of humidity in the nest can be crucial for the survival and growth of the brood. Though much is known on how nest excavating social insects respond to environmental humidity, little is known about how ants that build on to pre-existing cavities respond. Here we use the rock ant Temnothorax rugatulus to determine whether and how colonies respond to environmental humidity by building and changing their nest architectures in pre-existing nest spaces. We specifically test the hypothesis that T. rugatulus colonies build different nest walls, e.g. wider or denser ones, in response to lower environmental humidity. We allowed T. rugatulus colonies to build nest walls with two substrates across a 0-100% relative humidity gradient. We further compare the porosity - empty volume in built nest walls - of natural T. rugatulus nest walls with these artificial building substrates and the substrate compositions of built walls from our experiment. We found that humidity did not influence the nest walls T. rugatulus colonies built in our experiment, concluding that regulating humidity is likely not a key function of T. rugatulus nest wall architecture. We also found that the porosities of the artificial substrate that was predominantly used by the ants in our experiment were like the porosity of natural T. rugatulus nest walls, indicating that ants had constant preferences for particular substrates. Physical nest wall features, including porosity, are therefore unlikely to be flexibly regulated in response to external humidity, but may be adaptations in other ways.

animal behavior and cognition↗

bioRxiv2022

Nest shape influences colony organization in ants: spatial distribution and connectedness of colony members differs from that predicted by random movement and is affected by nest space

Many animals inhabit nests that protect them from adverse environments. However, the effects of living in a built or found structure are not limited to protection: the physical space can shape and organize behavior, particularly in self-organized collective systems. In addition, the geometry of nest space may not be under the animals control, raising the question whether animals can compensate for the effects that unexpected or suboptimal geometries may have. Here we examine how the shape of a nest cavity affects spatial organization of colonies in the ant Temnothorax rugatulus, a species that adapted to nest cavities of unmodifiable internal dimensions, since they inhabit rock crevices with rigid walls. We show that the emerging spatial relationships of workers, brood, queens, and young alates, as well as their relationships and distances to significant points in the nest, are all significantly influenced by nest shape, with the brood distributions most affected. However, we also found that the size of worker spatial fidelity zones, i.e. the areas in the nest that individual workers occupy and that may be key regulators of division of labor, are overall not affected by nest shape. These findings indicate that ants may actively regulate which areas of a nest they occupy, and that they may compensate for effects of nest architecture constraints. Physical properties of nests can thus influence the organization of ant colonies, highlighting the need to explore spatial constraints as a direct influence on the organization, movement, and communication of evolved or engineered self-organized systems.

animal behavior and cognition↗

bioRxiv2019

Predictors of colony extinction vary by habitat type in social spiders

Many animal societies are susceptible to mass mortality events and collapse. Elucidating how environmental pressures determine patterns of collapse is key for our understanding of social evolution. Using the social spider Stegodyphus dumicola we investigated the environmental drivers of colony extinction along two precipitation gradients across southern Africa, using the Namib and Kalahari deserts versus wetter savanna habitats to the north and east. We deployed experimental colonies (n = 242) along two 800km transects and returned to assess colony success in the field after two months. Specifically, we noted colony extinction events after the two-month duration and collected environmental data on the correlates of those extinction events (e.g., evidence of ant attacks, # prey captured). We found that colony extinction events at desert sites were more frequently associated with attacks by predatory ants as compared to savanna sites, while colony extinctions in wetter savannas sites were more tightly associated with fungal outbreaks. Our findings support the hypothesis that environments vary in the selection pressures that they impose on social organisms, which may explain why different social phenotypes are often favored in each habitat.

ecology↗