Changes in transmission rates drive seasonal patterns of shrimp black gill disease

Quantifying the processes affecting disease dynamics is critical for informing management strategies of fisheries. We present the results of a series of experiments and mechanistic models to disentangle the roles of transmission, mortality, and recovery in driving seasonal prevalence of shrimp Black Gill (sBG) disease in penaeid shrimp. We quantified seasonal sBG transmission to uninfected sentinel shrimp deployed into the environment. Next, we manipulated temperature and infection status in laboratory experiments to quantify drivers of host mortality and recovery. We then utilized these experiments to parameterize a series of mechanistic models to determine if disease dynamics were driven by host density-dependent or independent factors. Transmission was highest during the summer, with 75-91% of shrimp acquiring infection, but declined substantially in all other seasons (0-10% infection prevalence). In our lab experiments, we observed little disease-induced mortality and complete recov..., , # Changes in transmission rates drive seasonal patterns of shrimp black gill disease

Dataset DOI: [10.5061/dryad.mw6m9068b](10.5061/dryad.mw6m9068b)

## Description of the data and file structure

The code for the manuscript contains three parts: a field-based transmission experiment, an in-lab mortality and recovery experiment, and a mathematical model. The information below is divided to reflect this structure of the manuscript.

### Files and variables

## Transmission Experiment

#### File: Transmission_Exp_StatsV2.R

**Description:** This code contains the R script used to produce the results for the Transmission Experiment section and to create Figure 1, Appendix 3, and Table S1.

#### File: All_Estuaries_Trim_date.csv

**Description:** This file contains the diagnostic information for shrimp collected from the Wild and is used to compare the prevalence of deployed shrimp after the transmission experiments conclusion.

##### Variables

* PCR_binom: binary variable indicating *Hya...,