Table S1. Summary table of N. ceranae and N. apis prevalence from studies conducted across several years and countries. Prevalence varies considerably across space and time, though absolute estimates probably depend to some extent on methods of detection employed (efficiency of DNA/RNA extraction, PCR primers employed), sample size (number of workers per colony analysed) and when they were collected during the flight season. Country Spain Spain Spain Spain Spain Montane Spain supra-mediterranean Spain Colline Spain Meso-mediterranean Spain Termo-mediterranean Spain Andalusia Spain Andalusia Spain Catalonia Spain Catalonia Spain Valencia Spain Valencia Spain Andalusia Spain Spain (Canary Islands) Spain (Canary Islands) Spain (Canary Islands) Spain (Canary Islands) Spain Spain N. ceranae prevalence (%) 46 43 47 44 35 38 42 56 57 29 65 7 22 27 47 95 67 0 36 32 49 50 70 N. apis prevalence (%) 15 10 8 11 16 17 3 10 6 10 8 7 0 24 12 19 21 0 0 0 0 14 13 Source [1] [1] [1] [1] [1] [1] [1] [1] [1] [2] [2] [2] [2] [2] [2] [3] [3] [4] [4] [4] [4] [5] [5] No colonies screened 629 454 526 329 301 454 191 492 256 80 80 30 9 34 17 446 604 18 44 44 45 113 115 Year 2006spring 2006autumn 2007spring 2007autumn 2006/07 2006/07 2006/07 2006/07 2006/07 2002 2007 2002 2007 2002 2007 2006/07 2007 1998 2008 2010 2011 2006 2010 Scotland 78 73 Germany 7 20 Germany 10 24 Germany 19 12 Germany 19 27 Germany 16 22 Germany 5 8 Germany 2 8 Germany 2 5 Germany 2 3 Sweden 3 33 Lithuania 64 68 a Balkans 84 <1a Florida/California 60 20 a Average across Serbia, Bosnia and Herzegovina, Montenegro and FYROM [6] [7] [7] [7] [7] [7] [7] [7] [7] [7] [8] [9] [10] [11] 71 220 238 228 209 210 237 226 219 210 967 129 325 76 2011 2005spring 2006spring 2007spring 2008spring 2009spring 2005 autumn 2006autumn 2007autumn 2008autumn 2007 2011 2002/09 2007 References 1. Martín-Hernández R, Botías C, Bailón EG, Martínez-Salvador A, Prieto L, Meana A, Higes M. 2012 Microsporidia infecting Apis mellifera: coexistence or competition. Is Nosema ceranae replacing Nosema apis? Environ. Microbiol. 14, 2127–38. (doi:10.1111/j.14622920.2011.02645.x) 2. Botías C, Martín-Hernández R, Garrido-Bailón E, González-Porto A, Martínez-Salvador A, De la Rúa P, Meana A, Higes M. 2012 The growing prevalence of Nosema ceranae in honey bees in Spain, an emerging problem for the last decade. Res. Vet. Sci. 93, 150–5. (doi:10.1016/j.rvsc.2011.08.002) 3. Fernández JM, Puerta F, Cousinou M, Dios-Palomares R, Campano F, Redondo L. 2012 Asymptomatic presence of Nosema spp. in Spanish commercial apiaries. J. Invertebr. Pathol. 111, 106–10. (doi:10.1016/j.jip.2012.06.008) 4. Muñoz I, Cepero A, Pinto MA, Martín-Hernández R, Higes M, De la Rúa P. 2014 Presence of Nosema ceranae associated with honeybee queen introductions. Infect. Genet. Evol. 23, 161–8. (doi:10.1016/j.meegid.2014.02.008) 5. Jara L, Cepero A, Garrido-Bailón E, Martín-Hernández R, Higes M, De la Rúa P. 2012 Linking evolutionary lineage with parasite and pathogen prevalence in the Iberian honey bee. J. Invertebr. Pathol. 110, 8–13. (doi:10.1016/j.jip.2012.01.007) 6. Bollan KA, Hothersall JD, Moffat C, Durkacz J, Saranzewa N, Wright GA, Raine NE, Highet F, Connolly CN. 2013 The microsporidian parasites Nosema ceranae and Nosema apis are widespread in honeybee (Apis mellifera) colonies across Scotland. Parasitol. Res. 112, 751–9. (doi:10.1007/s00436-012-3195-0) 7. Gisder S, Hedtke K, Möckel N, Frielitz MC, Linde A, Genersch E. 2010 Five-year cohort study of Nosema spp. in Germany: does climate shape virulence and assertiveness of Nosema ceranae? Appl. Environ. Microbiol. 76, 3032–3038. (doi:10.1128/aem.03097-09) 8. Forsgren E, Fries I. 2013 Temporal study of Nosema spp. in a cold climate. Environ. Microbiol. Rep. 5, 78–82. (doi:10.1111/j.17582229.2012.00386.x) 9. Blažytė-Čereškienė L, Skrodenytė-Arbačiauskienė V, Būda V. 2014 Microsporidian parasites of honey bees Nosema ceranae and N. apis in Lithuania: supplementary data on occurrence along Europe. J. Apic. Res. 53, 374–376. (doi:10.3896/IBRA.1.53.3.04) 10. Stevanovic J, Stanimirovic Z, Genersch E, Kovacevic SR, Ljubenkovic J, Radakovic M, Aleksic N. 2011 Dominance of Nosema ceranae in honey bees in the Balkan countries in the absence of symptoms of colony collapse disorder. Apidologie 42, 49–58. (doi:10.1051/apido/2010034) 11. Vanengelsdorp D, et al. 2009 Colony collapse disorder: a descriptive study. PLoS One 4, e6481. (doi:10.1371/journal.pone.0006481)