Age‐specific infectious period shapes dynamics of pneumonia in bighorn sheep

Plowright, Raina K.; Manlove, Kezia R.; Besser, Thomas E.; Páez, David J.; Andrews, Kimberly R.; Matthews, Patrick E.; Waits, Lisette P.; Hudson, Peter J.; Cassirer, E. Frances

doi:10.1111/ele.12829

Cited by 46 publications

(64 citation statements)

References 69 publications

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“…Each winter from 2011 to 2016, we captured six‐ to nine‐month‐old lambs, yearlings and adults using baited corral traps and ground‐darting; sampling of adults focused primarily on females (Table b, Supporting Information Table S2). We estimated the age of each individual based on morphology (for lambs), tooth eruption and capture history (Plowright et al., ), and collected blood and tissue samples (Table b, Supporting Information Table S2). We also collected faecal samples from unmarked individuals after they defecated.…”

Section: Methodsmentioning

confidence: 99%

“…A total of 22 microsatellite loci were PCR amplified for each Mexican gray wolf sample (see Supporting Information Appendix S1 for PCR conditions), and a total of 15 microsatellite loci were PCR amplified in two multiplexes for each bighorn sheep sample (see Plowright et al., for PCR conditions). All PCRs were run with a negative control to test for reagent contamination.…”

Section: Methodsmentioning

confidence: 99%

“…The ability to identify the parents of individuals in wild populations can provide insight into a wide range of topics including inbreeding levels (Dunn, Clancey, Waits, & Byers, 2011;Pemberton, 2004), translocation success (Hogg, Forbes, Steele, & Luikart, 2006;Marker et al, 2008), hybridization (Adams, Kelly, & Waits, 2003;Steyer et al, 2016), demographic processes (D'Aloia et al, 2015;Douhard, Festa-Bianchet, & Pelletier, 2016), mating system (Dugdale, Macdonald, Pope, & Burke, 2007;Hogg & Forbes, 1997;Jones, Kvarnemo, Moore, Simmons, & Avise, 1998), disease transmission (Plowright et al, 2017) and quantitative genetics (DiBattista, Feldheim, Garant, Gruber, & Hendry, 2009;Janeiro, Coltman, Festa-Bianchet, Pelletier, & Morrissey, 2017;Nguyen, Hayes, & Ingram, 2014). Genetic data can provide a powerful tool for identifying parents, and currently the main type of genetic marker used for parentage analysis in wild populations is microsatellites (Jones, Small, Paczolt, & Ratterman, 2010;Pemberton, 2008).…”

Section: Introductionmentioning

confidence: 99%

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A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

Andrews

Adams

Cassirer

et al. 2018

Molecular Ecology Resources

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The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

Andrews

Adams

Cassirer

et al. 2018

Molecular Ecology Resources

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“…We used the approximate median date of lambing in North Dakota (15 May; Wiedmann and Hosek ) as the origin for age‐specific and annual survival. We left‐truncated survival records at age 2 because bighorn sheep were >1 year old when they were marked and because subadults (≤2 yrs old) and adults (>2 yrs old) may be differentially susceptible to various causes of mortality (Kelly , Plowright et al , Manlove et al , Plowright et al ). When date of death was uncertain, we used the midpoint of the interval between the last live observation and detection of death unless the extent of decomposition suggested otherwise (Bleich and Taylor ).…”

Section: Methodsmentioning

confidence: 99%

Ecotypic variation in population dynamics of reintroduced bighorn sheep

2017

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Selection of bighorn sheep (Ovis canadensis) for translocation historically has been motivated by preservation of subspecific purity rather than by adaptation of source stocks to similar environments. Our objective was to estimate cause-specific, annual, and age-specific mortality of introduced bighorn sheep that originated at low elevations in southern British Columbia, Canada (BC ecotype), or in the Missouri River Breaks region of central Montana, USA (MT ecotype). In North Dakota, USA, mortality was similar and typically low for adult female bighorn sheep from Montana (0.09 AE 0.029 [SE]) and British Columbia (0.08 AE 0.017) during 2000-2016. Median life expectancy was 11 years for females that reached adulthood (2 yrs old); however, mortality accelerated with age and reached 86% by age 16. Mortalities resulted primarily from low rates of predation, disease, accidents, and unknown natural causes (<0.04 [upper 90% CI]). Similar survival rates of female bighorn sheep from British Columbia and Montana, coupled with greater recruitment of bighorn sheep from Montana, resulted in a greater projected rate of increase for the MT ecotype (l ¼ 1.21) than for the BC ecotype (1.02), and a more youthful age structure. These results support translocation of bighorn sheep from areas that are environmentally similar to areas that will be stocked. Potential benefits include more rapid population growth, greater resilience to and more rapid recovery from densityindependent losses, an increased possibility that rapidly growing populations will expand into adjacent habitat, increased hunter opportunity, increased connectivity among herds, and a more complete restoration of ecosystem processes. Ó 2017 The Wildlife Society.

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“…Once clinical signs of pneumonia appear in lambs, generally at 6–9 weeks of age, lamb mortality rates also increase (Spraker et al , Coggins and Matthews , Cassirer et al ). Pneumonia epizootics have caused all‐age die‐offs and suppressed lamb recruitment in populations for many years (Singer et al , Monello et al , Miller , George et al ) because at least some survivors become carriers and transmit pathogens to naïve animals (Foreyt , Coggins and Matthews , Besser et al , Fox et al , Plowright et al ).…”

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confidence: 99%

Respiratory disease, behavior, and survival of mountain goat kids

Blanchong¹,

Anderson²,

Clark³

et al. 2018

J Wildl Manag

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Bacterial pneumonia is a threat to bighorn sheep (Ovis canadensis) populations. Bighorn sheep in the East Humboldt Mountain Range (EHR), Nevada, USA, experienced a pneumonia epizootic in 2009–2010. Testing of mountain goats (Oreamnos americanus) that were captured or found dead on this range during and after the epizootic detected bacteria commonly associated with bighorn sheep pneumonia die‐offs. Additionally, in years subsequent to the bighorn sheep epizootic, the mountain goat population had low kid:adult ratios, a common outcome for bighorn sheep populations that have experienced a pneumonia epizootic. We hypothesized that pneumonia was present and negatively affecting mountain goat kids in the EHR. From June–August 2013–2015, we attempted to observe mountain goat kids with marked adult females in the EHR at least once per week to document signs of respiratory disease; identify associations between respiratory disease, activity levels, and subsequent disappearance (i.e., death); and estimate weekly survival. Each time we observed a kid with a marked adult female, we recorded any signs of respiratory disease and collected behavior data that we fit to a 3‐state discrete hidden Markov model (HMM) to predict a kid's state (active vs. sedentary) and its probability of disappearing. We first observed clinical signs of respiratory disease in kids in late July–early August each summer. We observed 8 of 31 kids with marked adult females with signs of respiratory disease on 13 occasions. On 11 of these occasions, the HMM predicted that kids were in the sedentary state, which was associated with increased probability of subsequent death. We estimated overall probability of kid survival from June–August to be 0.19 (95% CI = 0.08–0.38), which was lower than has been reported in other mountain goat populations. We concluded that respiratory disease was present in the mountain goat kids in the EHR and negatively affected their activity levels and survival. Our results raise concerns about potential effects of pneumonia to mountain goat populations and the potential for disease transmission between mountain goats and bighorn sheep where the species are sympatric. © 2018 This article is a U.S. Government work and is in the public domain in the USA.

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Age‐specific infectious period shapes dynamics of pneumonia in bighorn sheep

Cited by 46 publications

References 69 publications

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

Ecotypic variation in population dynamics of reintroduced bighorn sheep

Respiratory disease, behavior, and survival of mountain goat kids

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