Woolhouse MEJ, Gowtage-Sequeria S. Host vary and rising and reemerging pathogens. Emerg Infect Dis. 2005;11:1842–7.
Google Scholar
Allen T, Murray KA, Zambrana-Torrelio C, Morse SS, Rondinini C, Di Marco M, et al. International hotspots and correlates of rising zoonotic illnesses. Nat Commun. 2017;8:1–10.
Google Scholar
Van Kerkhove MD, Ly S, Holl D, Guitian J, Mangtani P, Ghani AC, et al. Frequency and patterns of contact with home poultry and potential danger of H5N1 transmission to people residing in rural Cambodia. Influenza Different Respir Viruses. 2008;2:155–63.
Google Scholar
Gaythorpe KAM, Hamlet A, Cibrelus L, Garske T, Ferguson NM. The impact of local weather change on yellow fever illness burden in Africa. eLife. 2020;9:1–27.
Faust CL, McCallum HI, Bloomfield LSP, Gottdenker NL, Gillespie TR, Torney CJ, et al. Pathogen spillover throughout land conversion. Ecol Lett. 2018;21:471–83.
Google Scholar
Gog J, Woodroffe R, Swinton J. Illness in endangered metapopulations: The significance of other hosts. Proc R Soc B Biol Sci. 2002;269:671–6.
Jones BA, Grace D, Kock R, Alonso S, Rushton J, Mentioned MY, et al. Zoonosis emergence linked to agricultural intensification and environmental change. Proc Natl Acad Sci USA. 2013;110:8399–404.
Google Scholar
White LA, Forester JD, Craft ME. Illness outbreak thresholds emerge from interactions between motion habits, panorama construction, and epidemiology. Proc Natl Acad Sci USA. 2018;115:7374–9.
Google Scholar
Altizer S, Bartel R, Han BA. Animal migration and infectious illness danger. Science. 2011;331:296–302.
Google Scholar
Ludwig SC, Roos S, Bubb D, Baines D. Lengthy-term developments in abundance and breeding success of purple grouse and hen harriers in relation to altering administration of a Scottish grouse moor. Wildl Biol. 2017;2017:wlb.00246.
Newton I. Climate-related mass-mortality occasions in migrants. Ibis. 2007;149:453–67.
Ropert-Coudert Y, Kato A, Meyer X, Pellé M, MacIntosh AJJ, Angelier F, et al. A whole breeding failure in an Adélie penguin colony correlates with uncommon and excessive environmental occasions. Ecography. 2015;38:111–3.
Newmark WD, Stanley TR. Habitat fragmentation reduces nest survival in an Afrotropical chicken group in a biodiversity hotspot. Proc Natl Acad Sci USA. 2011;108:11488–93.
Google Scholar
Tuyttens FaM, Macdonald DW, Rogers LM, Cheeseman CL, Roddam AW. Comparative examine on the implications of culling badgers (Meles meles) on biometrics, inhabitants dynamics and motion. J Anim Ecol. 2000;69:567–80.
Frafjord Okay. Affect of reproductive standing: House vary dimension in water voles (Arvicola amphibius). PLoS ONE. 2016;11:1–13.
Begg CM, Begg KS, Du Toit JT, Mills MGL. Spatial group of the honey badger Mellivora capensis within the southern Kalahari: House-range dimension and motion patterns. J Zool. 2005;265:23–35.
Bronikowski AM, Cords M, Alberts SC, Altmann J, Brockman DK, Fedigan LM, et al. Feminine and male life tables for seven wild primate species. Sci Knowledge. 2016;3:1–8.
Mitchell GW, Woodworth BK, Taylor PD, Norris DR. Automated telemetry reveals age particular variations in flight period and pace are pushed by wind situations in a migratory songbird. Mov Ecol. 2015;3:1–13.
Frankish CK, Manica A, Phillips RA. Results of age on foraging habits in two carefully associated albatross species. Mov Ecol. 2020;8:1–17.
Tirpak JM, Giuliano WM, Allen TJ, Bittner S, Edwards JW, Friedhof S, et al. Ruffed grouse-habitat choice within the central and southern Appalachians. Ecol Manag. 2010;260:1525–38.
Zhu WW, Garber PA, Bezanson M, Qi XG, Li BG. Age- and sex-based patterns of positional habits and substrate utilization within the golden snub-nosed monkey (Rhinopithecus roxellana). Am J Primatol. 2015;77:98–108.
Google Scholar
Tian H, Yu P, Bjørnstad ON, Cazelles B, Yang J, Tan H, et al. Anthropogenically pushed environmental adjustments shift the ecological dynamics of hemorrhagic fever with renal syndrome. PLOS Pathog. 2017;13:e1006198.
Google Scholar
George DB, Webb CT, Farnsworth ML, O’Shea TJ, Bowen RA, Smith DL, et al. Host and viral ecology decide bat rabies seasonality and upkeep. Proc Natl Acad Sci USA. 2011;108:10208–13.
Google Scholar
van Dijk JG, Verhagen JH, Wille M, Waldenström J. Host and virus ecology as determinants of influenza A virus transmission in wild birds. Curr Opin Virol. 2018;28:26–36.
Google Scholar
Chong R, Shi M, Grueber CE, Holmes EC, Hogg CJ, Belov Okay, et al. Fecal Viral Range of Captive and Wild Tasmanian Devils Characterised Utilizing Virion-Enriched Metagenomics and Metatranscriptomics. J Virol. 2019;93:e00205–19.
Google Scholar
François S, Pybus OG. In the direction of an understanding of the avian virome. J Gen Virol. 2020;101:785–90.
Google Scholar
Springer A, Fichtel C, Al-Ghalith GA, Koch F, Amato KR, Clayton JB, et al. Patterns of seasonality and group membership characterize the intestine microbiota in a longitudinal examine of untamed Verreaux’s sifakas (Propithecus verreauxi). Ecol Evol. 2017;7:5732–45.
Google Scholar
Aivelo T, Laakkonen J, Jernvall J. Inhabitants-and individual-level dynamics of the intestinal microbiota of a small primate. Appl Environ Microbiol. 2016;82:3537–45.
Google Scholar
van Dongen WFD, White J, Brandl HB, Moodley Y, Merkling T, Leclaire S, et al. Age-related variations within the cloacal microbiota of a wild chicken species. BMC Ecol. 2013;13:11.
Cleaveland S, Laurenson MK, Taylor LH. Ailments of people and their home mammals: Pathogen traits, host vary and the danger of emergence. Philos Trans R Soc B Biol Sci. 2001;356:991–9.
Google Scholar
Wille M, Shi M, Damage AC, Klaassen M, Holmes EC. RNA virome abundance and variety is related to host age in a chicken species. Virology. 2021;561:98–106.
Google Scholar
Negrey JD, Thompson ME, Langergraber KE, Machanda ZP, Mitani JC, Muller MN, et al. Demography, life-history trade-offs, and the gastrointestinal virome of untamed chimpanzees. Philos Trans R Soc B Biol Sci. 2020;375:20190613.
Hill SC, Manvell RJ, Schulenburg B, Shell W, Wikramaratna PS, Perrins C, et al. Antibody responses to avian influenza viruses in wild birds broaden with age. Proc R Soc B Biol Sci. 2016;283:20162159.
Perrins CM, Ogilvie MA. A examine of the Abbotsbury mute swans (Cygnus olor). Wildfowl. 1981;32:35–47.
Perrins CM, McCleery RH, Ogilvie MA. A examine of the breeding Mute Swans Cygnus olor at Abbotsbury. Wildfowl. 1994;45:1–14.
Perrins C. Survival charges of younger mute swans Cygnus olor. Wildfowl Suppl. 1991;45:95–103.
McCleery RH, Perrins C, Wheeler D, Groves S. Inhabitants construction, survival charges and productiveness of mute swans breeding in a colony at Abbotsbury, Dorset, England. Waterbirds Waterbird Soc. 2002;25:201.
Matrozis R A 30-year (1988–2017) examine of Mute Swans Cygnus olor in Riga, Latvia. Wildfowl. 2019;14:164–77.
Charmantier A, Perrins C, McCleery RH, Sheldon BC. Quantitative genetics of age at replica in wild swans: Assist for antagonistic pleiotropy fashions of senescence. Proc Natl Acad Sci USA. 2006;103:6587–92.
Google Scholar
Hill SC, Hansen R, Watson S, Coward V, Russell C, Cooper J, et al. Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild chicken inhabitants. Philos Trans R Soc B Biol Sci. 2019;374:20180259.
Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P, et al. Full genome virus detection in fecal samples utilizing delicate nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm. PLoS ONE. 2014;9:e93269.
Google Scholar
Growth R, Sol CJA, Salimans MMM, Janses CL, Wertheim Van Dillen PME, Van Der Noordaa J. Speedy and easy methodology for purification of nucleic acids R. J Clin Microbiol. 1990;28:495–503.
Google Scholar
Endoh D, Mizutani T, Kirisawa R, Maki Y, Saito H, Kon Y, et al. Species-independent detection of RNA virus by representational distinction evaluation utilizing non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res. 2005;33:1–11.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMB. 2011;17:10–12.
Zerbino DR, Birney E. Velvet: algorithms for de novo quick learn meeting utilizing de Bruijn graphs. Genome Res. 2008;18:821–9.
Google Scholar
Buchfink B, Xie C, Huson DH. Quick and delicate protein alignment utilizing DIAMOND. Nat Strategies. 2014;12:59–60.
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Primary native alignment search instrument. J Mol Biol. 1990;215:403–10.
Google Scholar
Langmead B Aligning quick sequencing reads with Bowtie. Curr Protoc Bioinforma. 2010; Chapter 11: Unit 11.7.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Primary: an built-in and extendable desktop software program platform for the group and evaluation of sequence information. Bioinforma Oxf Engl. 2012;28:1647–9.
Katoh Okay, Misawa Okay, Kuma Okay, Miyata T. MAFFT: a novel methodology for speedy a number of sequence alignment based mostly on quick Fourier rework. Nucleic Acids Res. 2002;30:3059–66.
Google Scholar
Katoh Okay, Standley DM. MAFFT a number of sequence alignment software program model 7: Enhancements in efficiency and usefulness. Mol Biol Evol. 2013;30:772–80.
Google Scholar
Edgar RC. MUSCLE: a number of sequence alignment with excessive accuracy and excessive throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Muhire BM, Varsani A, Martin DP SDT: A virus classification instrument based mostly on pairwise sequence alignment and identification calculation. PLoS ONE. 2014;9:e108277.
Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: quick number of best-fit fashions of protein evolution. Bioinforma Oxf Engl. 2011;27:1164–5.
Google Scholar
Stamatakis A. RAxML model 8: A instrument for phylogenetic evaluation and post-analysis of enormous phylogenies. Bioinformatics. 2014;30:1312–3.
Google Scholar
Kapoor A, Simmonds P, Lipkin WI, Zaidi S, Delwart E. Use of nucleotide composition evaluation to deduce hosts for 3 novel picorna-like viruses. J Virol. 2010;84:10322–8.
Google Scholar
Wooden DE, Salzberg SL Kraken: Ultrafast metagenomic sequence classification utilizing precise alignments. Genome Biol. 2014;15:R46.
Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: estimating species abundance in metagenomics information. PeerJ Comput Sci. 2017;3:e104.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Solar Y, et al. Ribosomal Database Venture: Knowledge and instruments for top throughput rRNA evaluation. Nucleic Acids Res. 2014;42:633–42.
R Core Crew. R: A Language and Surroundings for Statistical Computing. 2019. R Basis for Statistical Computing, Vienna, Austria.
RStudio Crew. RStudio: Built-in Improvement for R. 2015. Boston, MA, USA.
Dixon P. VEGAN, a bundle of R features for group ecology. J Veg Sci. 2003;14:927–30.
Anderson MJ. A brand new methodology for non-parametric multivariate evaluation of variance. Austral Ecol. 2001;26:32–46.
Benjamini Y, Hochberg Y. Controlling the false discovery charge: a sensible and highly effective strategy to a number of testing. J R Stat Soc Ser B Methodol. 1995;57:289–300.
Benjamini Y, Yekutieli D. The management of the false discovery charge in a number of testing below dependency. Ann Stat. 2001;29:1165–88.
Oakley BB, Lillehoj HS, Kogut MH, Kim WK, Maurer JJ, Pedroso A, et al. The rooster gastrointestinal microbiome. FEMS Microbiol Lett. 2014;360:100–12.
Google Scholar
Waite DW, Taylor MW. Characterizing the avian intestine microbiota: Membership, driving influences, and potential perform. Entrance Microbiol. 2014;5:1–12.
Waite DW, Taylor MW. Exploring the avian intestine microbiota: Present developments and future instructions. Entrance Microbiol. 2015;6:1–12.
Zell R, Delwart E, Gorbalenya AE, Hovi T, King AMQ, Knowles NJ, et al. ICTV virus taxonomy profile: Picornaviridae. J Gen Virol. 2017;98:2421–2.
Google Scholar
Cotmore SF, Agbandje-McKenna M, Canuti M, Chiorini JA, Eis-Hubinger AM, Hughes J, et al. ICTV virus taxonomy profile: Parvoviridae. J Gen Virol. 2019;100:367–8.
Google Scholar
Bosch A, Guix S, Krishna N, Méndez E, Monroe SS, Pantin-Jackwood M, et al. Astroviridae. In: King A, Adams M, Carstens E, Lefkowitz E (eds). Virus taxonomy. Classification and nomenclature of viruses: ninth report of the Worldwide Committee on the Taxonomy of Viruses. 2011. Elsevier, London, pp 953-9.
Risely A. Making use of the core microbiome to grasp host–microbe techniques. J Anim Ecol. 2020;89:1549–58.
Google Scholar
Piepenbring AK, Enderlein D, Herzog S, Kaleta EF, Heffels-Redmann U, Ressmeyer S, et al. Pathogenesis of avian bornavirus in experimentally contaminated Cockatiels. Emerg Infect Dis. 2012;18:234–41.
Google Scholar
Anzil AP, Blinzinger Okay, Mayr A. Persistent Borna virus an infection in grownup hamsters. Arch Für Gesamt Virusforsch. 1973;40:52–57.
Google Scholar
Heffels-Redmann U, Enderlein D, Herzog S, Piepenbring A, Bürkle M, Neumann D, et al. Observe-Up Investigations on Totally different Programs of Pure Avian Bornavirus Infections in Psittacines. Avian Dis. 2012;56:153–9.
Google Scholar
Rubbenstroth D, Brosinski Okay, Rinder M, Olbert M, Kaspers B, Korbel R, et al. No contact transmission of avian bornavirus in experimentally contaminated cockatiels (Nymphicus hollandicus) and home canaries (Serinus canaria forma domestica). Vet Microbiol. 2014;172:146–56.
Google Scholar
Olsen I The Household Fusobacteriaceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Firmicutes and Tenericutes, 4th ed. 2014. pp 109-32.
Imhoff JF The Household Chlorobiaceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Different Main Lineages of Micro organism and The Archaea, 4th ed. 2014. pp 501-14.
Cho JC The Household Lentisphaeraceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Different Main Lineages of Micro organism and The Archaea, 4th ed. 2014. pp 705-10.
Karami A, Sarshar M, Ranjbar R, Zanjani RS The Phylum Spirochaetaceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Different Main Lineages of Micro organism and The Archaea, 4th ed. 2014. pp 915-29.
McBride MJ The Household Flavobacteriaceae. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds). The Prokaryotes: Different Main Lineages of Micro organism and The Archaea, 4th ed. 2014. pp 643-76.
Van Dijk JGB, Hoye BJ, Verhagen JH, Nolet BA, Fouchier RAM, Klaassen M. Juveniles and migrants as drivers for seasonal epizootics of avian influenza virus. J Anim Ecol. 2014;83:266–75.
Google Scholar
Chevalier V, Marsot M, Molia S, Rasamoelina H, Rakotondravao R, Pedrono M, et al. Serological proof of West Nile and Usutu viruses circulation in home and wild birds in wetlands of Mali and Madagascar in 2008. Int J Environ Res Public Well being. 2020;17:1998.
Man, JS Turkey Viral Hepatitis. Ailments of Poultry, twelfth Version. 2008. Wiley Blackwell, pp 426-30.
Davies ZG, Fuller RA, Dallimer M, Loram A, Gaston KJ. Family components influencing participation in chicken feeding exercise: a nationwide scale evaluation. PLOS ONE. 2012;7:e39692.
Google Scholar
Shutt JD, Trivedi UH, Nicholls JA. Faecal metabarcoding reveals pervasive long-distance impacts of backyard chicken feeding. Proc R Soc B Biol Sci. 2021;288:20210480.
Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. Quantifying and understanding well-to-well contamination in microbiome analysis. mSystems. 2019;4:e00186–19.
Google Scholar
