References
Almasi, B., Béziers, P., Roulin, A., & Jenni, L. (2015). Agricultural land use and human presence around breeding sites increase stress-hormone levels and decrease body mass in barn owl nestlings.Oecologia , 179(1), 89-101. https://doi.org/10.1007/s00442-015-3318-2
Andreasen, C., Jensen, H. A., & Jensen, S. M. (2018). Decreasing diversity in the soil seed bank after 50 years in Danish arable fields.Agriculture, Ecosystems & Environment , 259, 61-71. https://doi.org/10.1016/j.agee.2018.02.034
Andújar, C., Arribas, P., Yu, D. W., Vogler, A. P., & Emerson, B. C. (2018). Why the COI barcode should be the community DNA metabarcode for the metazoa. Molecular Ecology, 27(20), 3968-3975. https://doi.org/10.1111/mec.14844
Bass, D., Stentiford, G. D., Littlewood, D. T. J., & Hartikainen, H. (2015). Diverse applications of environmental DNA methods in parasitology. Trends in parasitology31 (10), 499-513. https://doi.org/10.1016/j.pt.2015.06.013
Benton, T. G., Bryant, D. M., Cole, L., & Crick, H. Q. (2002). Linking agricultural practice to insect and bird populations: a historical study over three decades. Journal of Applied Ecology, 39(4), 673-687. https://doi.org/10.1046/j.1365-2664.2002.00745.x
Benton, T. G., Vickery, J. A., & Wilson, J. D. (2003). Farmland biodiversity: is habitat heterogeneity the key?. Trends in ecology & evolution , 18(4), 182-188. https://doi.org/10.1016/S0169-5347(03)00011-9
Bohmann, K., Evans, A., Gilbert, M. T. P., Carvalho, G. R., Creer, S., Knapp, M., … & De Bruyn, M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. Trends in ecology & evolution , 29(6), 358-367. https://doi.org/10.1016/j.tree.2014.04.003
Bowler, D. E., Heldbjerg, H., Fox, A. D., de Jong, M., & Böhning‐Gaese, K. (2019). Long‐term declines of European insectivorous bird populations and potential causes. Conservation Biology , 33(5), 1120-1130. https://doi.org/10.1111/cobi.13307
Browne, S. J., Aebischer, N. J., Moreby, S. J., & Teague, L. (2006). The diet and disease susceptibility of grey partridges Perdix perdix on arable farmland in East Anglia, England. Wildlife Biology , 12(1), 3-10. https://doi.org/10.2981/0909-6396(2006)12[3:TDADSO]2.0.CO;2
Bravo, C., Cuscó, F., Morales, M., & Mañosa, S. (2017). Diet composition of a declining steppe bird the Little Bustard (Tetrax tetrax ) in relation to farming practices. Avian Conservation and Ecology , 12(1). https://doi.org/10.5751/ACE-00938-120103
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., & Coissac, E. (2016). obitools: A unix‐inspired software package for DNA metabarcoding. Molecular ecology resources , 16(1), 176-182. https://doi.org/10.1111/1755-0998.12428
Cabodevilla, X., Aebischer, J. N., Mougeot, F., Morales, M. B. & Arroyo, B. (2020). Are population changes of endangered little bustards associated with releases of red-legged partridges for hunting? A large-scale study from central Spain. European Journal of Wildlife Research , 66(2), 1-10. https://doi.org/10.1007/s10344-020-1366-3
Clarke, L. J., Soubrier, J., Weyrich, L. S., & Cooper, A. (2014). Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Molecular ecology resources , 14(6), 1160-1170. https://doi.org/10.1111/1755-0998.12265
Chamberlain, D. E., Fuller, R. J., Bunce, R. G., Duckworth, J. C., & Shrubb, M. (2000). Changes in the abundance of farmland birds in relation to the timing of agricultural intensification in England and Wales. Journal of applied ecology , 37(5), 771-788. https://doi.org/10.1046/j.1365-2664.2000.00548.x
Chapman, C. A., Wasserman, M. D., Gillespie, T. R., Speirs, M. L., Lawes, M. J., Saj, T. L., & Ziegler, T. E. (2006). Do food availability, parasitism, and stress have synergistic effects on red colobus populations living in forest fragments? American Journal of Physical Anthropology , 131(4), 525-534. https://doi.org/10.1002/ajpa.20477
Cheng, T., Xu, C., Lei, L., Li, C., Zhang, Y., & Zhou, S. (2016). Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Molecular Ecology Resources16 (1), 138-149. https://doi.org/10.1111/1755-0998.12438
Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., … & Tiedje, J. M. (2014). Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic acids research , 42(D1), D633-D642. https://doi.org/10.1093/nar/gkt1244
Coop, R. L., & Holmes, P. H. (1996). Nutrition and parasite interaction. International journal for parasitology , 26(8-9), 951-962. https://doi.org/10.1016/S0020-7519(96)80070-1
Deagle, B. E., Eveson, J. P., & Jarman, S. N. (2006). Quantification of damage in DNA recovered from highly degraded samples–a case study on DNA in faeces. Frontiers in zoology , 3(1), 11. https://doi.org/10.1186/1742-9994-3-11
Deagle, B. E., Gales, N. J., Evans, K., Jarman, S. N., Robinson, S., Trebilco, R., & Hindell, M. A. (2007). Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLoS One , 2(9), e831. https://doi.org/10.1371/journal.pone.0000831
Djurhuus, A., Closek, C. J., Kelly, R. P., Pitz, K. J., Michisaki, R. P., Starks, H. A., … & Montes, E. (2020). Environmental DNA reveals seasonal shifts and potential interactions in a marine community.Nature Communications , 11(1), 1-9. https://doi.org/10.1038/s41467-019-14105-1
Dunn, J. C., Goodman, S. J., Benton, T. G., & Hamer, K. C. (2014). Active blood parasite infection is not limited to the breeding season in a declining farmland bird. Journal of Parasitology , 100(3), 260-266. https://doi.org/10.1645/13-256.1
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics , 26(19), 2460-2461. https://doi.org/10.1093/bioinformatics/btq461
Edgar, R. (2018). Taxonomy annotation and guide tree errors in 16S rRNA databases. PeerJ6 , e5030. https://doi.org/10.7717/peerj.5030
Eng, M. L., Stutchbury, B. J., & Morrissey, C. A. (2019). A neonicotinoid insecticide reduces fueling and delays migration in songbirds. Science , 365(6458), 1177-1180. https://doi.org/10.1126/science.aaw9419
Epp, L. S., Boessenkool, S., Bellemain, E. P., Haile, J., Esposito, A., Riaz, T., … & Stenøien, H. K. (2012). New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular ecology , 21(8), 1821-1833. https://doi.org/10.1111/j.1365-294X.2012.05537.x
Evans, N. T., Olds, B. P., Renshaw, M. A., Turner, C. R., Li, Y., Jerde, C. L., … & Lodge, D. M. (2016). Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources16 (1), 29-41. https://doi.org/10.1111/1755-0998.12433
Faria, N., Rabaça, J. E., & Morales, M. B. (2012). Linking plant composition and arthropod abundance to establish little bustard breeding requirements in pastureland dominated landscapes. Biodiversity and Conservation , 21(8), 2109-2125. https://doi.org/10.1007/s10531-012-0300-8
Ficetola, G. F., Coissac, E., Zundel, S., Riaz, T., Shehzad, W., Bessière, J., … & Pompanon, F. (2010). An in silico approach for the evaluation of DNA barcodes. BMC genomics , 11(1), 434. https://doi.org/10.1186/1471-2164-11-434
Fonderflick, J., Besnard, A., Chardès, M. C., Lanuzel, L., Thill, C., & Pointereau, P. (2020). Impacts of agricultural intensification on arable plants in extensive mixed crop-livestock systems. Agriculture, Ecosystems & Environment , 290, 106778. https://doi.org/10.1016/j.agee.2019.106778
Greige, S., El Safadi, D., Bécu, N., Gantois, N., Pereira, B., Chabé, M., … & Viscogliosi, E. (2018). Prevalence and subtype distribution of Blastocystis sp. isolates from poultry in Lebanon and evidence of zoonotic potential. Parasites & vectors , 11(1), 389. https://doi.org/10.1186/s13071-018-2975-5
Hadziavdic, K., Lekang, K., Lanzen, A., Jonassen, I., Thompson, E. M., & Troedsson, C. (2014). Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PloS one , 9(2), e87624. https://doi.org/10.1371/journal.pone.0087624
Hajibabaei, M., Smith, M. A., Janzen, D. H., Rodriguez, J. J., Whitfield, J. B., & Hebert, P. D. (2006). A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes , 6(4), 959-964. https://doi.org/10.1111/j.1471-8286.2006.01470.x
Hajibabaei, M., Singer, G. A., Hebert, P. D., & Hickey, D. A. (2007). DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. TRENDS in Genetics , 23(4), 167-172. https://doi.org/10.1016/j.tig.2007.02.001
Hoi-Leitner, M., Romero-Pujante, M., Hoi, H., & Pavlova, A. (2001). Food availability and immune capacity in serin (Serinus serinus ) nestlings. Behavioral Ecology and Sociobiology , 49(5), 333-339. https://doi.org/10.1007/s002650000310
Holland, J. M., Hutchison, M. A. S., Smith, B., & Aebischer, N. J. (2006). A review of invertebrates and seed‐bearing plants as food for farmland birds in Europe. Annals of Applied Biology , 148(1), 49-71. https://doi.org/10.1111/j.1744-7348.2006.00039.x
Holland, J. M., Smith, B. M., Birkett, T. C., & Southway, S. (2012). Farmland bird invertebrate food provision in arable crops. Annals of Applied Biology , 160(1), 66-75. https://doi.org/10.1111/j.1744-7348.2011.00521.x
Jetz, W., Wilcove, D. S., & Dobson, A. P. (2007). Projected impacts of climate and land-use change on the global diversity of birds. PLoS biology , 5(6). https://doi.org/10.1371/journal.pbio.0050157
Jiguet, F. (2002). Arthropods in diet of Little Bustards Tetrax tetrax during the breeding season in western France. Bird Study , 49(2), 105-109. https://doi.org/10.1080/00063650209461253
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., … & Thierer, T. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics , 28(12), 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
Kerley, G. I., Landman, M., Ficetola, G. F., Boyer, F., Bonin, A., Rioux, D., Taberlet, P., & Coissac, E. (2018). Diet shifts by adult flightless dung beetles Circellium bacchus , revealed using DNA metabarcoding, reflect complex life histories. Oecologia188 (1), 107-115. https://doi.org/10.1007/s00442-018-4203-6
Kitaysky, A. S., Wingfield, J. C., & Piatt, J. F. (1999). Dynamics of food availability, body condition and physiological stress response in breeding black‐legged kittiwakes. Functional Ecology , 13(5), 577-584. https://doi.org/10.1046/j.1365-2435.1999.00352.x
Kitaysky, A. S., Piatt, J. F., & Wingfield, J. C. (2007). Stress hormones link food availability and population processes in seabirds.Marine Ecology Progress Series , 352, 245-258. https://doi.org/10.3354/meps07074
Korschgen, C. E., Gibbs, H. C., & Mendall, H. L. (1978). Avian cholera in eider ducks in Maine. Journal of Wildlife Diseases , 14(2), 254-258. https://doi.org/10.7589/0090-3558-14.2.254
Krehenwinkel, H., Kennedy, S. R., Rueda, A., Lam, A., & Gillespie, R. G. (2018). Scaling up DNA barcoding–Primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing. Methods Ecology Evolution9 (11), 2181-2193. https://doi.org/10.1111/2041-210X.13064
Lafferty, K. D. (1997). Environmental parasitology: what can parasites tell us about human impacts on the environment?. Parasitology today , 13(7), 251-255. https://doi.org/10.1016/S0169-4758(97)01072-7
Lamb, P. D., Hunter, E., Pinnegar, J. K., Creer, S., Davies, R. G., & Taylor, M. I. (2019). How quantitative is metabarcoding: A meta‐analytical approach. Molecular ecology , 28(2), 420-430. https://doi.org/10.1111/mec.14920
Lantz, P. G., Matsson, M., Wadström, T., & Rådström, P. (1997). Removal of PCR inhibitors from human faecal samples through the use of an aqueous two-phase system for sample preparation prior to PCR.Journal of Microbiological Methods , 28(3), 159-167. https://doi.org/10.1016/S0167-7012(97)00979-2
Lopez-Antia, A., Ortiz-Santaliestra, M. E., Mougeot, F., & Mateo, R. (2015). Imidacloprid-treated seed ingestion has lethal effect on adult partridges and reduces both breeding investment and offspring immunity.Environmental research , 136, 97-107. https://doi.org/10.1016/j.envres.2014.10.023
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal , 17(1), 10-12. https://doi.org/10.14806/ej.17.1.200
Matson, P. A., Parton, W. J., Power, A. G., & Swift, M. J. (1997). Agricultural intensification and ecosystem properties. Science , 277(5325), 504-509. https://doi.org/10.1126/science.277.5325.504
Meyer, W. B., & Turner, B. L. (1992). Human population growth and global land-use/cover change. Annual review of ecology and systematics , 23(1), 39-61. https://doi.org/10.1146/annurev.es.23.110192.000351
Millot, F., Decors, A., Mastain, O., Quintaine, T., Berny, P., Vey, D., … & Bro, E. (2017). Field evidence of bird poisonings by imidacloprid-treated seeds: a review of incidents reported by the French SAGIR network from 1995 to 2014. Environmental Science and Pollution Research , 24(6), 5469-5485. https://doi.org/10.1007/s11356-016-8272-y
Moreby, S. J. (1988). An aid to the identification of arthropod fragments in the faeces of gamebird chicks (Galliformes). Ibis , 130(6), 519-526. https://doi.org/10.1111/j.1474-919X.1988.tb02717.x
Murray, D. L., Keith, L. B., & Cary, J. R. (1998). Do parasitism and nutritional status interact to affect production in snowshoe hares?.Ecology , 79(4), 1209-1222. https://doi.org/10.1890/0012-9658(1998)079[1209:DPANSI]2.0.CO;2
Newton, I. (1998). Bird conservation problems resulting from agricultural intensification in Europe. Avian conservation: research and management . Island Press, Washington, DC, 307-322.
Newton, I. (2004). The recent declines of farmland bird populations in Britain: an appraisal of causal factors and conservation actions.Ibis , 146(4), 579-600. https://doi.org/10.1111/j.1474-919X.2004.00375.x
Nordling, D., Andersson, M., Zohari, S., & Lars, G. (1998). Reproductive effort reduces specific immune response and parasite resistance. Proceedings of the Royal Society B: Biological Sciences , 265(1403), 1291-1298. https://doi.org/10.1098/rspb.1998.0432
Okulewicz, A., & Sitko, J. (2012). Parasitic helminthes—probable cause of death of birds. Helminthologia , 49(4), 241-246. https://doi.org/10.2478/s11687-012-0045-7
Pain, D. J., & Pienkowski, M. W. (1997). Farming and birds in Europe: the Common Agricultural Policy and its implications for bird conservation . Academic Press.
Pigeon, G., Baeta, R., Bélisle, M., Garant, D., & Pelletier, F. (2013). Effects of agricultural intensification and temperature on immune response to phytohemagglutinin in Tree Swallows (Tachycineta bicolor ). Canadian journal of zoology , 91(2), 56-63. https://doi.org/10.1139/cjz-2012-0176
Pimm, S. L., Russell, G. J., Gittleman, J. L., & Brooks, T. M. (1995). The future of biodiversity. Science , 269(5222), 347-349. https://doi.org/10.1126/science.269.5222.347
Piñol, J., Senar, M. A., & Symondson, W. O. (2019). The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative. Molecular ecology , 28(2), 407-419. https://doi.org/10.1111/mec.14776
Pompanon, F., Deagle, B. E., Symondson, W. O., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: diet assessment using next generation sequencing. Molecular ecology , 21(8), 1931-1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Presswell, B., & Lagrue, C. (2016). Assessing parasite infections from avian faecal samples: the old methods are still the best.Notornis , 63, 32-36.
Prosser, P., & Hart, A. D. M. (2005). Assessing potential exposure of birds to pesticide-treated seeds. Ecotoxicology , 14(7), 679-691. https://doi.org/10.1007/s10646-005-0018-4
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., … & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research , 41(D1), D590-D596. https://doi.org/10.1093/nar/gks1219
Prosser, S. W., Velarde‐Aguilar, M. G., León‐Règagnon, V., & Hebert, P. D. (2013). Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes.Molecular Ecology Resources13 (6), 1108-1115. https://doi.org/10.1111/1755-0998.12082
Rådström, P., Knutsson, R., Wolffs, P., Lövenklev, M., & Löfström, C. (2004). Pre-PCR processing. Molecular biotechnology , 26(2), 133-146. https://doi.org/10.1385/MB:26:2:133
R Core Team (2019) R: A language and environment for statistical computing . Vienna, Austria: R Foundation for Statistical Computing. URL https://www.Rproject.org/
Rengifo-Herrera, C., Ferre, I., Ortega-Mora, L. M., Rojo-Montejo, S., García-Moreno, F. T., García-Párraga, D., … & Pedraza-Díaz, S. (2014). Helminth parasites found in faecal samples of phocids from the Antarctic Peninsula. Polar biology , 37(5), 685-695. https://doi.org/10.1007/s00300-014-1469-y
Salamolard, M., & Moreau, C. (1999). Habitat selection by Little Bustard Tetrax tetrax in a cultivated area of France. Bird Study , 46(1), 25-33. https://doi.org/10.1080/00063659909461112
Santoro, M., Tripepi, M., Kinsella, J. M., Panebianco, A., & Mattiucci, S. (2010). Helminth infestation in birds of prey (Accipitriformes and Falconiformes) in Southern Italy. The Veterinary Journal , 186(1), 119-122. https://doi.org/10.1016/j.tvjl.2009.07.001
Scanlan, P. D. (2012). Blastocystis : past pitfalls and future perspectives. Trends in parasitology , 28(8), 327-334. https://doi.org/10.1016/j.pt.2012.05.001
Shokralla, S., Spall, J. L., Gibson, J. F., & Hajibabaei, M. (2012). Next‐generation sequencing technologies for environmental DNA research.Molecular ecology , 21(8), 1794-1805. https://doi.org/10.1111/j.1365-294X.2012.05538.x
Sonnenberg, R., Nolte, A. W., & Tautz, D. (2007). An evaluation of LSU rDNA D1-D2 sequences for their use in species identification.Frontiers in zoology , 4(1), 6. https://doi.org/10.1186/1742-9994-4-6
Srivathsan, A., Ang, A., Vogler, A. P., & Meier, R. (2016). Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Frontiers in Zoology , 13(1), 17. https://doi.org/10.1186/s12983-016-0150-4
Stockdale, J. E., Dunn, J. C., Goodman, S. J., Morris, A. J., Sheehan, D. K., Grice, P. V., & Hamer, K. C. (2015). The protozoan parasiteTrichomonas gallinae causes adult and nestling mortality in a declining population of European Turtle Doves, Streptopelia turtur . Parasitology , 142(3), 490-498. https://doi.org/10.1017/S0031182014001474
Storkey, J., Meyer, S., Still, K. S., & Leuschner, C. (2012). The impact of agricultural intensification and land-use change on the European arable flora. Proceedings of the Royal Society B: Biological Sciences , 279(1732), 1421-1429. https://doi.org/10.1098/rspb.2011.1686
Taberlet, P., Coissac, E., Hajibabaei, M., & Rieseberg, L. H. (2012a). Environmental DNA. Molecular ecology , 21(8), 1789-1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev, E. (2012b). Towards next‐generation biodiversity assessment using DNA metabarcoding. Molecular ecology , 21(8), 2045-2050. https://doi.org/10.1111/j.1365-294X.2012.05470.x
Tan, K. S. (2008). New insights on classification, identification, and clinical relevance of Blastocystis spp. Clinical microbiology reviews , 21(4), 639-665. https://doi.org/10.1128/CMR.00022-08
Van Steenkiste, N., Locke, S. A., Castelin, M. , Marcogliese, D. J. & Abbott, C. L. (2015), New primers for DNA barcoding of digeneans and cestodes (Platyhelminthes). Molecular Ecology Resources , 15: 945-952. https://doi.org/10.1111/1755-0998.12358
Vestheim, H., & Jarman, S. N. (2008). Blocking primers to enhance PCR amplification of rare sequences in mixed samples–a case study on prey DNA in Antarctic krill stomachs. Frontiers in zoology , 5(1), 12. https://doi.org/10.1186/1742-9994-5-12
Villanúa, D., Pérez-Rodríguez, L., Casas, F., Alzaga, V., Acevedo, P., Viñuela, J., & Gortázar, C. (2008). Sanitary risks of red-legged partridge releases: introduction of parasites. European Journal of Wildlife Research , 54(2), 199-204. https://doi.org/10.1007/s10344-007-0130-2
Wakelin, D. (1996). Immunity to parasites: how parasitic infections are controlled . Cambridge University Press.
Wickham H (2016) Ggplot2: Elegant Graphics for Data Analysis . Springer-Verlag New York
Wilson, I. G. (1997). Inhibition and facilitation of nucleic acid amplification. Applied and environmental microbiology , 63(10), 3741.
Wilson, J. D., Morris, A. J., Arroyo, B. E., Clark, S. C., & Bradbury, R. B. (1999). A review of the abundance and diversity of invertebrate and plant foods of granivorous birds in northern Europe in relation to agricultural change. Agriculture, Ecosystems & Environment , 75(1-2), 13-30. https://doi.org/10.1016/S0167-8809(99)00064-X
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012). Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution , 3(4), 613-623. https://doi.org/10.1111/j.2041-210X.2012.00198.x