Hoberg EP, Kocan AA, Rickard LG. Gastrointestinal strongyles in wild ruminants. In: William SM, Pybus MJ, Kocan AA, editors. Parasitic diseases of wild mammals. Ames: Iowa State University Press; 2001. p. 193–227.
Google Scholar
Roeber F, Jex AR, Gasser RB. Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance—an Australian perspective. Parasites Vectors. 2013;6:153.
PubMed
PubMed Central
Google Scholar
Craig BH, Pilkington JG, Pemberton JM. Gastrointestinal nematode species burdens and host mortality in a feral sheep population. Parasitology. 2006;133:485–96.
CAS
PubMed
Google Scholar
Leivesley JA, Bussière LF, Pemberton JM, Pilkington JG, Wilson K, Hayward AD. Survival costs of reproduction are mediated by parasite infection in wild Soay sheep. Ecol Lett. 2019;22:1203–13.
PubMed
Google Scholar
Kelehear C, Brown GP, Shine R. Influence of lung parasites on the growth rates of free-ranging and captive adult cane toads. Oecologia. 2011;165:585–92.
PubMed
Google Scholar
Tompkins DM, Wilson K. Wildlife disease ecology: from theory to policy. Trends Ecol Evol. 1998;13:476–8.
CAS
PubMed
Google Scholar
Gunn A, Irvine RJ. Subclinical parasitism and ruminant foraging strategies—a review. Wildl Soc Bull. 2003;31:117–26.
Google Scholar
Thompson RCA, Lymbery AJ, Smith A. Parasites, emerging disease and wildlife conservation. Int J Parasitol. 2010;40:1163–70.
CAS
PubMed
Google Scholar
Lochmiller RL, Deerenberg C. Trade-offs in evolutionary immunology: just what is the cost of immunity? Oikos. 2000;88:87–98.
Google Scholar
Gilot-Fromont E, Jégo M, Bonenfant C, Gibert P, Rannou B, Klein F, et al. Immune phenotype and body condition in roe deer: individuals with high body condition have different, not stronger immunity. PLoS ONE. 2012;7:e45576.
CAS
PubMed
PubMed Central
Google Scholar
Beldomenico PM, Begon M. Disease spread, susceptibility and infection intensity: vicious circles? Trends Ecol Evol. 2010;25:21–7.
PubMed
Google Scholar
Tompkins DM, Dunn AM, Smith MJ, Telfer S. Wildlife diseases: from individuals to ecosystems. J Anim Ecol. 2011;80:19–38.
PubMed
Google Scholar
Body G, Ferté H, Gaillard J-M, Delorme D, Klein F, Gilot-Fromont E. Population density and phenotypic attributes influence the level of nematode parasitism in roe deer. Oecologia. 2011;167:635–46.
PubMed
Google Scholar
Aleuy OA, Ruckstuhl K, Hoberg EP, Veitch A, Simmons N, Kutz SJ. Diversity of gastrointestinal helminths in Dall’s sheep and the negative association of the abomasal nematode, Marshallagia marshalli, with fitness indicators. PLoS ONE. 2018;13:e0192825.
PubMed
PubMed Central
Google Scholar
Sinclair R, Melville L, Sargison F, Kenyon F, Nussey D, Watt K, et al. Gastrointestinal nematode species diversity in Soay sheep kept in a natural environment without active parasite control. Vet Parasitol. 2016;227:1–7.
PubMed
Google Scholar
Gruver AL, Hudson LL, Sempowski GD. Immunosenescence of ageing. J Pathol. 2007;211:144–56.
CAS
PubMed
PubMed Central
Google Scholar
Peters A, Delhey K, Nakagawa S, Aulsebrook A, Verhulst S. Immunosenescence in wild animals: meta-analysis and outlook. Ecol Lett. 2019;22:1709–22.
PubMed
Google Scholar
Budischak SA, O’Neal D, Jolles AE, Ezenwa VO. Differential host responses to parasitism shape divergent fitness costs of infection. Funct Ecol. 2018;32:324–33.
Google Scholar
Bourgoin G, Portanier E, Poirel M-T, Itty C, Duhayer J, Benabed S, et al. Reproductive females and young mouflon (Ovis gmelini musimon × Ovis sp.) in poor body condition are the main spreaders of gastrointestinal parasites. Parasitology. 2021;148:809–18.
CAS
PubMed
Google Scholar
Hayward AD. Causes and consequences of intra- and inter-host heterogeneity in defence against nematodes. Parasite Immunol. 2013;35:362–73.
CAS
PubMed
Google Scholar
Klein SL. The effects of hormones on sex differences in infection: from genes to behavior. Neurosci Biobehav Rev. 2000;24:627–38.
CAS
PubMed
Google Scholar
Moore SL, Wilson K. Parasites as a viability cost of sexual selection in natural populations of mammals. Science. 2002;297:2015–8.
CAS
PubMed
Google Scholar
Markle JG, Fish EN. SeXX matters in immunity. Trends Immunol. 2014;35:97–104.
CAS
PubMed
Google Scholar
Froeschke G, Harf R, Sommer S, Matthee S. Effects of precipitation on parasite burden along a natural climatic gradient in southern Africa—implications for possible shifts in infestation patterns due to global changes. Oikos. 2010;119:1029–39.
Google Scholar
Cheynel L, Lemaître J-F, Gaillard J-M, Rey B, Bourgoin G, Ferté H, et al. Immunosenescence patterns differ between populations but not between sexes in a long-lived mammal. Sci Rep. 2017;7:13700.
CAS
PubMed
PubMed Central
Google Scholar
Davidson RK, Ličina T, Gorini L, Milner JM. Endoparasites in a Norwegian moose (Alces alces) population—Faunal diversity, abundance and body condition. Int J Parasitol Parasites Wildl. 2015;4:29–36.
PubMed
PubMed Central
Google Scholar
Oliver-Guimerá A, Martínez-Carrasco C, Tvarijonaviciute A, Ruiz de Ybáñez MR, Martínez-Guijosa J, López-Olvera JR, et al. The physiological cost of male-biased parasitism in a nearly monomorphic mammal. Parasites Vectors. 2017;10:200.
PubMed
PubMed Central
Google Scholar
Dobson A, Lafferty KD, Kuris AM, Hechinger RF, Jetz W. Homage to Linnaeus: how many parasites? How many hosts? Proc Natl Acad Sci USA. 2008;105:11482–9.
CAS
PubMed
PubMed Central
Google Scholar
Goater TM, Goater CP, Esch GW. Parasitism: the diversity and ecology of animal parasites. Cambridge: Cambridge University Press; 2013.
Google Scholar
Taylor MA, Coop RL, Wall RL. Veterinary parasitology. 4th ed. Chichester: Wiley Blackwell; 2015.
Google Scholar
Aivelo T, Medlar A. Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology. 2018;145:608–21.
PubMed
Google Scholar
Avramenko RW, Redman EM, Lewis R, Yazwinski TA, Wasmuth JD, Gilleard JS. Exploring the gastrointestinal “Nemabiome”: deep amplicon sequencing to quantify the species composition of parasitic nematode communities. PLoS ONE. 2015;10(12):e0143559.
PubMed
PubMed Central
Google Scholar
Barone CD, Wit J, Hoberg EP, Gilleard JS, Zarlenga DS. Wild ruminants as reservoirs of domestic livestock gastrointestinal nematodes. Vet Parasitol. 2020;279:109041.
CAS
PubMed
Google Scholar
Obanda V, Maingi N, Muchemi G, Ng’ang’a CJ, Angelone S, Archie EA. Infection dynamics of gastrointestinal helminths in sympatric non-human primates, livestock and wild ruminants in Kenya. PLoS ONE. 2019;14:e0217929.
CAS
PubMed
PubMed Central
Google Scholar
Walker JG, Morgan ER. Generalists at the interface: nematode transmission between wild and domestic ungulates. Int J Parasitol Parasites Wildl. 2014;3:242–50.
PubMed
PubMed Central
Google Scholar
Borgsteede FHM, Jansen J, Van Nispen tot Pannerden HPM, Van Der Burg WPJ, Noorman N, Poutsma J, et al. Untersuchungen über die helminthen-fauna beim reh (Capreolus capreolus L.) in den Niederlanden. Z Jagdwiss. 1990;36:104–9.
Google Scholar
Pato FJ, Vázquez L, Díez-Baños N, López C, Sánchez-Andrade R, Fernández G, et al. Gastrointestinal nematode infections in roe deer (Capreolus capreolus) from the NW of the Iberian Peninsula: assessment of some risk factors. Vet Parasitol. 2013;196:136–42.
CAS
PubMed
Google Scholar
Zaffaroni E, Teresa Manfredi M, Citterio C, Sala M, Piccolo G, Lanfranchi P. Host specificity of abomasal nematodes in free ranging alpine ruminants. Vet Parasitol. 2000;90:221–30.
CAS
PubMed
Google Scholar
Segonds-Pichon A, Ferté H, Gaillard J-M, Lamarque F, Duncan P. Nematode infestation and body condition in roe deer (Capreolus capreolus). Game Wildl Sci. 2000;17:241–58.
Google Scholar
Pettorelli N, Gaillard J-M, Duncan P, Maillard D, Van Laere G, Delorme D. Age and density modify the effects of habitat quality on survival and movements of roe deer. Ecology. 2003;84:3307–16.
Google Scholar
Gaillard J-M, Duncan P, Delorme D, Van Laere G, Pettorelli N, Maillard D, et al. Effects of hurricane Lothar on the population dynamics of European roe deer. J Wildl Manag. 2003;67:767–73.
Google Scholar
Gaudry W, Gaillard J-M, Saïd S, Bonenfant C, Mysterud A, Morellet N, et al. Same habitat composition but different use: evidence of context-dependent habitat selection in roe deer females. Sci Rep. 2018;8:5102.
Google Scholar
Gaillard J-M, Delorme D, Boutin J-M, Van Laere G, Boisaubert B, Pradel R. Roe deer survival patterns: a comparative analysis of contrasting populations. J Anim Ecol. 1993;62:778–91.
Google Scholar
O’Connor LJ, Walkden-Brown SW, Kahn LP. Ecology of the free-living stages of major trichostrongylid parasites of sheep. Vet Parasitol. 2006;142:1–15.
PubMed
Google Scholar
Raynaud J-P, William G, Brunault G. Etude de l’efficacité d’une technique de coproscopie quantitative pour le diagnostic de routine et le contrôle des infestations parasitaires des bovins, ovins, équins et porcins. Ann Parasitol Hum Comp. 1970;45:321–42.
CAS
PubMed
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
CAS
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Google Scholar
Taberlet P, Bonin A, Zinger L, Coissac E. Environmental DNA: for biodiversity research and monitoring. Oxford: Oxford University Press; 2018.
Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:140.
PubMed
PubMed Central
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
CAS
PubMed
Google Scholar
Workentine ML, Chen R, Zhu S, Gavriliuc S, Shaw N, de Rijke J, et al. A database for ITS2 sequences from nematodes. BMC Genet. 2020;21:74.
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
CAS
PubMed
PubMed Central
Google Scholar
Schnell IB, Bohmann K, Gilbert MTP. Tag jumps illuminated—reducing sequence-to-sample misidentifications in metabarcoding studies. Mol Ecol Resour. 2015;15:1289–303.
CAS
PubMed
Google Scholar
Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:160–74.
CAS
PubMed
Google Scholar
Posada D, Crandall KA. modeltest: testing the model of DNA substitution. Bioinformatics. 1998;14:817–8.
CAS
PubMed
Google Scholar
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics Oxford Academic. 2011;27:592–3.
CAS
Google Scholar
Rambaut A. (2014). FigTree v1.4.4. http://tree.bio.ed.ac.uk/software/figtree/. Accessed 4 Dec 2020.
Wright ES. Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 2016;8:352–9.
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Roeland K, Legendre P, McGlinn D, et al. (2020). vegan: Community Ecology Package. R package v2.5–7. https://CRAN.R-project.org/package=vegan.
Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36.
Google Scholar
Shannon CE, Weaver W. A mathematical theory of communication. Urbana: University of Illinois Press; 1948.
Google Scholar
Simpson EH. Measurement of diversity. Nature. 1949;163:688.
Google Scholar
Dyson K. Custom community ecology helper R scripts [Internet]. 2018. https://github.com/kdyson/R_Scripts
Burnham KP, Anderson DR. Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. New York: Springer; 2002.
Google Scholar
Legendre P, Legendre L. Numerical ecology. 2nd ed. Amsterdam: Elsevier; 1998.
Google Scholar
Lienard E, Depaquit J, Ferté H. Spiculopteragia mathevossiani Ruchliadev, 1948 is the minor morph of Spiculopteragia spiculoptera (Gushanskaya, 1931): molecular evidence. Vet Res. 2006;37:683–94.
PubMed
Google Scholar
Wyrobisz-Papiewska A, Kowal J, Nosal P, Chovancová G, Rehbein S. Host specificity and species diversity of the Ostertagiinae Lopez-Neyra, 1947 in ruminants: a European perspective. Parasites Vectors. 2018;11:369.
PubMed
PubMed Central
Google Scholar
Wang C, Gao J-F, Chang QC, Zou FC, Zhao Q, Zhu X-Q. Sequence variability in four mitochondrial genes among Bunostomum trigonocephalum isolates from four provinces in China. J Helminthol. 2013;87:416–21.
CAS
PubMed
Google Scholar
Wyrobisz A, Kowal J, Nosal P. Insight into species diversity of the Trichostrongylidae Leiper, 1912 (Nematoda: Strongylida) in ruminants. J Helminthol. 2016;90:639–46.
CAS
PubMed
Google Scholar
Lehrter V, Jouet D, Liénard E, Decors A, Patrelle C. Ashworthius sidemi Schulz, 1933 and Haemonchus contortus (Rudolphi, 1803) in cervids in France: integrative approach for species identification. Infect Genet Evol. 2016;46:94–101.
PubMed
Google Scholar
Dróżdż J, Demiaszkiewicz A, Lachowicz J. Expansion of the Asiatic parasite Ashworthius sidemi (Nematoda, Trichostrongylidae) in wild ruminants in Polish territory. Parasitol Res. 2003;89:94–7.
Google Scholar
Vadlejch J, Kyriánová I, Rylková K, Zikmund M, Langrova I. Health risks associated with wild animal translocation: a case of the European bison and an alien parasite. Biol Invasions. 2017;19:1121–5.
Google Scholar
Santín-Durán M, Alunda JM, Hoberg EP, de la Fuente C. Age distribution and seasonal dynamics of abomasal helminths in wild red deer from central Spain. J Parasitol. 2008;94:1031–7.
PubMed
Google Scholar
Else KJ. Have gastrointestinal nematodes outwitted the immune system? Parasite Immunol. 2005;27:407–15.
CAS
PubMed
Google Scholar
Jégo M, Ferté H, Gaillard J-M, Klein F, Crespin L, Gilot-Fromont E, et al. A comparison of the physiological status in parasitized roe deer (Capreolus capreolus) from two different populations. Vet Parasitol. 2014;205:717–20.
PubMed
Google Scholar
Bordes F, Morand S. Coevolution between multiple helminth infestations and basal immune investment in mammals: cumulative effects of polyparasitism? Parasitol Res. 2009;106:33–7.
PubMed
Google Scholar
Inclan-Rico JM, Siracusa MC. First responders: innate immunity to helminths. Trends Parasitol. 2018;34:861–80.
CAS
PubMed
PubMed Central
Google Scholar
Martin LB, Weil ZM, Nelson RJ. Seasonal changes in vertebrate immune activity: mediation by physiological trade-offs. Philos Trans R Soc Lond B Biol Sci. 2008;363:321–39.
PubMed
Google Scholar
Bonenfant C, Gaillard J-M, Dray S, Loison A, Royer M, Chessel D. Testing sexual segregation and aggregation: old ways are best. Ecology. 2007;88:3202–8.
PubMed
Google Scholar
José CS, Lovari S, Ferrari N. Temporal evolution of vigilance in roe deer. Behav Processes. 1996;38:155–9.
PubMed
Google Scholar
Merceron G, Viriot L, Blondel C. Tooth microwear pattern in roe deer (Capreolus capreolus L.) from Chizé (Western France) and relation to food composition. Small Rumin Res. 2004;53:125–32.
Google Scholar
Habig B, Doellman MM, Woods K, Olansen J, Archie EA. Social status and parasitism in male and female vertebrates: a meta-analysis. Sci Rep. 2018;8:3629.
PubMed
PubMed Central
Google Scholar
Portanier E, Garel M, Devillard S, Duhayer J, Poirel M-T, Henri H, et al. Does host socio-spatial behavior lead to a fine-scale spatial genetic structure in its associated parasites? Parasite. 2019;26:64.
PubMed
PubMed Central
Google Scholar