Journal of Theoretical Biology

Zombie ants are ants manipulated by a fungal parasite (Ophiocordyceps sp.) to leave the nest and die biting the underside of a leaf. From there, the fungus grows from the ant and distributes spores to new ants. The model recreates how infected ants are walking from the nest to the biting locations. By altering the movement parameters of the ants, we investigate how walking style influences whether ants frequently end up on the biting locations. The model uses field data to inform the model setup, using 4 different nests with the real locations of the ant nest, foraging trails, and cadaver biting locations.

I. The program Poly_map_2age produces maps classifying possibility of polymorphism maintenance for 2-age population under cyclical selection for two cases: (i) maternal selection (Eq. 5), (ii) simple gene (Eq. 6) in text format. a. Output notation: 0 and 1 are monomorphism, 3 is polymorphism, 4 is bistability region. b. To start: poly_map_2age.exe INP x_s.csv x_m.csv c. C++ cod (“poly_map_2age.CPP”), Input, and Output files examples are given in the current directory; II. Color_maps.R (script in R) transforms text output (“x_s.csv” and “x_m.csv”) to color image III. Poly_int_uniform.R (script in R) allows constructing figures with a. coexistence conditions for four- and three-year cycles with value variations of the parameter m. Separetedly for maternal selection (Eq. 2) and .simple gene (Eq. 1) b. coexistence conditions for N-year cycles at any fixed value of m.

Source code for running all simulations

A template python script for running the simulations with explanation.

The included Mathematica notebooks allow for analysis of the model describing the population dynamical consequences of antagonism between partners sharing a mutualist. "FullModelAnalyses.nb" could be used to recover all of our results. "RegionPlots.nb" provide code necessary to recreate region plots used in the paper. The other files are the supplementary files that show brief methods for obtaining (1) population dynamics of different ecological scenarios beyond those explored in depth in the manuscript, (2) stability analyses of model equilibria, (3) direct and indirect effects as evidenced by press perturbation analyses. Both .nb and .cdf files are provided.

For the years 1989- 1993, data provides whether an observation is a US Sugar Corporation field was infected with CTV. A '1' indicates infection a 0 otherwise. Headers "hor" and "vert" specify the row and column where an observations is located in the field. The headers 89-93 correspond to years 1989- 1993 respectively.

Deep-GDAE Gene-Disease Association Extraction Deep-GDAE integrates the specificities of a Convolution Neural Network (CNN) and an Attention-based Bidirectional Long Short-Term Memory Network to classify Gene-Disease Associations.

Names-position-nodes.csv is a tab delimited file that contains 83 rows. Each row has 7 entries: the node number, its hemisphere (left or right), its anatomical name, its coordinates (x,y,z), and its associated region.

GraphLaplacian83.csv is a tab delimited file that contains the weighted graph Laplacian extracted from 418 different brains as explained in the main text.

All data for Goerlitz et al, J Theor Biol bat parameters, moth parameters, detection distances, buffer distances