Dawkins’ Weasel is a NetLogo model that illustrates the principle of evolution by natural selection. It is inspired by a thought experiment presented by Richard Dawkins in his book The Blind Watchmaker (1996).

Fertility Tradeoffs is a NetLogo model that illustrates the emergencent tradeoffs between the quality and quantity of offspring. Often, we associate high fitness with maximizing the number of offspring. However, under certain circumstances, it pays instead to optimize the number of offspring, having fewer offspring than is possible. When the number of offspring is reduced, more energy can be invested in each offspring, which can have fitness benefits.

This model simulates the Hawk-Dove game as first described by John Maynard Smith, and further elaborated by Richard Dawkins in “The Selfish Gene”. In the game, two strategies, Hawks and Doves, compete against each other, and themselves, for reproductive benefits. A third strategy can be introduced, Retaliators, which act like either Hawks or Doves, depending on the context.

This model replicates the Axelrod prisoner’s dilemma tournaments. The model takes as input a file of strategies and pits them against each other to see who achieves the best payoff in the end. Change the payoff structure to see how it changes the tournament outcome!

BEGET Classic includes previous versions used in the classroom and for publication. Please check out the latest version of B3GET here, which has several user-friendly features such as directly importing and exporting genotype and population files.

The classic versions of B3GET include: version one and version three were used in undergraduate labs at the University of Minnesota to demonstrate principles in primate behavioral ecology; version two first demonstrated proof of concept for creating virtual biological organisms using decision-vector algorithms; version four was presented at the 2017 annual meeting at the American Association of Physical Anthropologists; version five was presented in a 2019 publication from the Journal of Human Evolution (Crouse, Miller, and Wilson, 2019).

B3GET simulates populations of virtual organisms evolving over generations, whose evolutionary outcomes reflect the selection pressures of their environment. The model simulates several factors considered important in biology, including life history trade-offs, investment in fighting ability and aggression, sperm competition, infanticide, and competition over access to food and mates. Downloaded materials include starting genotype and population files. Edit the these files and see what changes occur in the behavior of virtual populations!

View the B3GET user manual here.

LethalGeometry was developed to examine whether territory size influences the mortality risk for individuals within that territory. For animals who live in territoral groups and are lethally aggressive, we can expect that most aggression occurs along the periphery (or border) between two adjacent territories. For territories that are relatively large, the periphery makes up a proportionately small amount of the of the total territory size, suggesting that individuals in these territories might be less likely to die from these territorial skirmishes. LethalGeometry examines this geometric relationship between territory size and mortality risk under realistic assumptions of variable territory size and shape, variable border width, and stochastic interactions and movement.

The individuals (agents) are programmed to walk randomly about their environment, search for and eat food to obtain energy, reproduce if they can, and act aggressively toward individuals of other groups. During each simulation step, individuals analyze their environment and internal state to determine which actions to take. The actions available to individuals include moving, fighting, and giving birth.

Identifying how organisms respond to environmental stressors remains of central importance as human impacts continue to shift the environmental conditions for countless species. Some mammals are able to mitigate these environmental stressors at the cellular level, but the mechanisms by which cells are able to do this and how these strategies vary among species is not well understood. At the cellular level, it is difficult to identify the temporal dynamics of the system through empirical data because fine-grained time course samples are both incomplete and limited by available resources. To help identify the mechanisms by which animal cells mitigate extreme environmental conditions, we propose an agent-based model to capture the dynamics of the system. In the model, agents are regulatory elements and genes, and are able to impact the behaviors of each other. Rather than imposing rules for these interactions among agents, we will begin with randomized sets of rules and calibrate the model based on empirical data of cellular responses to stress. We will apply a common-garden framework to cultured cells from 16 mammalian species, which will yield genomic data and measures of cell morphology and physiology when exposed to different levels of temperature, glucose, and oxygen. These species include humans, dolphins, bats, and camels, among others, which vary in how they respond to environmental stressors, offering a comparative approach for identifying mechanistic rules whereby cells achieve robustness to environmental stressors. For calibration of the model, we will iteratively select for rules that best lead to the emergent outcomes observed in the cellular assays. Our model is generalized for any species, any cell type, and any environmental stressor, offering many applications of the model beyond our study. This study will increase our understanding of how organisms mitigate environmental stressors at the cellular level such that we can better address how organisms are impacted by and respond to extreme environmental conditions.

While the world’s total urban population continues to grow, not all cities are witnessing such growth, some are actually shrinking. This shrinkage causes several problems to emerge including population loss, economic depression, vacant properties and the contraction of housing markets. Such problems challenge efforts to make cities sustainable. While there is a growing body of work on study shrinking cities, few explore such a phenomenon from the bottom up using dynamic computational models. To overcome this issue this paper presents an spatially explicit agent-based model stylized on the Detroit Tri-county area, an area witnessing shrinkage. Specifically, the model demonstrates how through the buying and selling of houses can lead to urban shrinkage from the bottom up. The model results indicate that along with the lower level housing transactions being captured, the aggregated level market conditions relating to urban shrinkage are also captured (i.e., the contraction of housing markets). As such, the paper demonstrates the potential of simulation to explore urban shrinkage and potentially offers a means to test polices to achieve urban sustainability.

The goal of the AG-Innovation agent-based model is to explore and compare the effects of two alternative mechanisms of innovation development and diffusion (exogenous, linear and endogenous, non-linear) on emergent properties of food and income distribution and adoption rates of different innovations. The model also assesses the range of conditions under which these two alternative mechanisms would be effective in improving food security and income inequality outcomes. Our modelling questions were: i) How do cross-scalar social-ecological interactions within agricultural innovation systems affect system outcomes of food security and income inequality? ii) Do foreign aid-driven exogenous innovation perpetuate income inequality and food insecurity and if so, under which conditions? iii) Do community-driven endogenous innovations improve food security and income inequality and if so, under which conditions? The Ag-Innovation model is intended to serve as a thinking tool for for the development and testing of hypotheses, generating an understanding of the behavior of agricultural innovation systems, and identifying conditions under which alternated innovation mechanisms would improve food security and income inequality outcomes.