Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen
Data files
May 06, 2024 version files 87.26 KB
-
Multistate_Datafile.csv
80.62 KB
-
README.md
6.63 KB
Abstract
Testing for intraspecific variation for host tolerance or resistance in wild populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test the importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) against Batrachochytrium dendrobatidis (Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease.
Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden, and survival for eight weeks. We used a multi-state modeling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture.
We found that WY boreal toads are more tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also appeared more resistant to Bd with a higher probability of infection clearance and an average of five days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that likely contribute to why population declines vary regionally across this species.
Our multi-state framework allowed us to gain inference on typically hidden disease processes when testing for host tolerance or resistance. Our findings demonstrate that describing an entire host species as ‘tolerant’ or ‘resistant’ (or lack thereof) is unwise without testing for intraspecific variation.
README: Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen
https://doi.org/10.5061/dryad.0rxwdbs82
The ‘Multistate_Datafile’ is a file formatted in the multi-state mark-recapture format for program MARK.
Description of Multistate_Datafile
Filler_1: /* required before individual identifier (id) entry for MARK software to separate individuals
id: individual animal identity
Filler_2: */ required after individual identifier (id) entry for MARK software to separate individuals
Day0: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day7: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day14: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day21: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day28: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day35: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day42: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day49: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Day56: Entry of an I (infected), C (cleared/not infected), or 0 (dead) to signify whether an individual was infected with Batrachochytrium dendrobatidis, not infected, or dead on the day of sampling.
Pop1: A 1 indicates the individual belonging to population 1. A 0 indicates not belonging to population 1.
Pop2: A 1 indicates the individual belonging to population 2. A 0 indicates not belonging to population 2.
Pop3: A 1 indicates the individual belonging to population 3. A 0 indicates not belonging to population 3.
Pop4: A 1 indicates the individual belonging to population 4. A 0 indicates not belonging to population 4.
Mid: A 1 indicates the individual was exposed to a mid dose of Batrachochytrium dendrobatidis at the start of the experiment.
Hi: A 1 indicates the individual was exposed to a high dose of Batrachochytrium dendrobatidis at the start of the experiment.
Day0LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 0
Day7LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 7
Day21LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 14
Day28LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 21
Day35LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 28
Day42LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 35
Day49LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 42
Day56LnBd: Value of pathogen load natural-log transformed for the individual sampled on day 49
MassDay0: Mass in grams of the individual measured on Day 0
MassDay7: Mass in grams of the individual measured on Day 7
MassDay14: Mass in grams of the individual measured on Day 14
MassDay21: Mass in grams of the individual measured on Day 21
MassDay28: Mass in grams of the individual measured on Day 28
MassDay35: Mass in grams of the individual measured on Day 35
MassDay42: Mass in grams of the individual measured on Day 42
MassDay49: Mass in grams of the individual measured on Day 49
MassDay56: Mass in grams of the individual measured on Day 56
Delta-7-0: The percent change in mass from day 0 to day -7
Delta0-7: The percent change in mass from day 0 to day 7
Delta0-14: The percent change in mass from day 0 to day 14
Delta0-21: The percent change in mass from day 0 to day 21
Delta0-28: The percent change in mass from day 0 to day 28
Delta0-35: The percent change in mass from day 0 to day 35
Delta0-42: The percent change in mass from day 0 to day 42
Delta0-49: The percent change in mass from day 0 to day 49
UNK1: An empty column placeholder for a potential unknown variable to be added later
UNK2: An empty column placeholder for a potential unknown variable to be added later
UNK3: An empty column placeholder for a potential unknown variable to be added later
UNK4: An empty column placeholder for a potential unknown variable to be added later
UNK5: An empty column placeholder for a potential unknown variable to be added later
UNK6: An empty column placeholder for a potential unknown variable to be added later
UNK7: An empty column placeholder for a potential unknown variable to be added later
UNK8: An empty column placeholder for a potential unknown variable to be added later
UNK9: An empty column placeholder for a potential unknown variable to be added later
UNK10: An empty column placeholder for a potential unknown variable to be added later
END: ; that indicates the end of the data string for each individual for MARK software
Concatenated: The concatenated string of data for each individual. All rows of the concatenated column can then be copied into a text file to be used as the input file (.inp ending) for MARK software to read.
Note that input values of -99 indicates a fill-in value that signals to program MARK to not treat the value as a real covariate. These are input when covariates cannot be measured for an individual because the individual is dead. A 0 would be inappropriate because the covariate would be read at a value of 0. -99 essentially marks missing data.
Sharing Access/Information
All data were generated during a live animal experiment. No data was used from other sources.
Methods
See main manuscript text and supporting information in Hardy et al.