This MALAGON_DATASET_ReadmeTemplate_2020-02-13.txt file was generated on 2020-02-13] by Daniel Malagon


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GENERAL INFORMATION
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1. Title of Dataset 

Host density and habitat structure influence host contact rates and Batrachochytrium salamandrivorans transmission

2. Author Information


  Principal Investigator Contact Information
        Name: Dr. Matt J. Gray
           Institution: University of TN-Knoxville
           Address: Ellington Plant Sciences Building UTIA
           Email: mgray11@utk.edu


  Associate or Co-investigator Contact Information
        Name: Daniel Malagon
           Institution: University of TN-Knoxville
           Address: Ellington Plant Sciences Building UTIA
           Email: dmalagon@vols.utk.edu


  Alternate Contact Information
           Name: Davis Carter
           Institution: University of TN-Knoxville
           Address: Ellington Plant Sciences Building UTIA
           Email: Ecarte27@utk.edu


3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>


2018-08-29-2018-12-15

4. Geographic location of data collection (where was data collected?): 

University of TN-Knoxville, UTIA JARTU

5. Information about funding sources that supported the collection of the data:


Partial support (LAM, OFP, SL) was provided by the National Institute for Mathematical and Biological Synthesis, an Institute supported by the National Science Foundation through NSF Award #DBI-1300426. National Science Foundation Division of Environmental Biology (DEB-#1814520) also provided partial support for DAM, EDC, MJG and DLM. This work was completed under Hatch Project 1012932 of the USDA National Institute of Food and Agriculture. Funding was also provided by the UT College Scholars Program Excellence Fund.


6. Abstract/description of the dataset:

Batrachochytrium salamandrivorans (Bsal) is an emerging invasive pathogen that is highly pathogenic to salamander species. Modeling infection dynamics in this system can facilitate proactive efforts to mitigate this pathogen’s impact on North American species. Given its widespread distribution and high abundance, the eastern newt (Notophthalmus viridescens) has the potential to significantly influence Bsal epidemiology. We designed experiments to 1) estimate contact rates given different host densities and habitat structure and 2) estimate the probability of transmission from infected to susceptible individuals. Using parameter estimates from data generated during these experiments, we modeled infection and disease outcomes for a population of newts using a system of differential equations. We found that host contact rates were density-dependent, and that adding habitat structure reduced contacts. The probability of Bsal transmission given contact between newts was very high (>90%) even at early stages of infection. Our simulations show rapid transmission of Bsal among individuals following pathogen introduction, with infection prevalence exceeding 90% within one month and >80% mortality of newts in three months. Estimates of basic reproductive rate (R0) of Bsal for eastern newts were 1.9 and 3.2 for complex and simple habitats, respectively. Although reducing host density and increasing habitat complexity might decrease transmission, these management strategies may be ineffective at stopping Bsal invasion in eastern newt populations due to this species’ hyper-susceptibility.

7: Keywords for the dataset (provide 3 - 5):

Bsal, newt, transmission, contact


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data:

None

2. Links to publications that cite or use the data:

To be provided later.

3. Links to other publicly accessible locations of the data:

None

4. Links/relationships to ancillary data sets:

None

5. Was data derived from another source?
           If yes, list source(s):

No

6. Recommended citation for the data:

To be provided.


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DATA & FILE OVERVIEW
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1. File List

   A. Filename: Host density and habitat structure influence host contact rates and Batrachochytrium salamandrivorans transmission r-script
	Short description: R script for statistical analysis of data collected.

   B. Filename: contactrates.csv
      Short description: Measured rates of contacts/hr for pools of newts with varying densities, and plant treatments. 

   C. Filename: InfectedLoads.csv
      Short description: Estimated loads of Bsal on individual newts across 3 swabs.

   D. Filename: DansSurvival.csv
      Short description: Survival Data of infected and susceptible newts.

   E. Filename: ContactLocation.csv
      Short description: The number of contacts and location of contact between individual newts being cohoused for varying amounts of time.

   F. Filename: Controls Survival Data.csv
      Short description: Survival data of control newts which were not exposed to Bsal		 during the experiment.

   G. Filename: NonLinFit.m
      Short description: Matlab script for creation of a non linear function.

   H. Filename: SEIParameterStructure4.m
      Short description: Matlab script for parameters used for the SEI model.

   I. Filename: SolveSEImodel6.m
      Short description: Matlab script for calculating a solution to SEI model 6 and        plotting code.

   J. Filename: objfun.m
      Short description: Matlab script for calculating contacts per newt density.

   K. Filename: MasterRun.m
      Short description: Matlab script for master run.

   L. Filename: SEImodel4
      Short description: Matlab script for creating SEI model 4.



2. Relationship between files:        

File A is an r script used to analyze files B,C,D,E, and F. Files G, H, I, J, K, and L are matlab scripts used to create and analyze the SEI model referenced in the paper.


3. Additional related data collected that was not included in the current data package:

None


4. Are there multiple versions of the dataset? no
   If yes, list versions:
           Name of file that was updated:
                     i. Why was the file updated? 
                ii. When was the file updated?
           Name of file that was updated:
                      i. Why was the file updated?
                    ii. When was the file updated?






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METHODOLOGICAL INFORMATION
--------------------------


1. Description of methods used for collection/generation of data: 
<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>


Methods
Model Organism
Adult eastern newts were collected from two wild populations in eastern Tennessee, USA, in Carter County (36.177 N, -82.113 W) and Knox County (35.847 N, -83.872 W) in May 2017 and August 2018 under Tennessee Wildlife Resources Agency Science Collection Permit #1504. Following capture, newts were transported by vehicle in <3 hrs to the Johnson Animal Research and Teaching Unit facility at the University of Tennessee and held in large mesocosm tanks at room temperature prior to the experiments. All experiments described herein were approved by the University of Tennessee approved Institutional Animal Care and Use Committee under protocol #2395.

Experiment 1: Estimating Contact Rates among Newt Densities and Habitat Complexity
Newts were randomly assigned to one of six circular 1-m2 aquatic mesocosms (i.e., experimental units) containing approximately 7 cm of aged, dechlorinated water and maintained at room temperature (20 – 22°C). Due to space limitations in the laboratory, we tested one host density treatment (2, 4, or 8 newts) per week. These densities represent a natural range of eastern newt densities in the wild and have been used in other density-focused studies. After each week, mesocosms were drained and refilled with aged, dechlorinated water in order to maintain favorable water quality, and we re-randomized newts into mesocosms at a new density to randomly distribute any biases associated with captive duration among experimental effects. For the complex habitat treatment, we repeated the experiment following the same weekly randomization with artificial plants present in the mesocosms. We placed nine artificial plants (ca. 9 cm in height) in a 3 x 3 grid in each mesocosm, with each plant equidistant from each other (ca. 15 cm apart). Newts were fed ad libitum by equally dispersing thawed brine shrimp daily throughout each mesocosm. The laboratory was set to 12 hours of light and dark per diel cycle, which is typical daylight duration in Tennessee during summer.    
To ensure observers did not influence movements, number of newt contacts per hour was estimated using a surveillance camera (Night Owl, Model: DVR-BBHDA10PB-82-RS; Naples, FL, USA) suspended ca. 170 cm above each mesocosm. Video was recorded for one hour during each of four diel periods (0-0600, 0600-1200, 1200-1800,1800-2400 hrs), resulting in four hours of video observed per mesocosm per day. We averaged number of newt contacts among the diel periods and days for each mesocosm to obtain a robust estimate of contacts per hour for each host density and plant treatment. One contact was defined as a noticeable contact between two newts, such that one newt responded to contact from the other. 
Experiment 2: Estimating the probability of Bsal transmission among disease states and contact frequencies 
A separate group of newts were collected from the wild for Experiment 2. Newts were housed individually in 2000-cm3 circular containers (diameter = 16.5 cm) with ca. 300 mL of aged, dechlorinated water and a PVC cover object. Because co-infection with B. dendrobatidis (Bd) could influence Bsal infection dynamics,33 we heat-treated eastern newts upon arrival to the laboratory in an environmental chamber held at 30°C for 9 days 73. We did not test the newts for Bd infection prior to heat treatment, because prior exposure to Bd does not seem to connote acquired immunity to Bsal33. After heat treatment, we decreased temperature over four days to 14°C and held them at that temperature for four additional days before starting the experiment. We verified that all newts were Bd-negative using quantitative PCR (protocol discussed below) prior to beginning the experiment. Every three days, we changed housing containers, cover objects and water, and fed newts 2% of their initial body mass in frozen bloodworms. 
After the heat treatment, newts were randomly assigned to two groups of either infected or susceptible hosts. Infected hosts (n = 15) were exposed to a standardized quantity of Bsal zoospores (5 x 106 zoospores/mL) in a 10-mL water bath for 24 hours. We cultured Bsal on TgHL plates and harvested them by flooding each plate with a total of 6 mL of autoclaved dechlorinated water and filtering the suspended zoospores through a 20-um filter. Zoospores were enumerated by hemocytometry and verified by flow cytometry. After 12, 18 and 24 days post exposure (i.e., referred to as disease states in this study), one infected newt was exposed to a susceptible newt through one of three contact frequency treatments: one-second forced contact, 10-min cohabitation, and 30-min cohabitation (n = 5 susceptible newts per treatment combination). The one-second contact involved ventrum (infected) to ventrum (susceptible) touching for <1 second then animal separation. For cohabitation, susceptible and infected individuals were co-housed in a 2000-cm3 circular containers with ca. 300 mL of aged, dechlorinated water for the specified duration. To relate cohabitation treatments to contacts, we recorded and enumerated contacts in each container. The average number of contacts in the 10- and 30-min cohabitation treatments were 19 + 2 and 41 + 6 (s.e.m.), respectively. Location of newt contacts also was recorded for five major body regions: head, tail, legs, dorsum and ventrum. 
Following the contact-exposure treatments, susceptible newts were housed in individual containers (same size as above) in environmental chambers at 14°C, newts were inspected daily for signs of Bsal chytridiomycosis, and animals euthanized using benzocaine hydrochloride (100 mg/L) at humane endpoints of disease progression. To test for Bsal infection, we swabbed infected and susceptible newts every six days following the standardized protocol for Bd. Genomic DNA was extracted from each swab using Qiagen DNeasy Blood and Tissue kits (Qiagen, Hilden, Germany), and Bsal presence and load on each swab estimated using qPCR methods similar to those described in Blooi et al 2013. All qPCR reactions were amplified using an Applied Biosystems Quantstudio 6 Flex qPCR instrument. Each swab sample was run in duplicate and considered positive if both replicates amplified within 50 cycles. We confirmed Bsal infection on a subset of animals representing each experiment by performing histological examinations of epidermal tissues. The experiment ended at 90 days post-exposure to an infected newt, which is sufficient duration for Bsal chytridiomycosis to develop in eastern newts. 

2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>

The data submitted have not been processed. 

3. Instrument- or software-specific information needed to interpret the data:

R software

MATLAB

4. Standards and calibration information, if appropriate:


5. Environmental/experimental conditions:

All experiments took place in temperature controlled incubators as described in the manuscript at UTIA JARTU.

6. Describe any quality-assurance procedures performed on the data:

All data and code used for statistical analyses were screened by Dr. Jim Fordyce. 

7. People involved with sample collection, processing, analysis and/or submission:


Daniel A. Malagon1, Luis A. Melara2, Olivia F. Prosper3,4, Suzanne Lenhart4, E. Davis Carter1, J. A. Fordyce5, Anna C. Peterson1, Debra L. Miller1,6, and Matthew J. Gray1*

1Center for Wildlife Health, Department of Forestry, Wildlife and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
2Department of Mathematics, Shippensburg University, Shippensburg, PA 17257 USA 
3Department of Mathematics, University of Kentucky, Lexington, KY 40506 USA
4Department of Mathematics, University of Tennessee, Knoxville, TN 37996 USA 
5 Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
6Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University 
of Tennessee, Knoxville, TN 37996 USA




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DATA-SPECIFIC INFORMATION FOR: contactrates.csv
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables: 6


2. Number of cases/rows: 672


3. Variable List

    A. Name: Density
       Description: Density of newts in a pool.



    B. Name: Plants
       Description: Whether artifical plants were present in pool at time of data collection.

    C. Name: Contacts/Hr
	Description: The number of observed contacts per hour.


 C. Name: Day
	Description: Which day (out of 30) the video data were taken.


 C. Name: Diel
	Description: The diel period during which the video was taken.

 C. Name: Pool
	Description: Replicate pool number.



4. Missing data codes:
None 

5. Specialized formats of other abbreviations used


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DATA-SPECIFIC INFORMATION FOR: InfectedLoads.csv
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables: 3


2. Number of cases/rows: 15


3. Variable List
    A. Name: ID
       Description: Newt ID code.



    B. Name: Swab
       Description: Number of swab corresponding to Bsal load.


    B. Name: Load
       Description: Estimated Bsal load.


4. Missing data codes:
        Code/symbol:       -9999 Definition: data point lost
      


5. Specialized formats of other abbreviations used


-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: DansSurvival.csv
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables:8


2. Number of cases/rows: 75


3. Variable List
    A. Name: ID
       Description: Newt ID



    B. Name: Treatment
       Description: The treatment for newts (either 12,18, or 24 days) or 5x10^6 (exposed directly to Bsal).


    C. Name: Date of Death
       Description: The date on which the individual was either euthanized or died.


   D. Name: Date Exposed
       Description: The date on which each individual was exposed to Bsal.


   E. Name: Days Survival
       Description: The number of days each newt survived after being exposed to Bsal.



  F. Name: Dead
       Description: Whether the individual died or was euthanized during the experiment (=1) or was euthanized during experiment shutdown (=0).



  G. Name: CT
       Description: Contact treatment (either 1 second, 10 minutes, or 30 minutes).


  
4. Missing data codes:
        Code/symbol:       NA  Definition: Does not apply to individual newts.


5. Specialized formats of other abbreviations used



-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: ContactLocation.csv
-----------------------------------------
<create sections for each dataset (or file if appropriate) included>


1. Number of variables: 7


2. Number of cases/rows: 30


3. Variable List

    A. Name: contactreplicate
       Description: Contact situation replicate number.

    B. Name: head
       Description: Number of observed contacts on head.

    C. Name: tail
       Description: Number of observed contacts on tail.

  D. Name: ventrum
       Description: Number of observed contacts on ventrum.

  E. Name: legs
       Description: Number of observed contacts on legs.

  F. Name: dorsum
       Description: Number of observed contacts on dorsum.

  G. Name: total
       Description: Total number of observed contacts.


4. Missing data codes:
 None


5. Specialized formats of other abbreviations used




-----------------------------------------
DATA-SPECIFIC INFORMATION FOR: Controls Survival Data.csv
-----------------------------------------

1. Number of variables:8


2. Number of cases/rows: 56


3. Variable List
    A. Name: ID
       Description: Newt ID



    B. Name: Treatment
       Description: The treatment for newts (either 12,18, or 24 days) or Control ( not exposed to Bsal).


    C. Name: Date of Death
       Description: The date on which the individual was either euthanized or died.


   D. Name: Date Exposed
       Description: The date on which each individual was exposed to Bsal.


   E. Name: Days Survival
       Description: The number of days each newt survived after being exposed to Bsal.



  F. Name: Dead
       Description: Whether the individual died or was euthanized during the experiment (=1) or was euthanized during experiment shutdown (=0).



  G. Name: CT
       Description: Contact treatment (either 1 second, 10 minutes, or 30 minutes).


  
4. Missing data codes:
        Code/symbol:       NA  Definition: Does not apply to individual newts.


5. Specialized formats of other abbreviations used




























