DOI: 10.5061/dryad.0rxwdbs82
title: Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen

description: 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.
description: See main manuscript text and supporting information in Hardy et
 al.
description: # Quantifying intraspecific variation in host resistance and tolerance to
 a lethal pathogen
 [https://doi.org/10.5061/dryad.0rxwdbs82](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.