DOI: 10.5061/dryad.fqz612jw1
title: Data and code for: Disease outbreaks select for mate choice and coat color in wolves

description: We know much about pathogen evolution and the emergence of new disease
 strains but less about host resistance and how it is signaled to other
 individuals and subsequently maintained. The cline in frequency of
 black-coated wolves across North America is hypothesized to result from a
 relationship with canine distemper virus (CDV) outbreaks. We test this
 hypothesis using cross-sectional data from wolf populations across North
 America that vary in the prevalence of CDV and the allele that makes coats
 black, longitudinal data from Yellowstone National Park, and modeling. The
 frequency of CDV outbreaks generates fluctuating selection that results in
 heterozygote advantage that in turn impacts the frequency of the black
 allele, the optimal mating behavior, and the black wolf cline across the
 continent.
description: Technical details about the
 analyses and the models are provided in the Material and Methods section
 of the article. 1 Survival analysis
 Data can be found in file
 'dataYNPsurvivalanalysis340.RData', codes and step-by-step
 guidance are available to run the analysis and visualize results (file :
 SurvivalAnalysis_Cubaynesetalarticle.Rmd.
 We used demographic data that
 included individual survival and immigration records, age, pack, and coat
 color phenotype and genotype for 340 wolves equipped with radio-collars in
 Yellowstone National Park, monitored between 1998 to 2020. Of these
 wolves, 181 were grey and 159 black (144 black heterozygotes, 10 black
 homozygotes, 5 of unknown genotype). We censored records at their last
 live sighting within the boundary of the park. 105 wolves were censored at
 the point they permanently dispersed outside of the National Park (n=101)
 or were killed by humans (n=4), deliberately or accidentally, within
 Yellowstone National Park.  During annual capture and radio-collaring
 efforts, the National Park Service routinely collects blood serum for
 serological analysis. All serum samples (n=425) were analyzed for CDV
 antibodies using a serum neutralization assay at Cornell University’s
 Animal Health Diagnostic Center (22,47). CDV exposure was a binary variable
 representing previous exposure (1, i.e., seropositive) or not (0, i.e.,
 seronegative). A result was seropositive when the titer dilution was equal
 or greater than the standard titer cutoff provided by the assay
 manufacturer. All wolf samples analyzed for this study were previously
 collected the National Park Service; no wolf was captured or handled for
 the purposes of this study. CDV outbreaks have occurred in 1999, 2005, 2008,
 2017 and 2018 in the Yellowstone wolf population. Reported exposure rate of wolves to CDV was
 near zero in non-outbreak years, and between 60% and 80% in outbreak
 years. We assumed no
 exposure occurred in non-outbreak years, unless a wolf seroconverted in
 that year. Given CDV’s extreme transmissibility within a pack, individuals
 were determined positive for CDV exposure if they, or at least one pup in
 their pack, seroconverted during an outbreak year. Given high exposure rates in outbreak
 years, we assumed that
 individuals that never tested negative for CDV at or after collaring were
 previously exposed to CDV if they were alive during an outbreak
 year. Introduced wolves
 that received a CDV vaccine as part of the release program were considered
 to have never been exposed to CDV (n=12). 
 In a year following first
 exposure to CDV, a wolf can either die or gain lifelong
 immunity. In our model, a
 wolf had two fates following its first CDV exposure: 1) die within the
 year of exposure, or 2) gain lifelong CDV immunity.
 We combined demographic,
 genetic and serological data to obtain the encounter histories of the 340
 wolves alive or dead of natural causes within Yellowstone National Park
 between 1998 and 2020.  2 Analysis across North American wolf
 populations Details about the data and sampling protocols
 are available in E.E. Brandell, et al. Patterns and processes
 of pathogen exposure in gray wolves across North America. Scientific
 reports, 11,1-14 (2021).  Data can be found in file
 'dataset_binary_reduced.csv', codes and step-by-step guidance
 are available to run the analysis and visualize results (files:
 'RunBayes_models_noCPV_allPops.r' and
 'WriteBayes_models'. 3 Projection
 Step-by-step guidance to run the population projection model is
 provided in the file
 Script_ProjectionModel_fromCubaynesetal2022.Rmd
description: open-source program R Excel or Libre
 Office text editor
description: # Data and code for: Disease outbreaks select for mate choice and coat
 color in wolves
 [https://doi.org/10.5061/dryad.fqz612jw1](https://doi.org/10.5061/dryad.fqz612jw1) ## Description of the data and file structure ### 1 - Survival analysis The file 'dataYNPsurvivalanalysis.RData' contains all data necessary to run the survival analysis described in Cubaynes et al.'s manuscript entitled 'Disease Outbreaks Select for Mate Choice and Coat Color in Wolves'. It can be imported in software R using the load() function. The list 'dataYNPsurvivalanalysis' contains the following components : * $ID a vector of characters of length n=340 containing wolves identification number, other objects are in same order. * $CR a matrix of 340 rows x 23 columns containing the capture history for each wolf (line), each year from 1998 to 2020 (column) with demographic and epidemiological status coded 1 : wolf alive inside YNP never exposed to CDV, 2: wolf alive inside YNP first exposure to CDV, 3 : wolf alive inside YNP already exposed to CDV, 4: wolf recovered dead from natural causes inside YNP, 0 : not detected * $first: for each wolf, vector of occasion of first capture (coded 1 to 22 for 1998 to 2020) * $last : for each wolf, vector of last occasion for left censoring for wolves that left YNP permanently r died of human-induced mortality inside YNP (coded 1 to 22 for 1998 to 2020) * $color : for each wolf, vector of coat color phenotype, 0 for gray phenotype, 1 for black phenotype * $geno : for each wolf, vector of coat color genotype, 1 for homozygote black, 2 for heterozygote black, 3 for homozygote gray, 4 unknown black genotype * $BHOM : for each wolf, vector of binary index for coat color genotype, 1 if homozygote black, 0 otherwise * $BHET : for each wolf, vector of binary index for coat color genotype, 1 if homozygote black, 0 otherwise * $GHOM : for each wolf, vector of binary index for coat color genotype, 1 if homozygote black, 0 otherwise * $UN : for each wolf, vector of binary index for coat color genotype, 1 if unknown black genotype, 0 otherwise * $age : for each wolf (line), each year (column) matrix of age class, 1 for wolf &lt; 7yo, 2 for senescent wolf 7+ yo * $pack : for each wolf (row), each year (column) matrix of pack code * $alive1 : for each wolf (row), each year (column) matrix of initial state matrix for running the state space model. * $packN : for each pack code (row) name of the corresponding pack. Codes with step-by-step instructions to run the survival analysis is available in file 'SurvivalAnalysis\_Cubaynesetalarticle.Rmd'. ### 2 - Analysis examining the relationship between coat color and canine distemper virus across North American wolf populations The file 'dataset\_serosurvey.csv' contains all data necessary to run the Bayesian analysis examining the relationship between coat color and CDV described in Cubaynes et al.'s manuscript entitled 'Disease Outbreaks Select for Mate Choice and Coat Color in Wolves'. The dataset used for this analysis is from (31) and presented in Figure 1(A). Statistical analyses used a reduced version of this dataset (Figure 1(B), 1(C)) whereby populations without coat color data – Montana (n = 351), northern Northwest Territories (n = 67), Michigan (n = 102) – or variation in coat color (the black phenotype is not known to exist due to geographic/management barriers) – Ellesmere Island (n = 11), Mexican wolves (n = 181) – were removed. In addition, wolves without age, sex, CDV, and coat color data were removed (n = 140). Below are covariates examined in the Bayesian analysis. See (31) and associated Supporting Information for additional details. Description of the dataset : * $pop: population ID = Alaska Peninsula (AK PEN), Denali National Park (DENALI), central-eastern Alaska (INT AK), Yukon-Charley National Preserve (YUCH), South Slave Northwest Territories (SS NWT), British Columbia (BC), southeastern Alaska (SE AK), Banff & Jasper National Parks (BAN JAS), Yellowstone National Park (YNP), Grand Teton National Park (GTNP), Ontario (ONT), and Superior National Forest (SNF). * $wolf: individual wolf ID. * $pack: pack ID that wolf was a member of at time of sampling. * $year: biological year; year starts according to the birth month in each population: April = British Columbia/Banff/Jasper National Parks and south, May = SE Alaska and north. * $age.cat1: age category as pup [0,1), subadult [1,3), and adult [3+]. * $sex: F female, M male, or NA. * $color: B black, G gray, or NA. * $social: A alpha, B beta, S subordinate, or NA. * $habitat+: index of habitat quality. * $human+: human density = the number of people per 1000-km2, and was used as a proxy for the presence of unvaccinated dogs and synanthropic animals (31). * $cumu.total.pop: population density = average population density (wolves/1000-km2/year). This was calculated as a basic average across years, but for populations with &gt;1 density estimate per year, density was first averaged by year, resulting in one density estimate per year. * $cumu.pack.size: pack size = average annual pack size (mean number of wolves/pack/year); pack sizes were averaged within a year, then averaged across years to provide one average annual pack size estimate per population. * $cdv.binary\*: serostatus for canine distemper virus, 1 positive, 0 negative, or NA. * $cpv.binary\*: serostatus for canine parvovirus, 1 positive, 0 negative, or NA. * $mesocarnivores: an integer from 0-3 representing presence of skunks (Mephitis mephitis), raccoons (Procyon lotor), and coyotes (Canis latrans); presence of each species was given a 1, and then summed, so that 3 meant all three species were present. * $forest+: a continuous variable calculated as the percent forest cover in a population (deciduous, coniferous, and mixed). +Populations are assumed to be the same size: a circle with radius 200-km2 (total area = 125664-km2) based on typical wolf territory size and dispersal distance. Centroids were the approximate center of samples, verified by resident expert biologists. \*See Brandell et al. 2021 (31) Supplementary Material for laboratory testing, titer cutoffs, and additional information on serological analyses). Codes with step-by-step instructions to run the analysis is available in files 'RunBayes\_models\_noCPV\_allPops.r' and 'WriteBayes\_models'. ### 3 - Population projection model Step-by-step instructions to run the population projection model is available in file : 'Script\_ProjectionModel\_fromCubaynesetal2022.Rmd'