# References

Andersen, Kenneth, Karen Lise Bird, Morten Rasmussen, James Haile, Henrik Breuning-Madsen, Kurt H Kjaer, Ludovic Orlando, M Thomas P Gilbert, and Eske Willerslev. 2012. “Meta-barcoding of ëdirtı́DNA from soil reflects vertebrate biodiversity.” Molecular Ecology 21 (8): 1966–79.
Baldwin, Darren S, Matthew J Colloff, Gavin N Rees, Anthony A Chariton, Garth O Watson, Leon N Court, Diana M Hartley, et al. 2013. “Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils.” Molecular Ecology 22 (6): 1746–58. https://doi.org/10.1111/mec.12190.
Boyer, Frédéric, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre Taberlet, and Eric Coissac. 2016. “obitools: a unix-inspired software package for DNA metabarcoding.” Molecular Ecology Resources 16 (1): 176–82. https://doi.org/10.1111/1755-0998.12428.
Caporaso, J Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, et al. 2010. “QIIME allows analysis of high-throughput community sequencing data.” Nature Methods 7 (5): 335–36. https://doi.org/10.1038/nmeth.f.303.
Chariton, Anthony A, Anthony C Roach, Stuart L Simpson, and Graeme E Batley. 2010. “Influence of the choice of physical and chemistry variables on interpreting patterns of sediment contaminants and their relationships with estuarine macrobenthic communities.” Marine and Freshwater Research. https://doi.org/10.1071/mf09263.
Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. 2010. “The Sanger FASTQ File Format for Sequences with Quality Scores, and the Solexa/Illumina FASTQ Variants.” Nucleic Acids Research 38 (6): 1767–71.
Deagle, Bruce E, Roger Kirkwood, and Simon N Jarman. 2009. “Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces.” Molecular Ecology 18 (9): 2022–38. https://doi.org/10.1111/j.1365-294X.2009.04158.x.
Kowalczyk, Rafał, Pierre Taberlet, Eric Coissac, Alice Valentini, Christian Miquel, Tomasz Kamiński, and Jan M Wójcik. 2011. “Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland).” Forest Ecology and Management 261 (4): 821–28. https://doi.org/10.1016/j.foreco.2010.11.026.
Lipman, D J, and W R Pearson. 1985. “Rapid and sensitive protein similarity searches.” Science 227 (4693): 1435–41. http://www.ncbi.nlm.nih.gov/pubmed/2983426.
Parducci, Laura, Tina Jørgensen, Mari Mette Tollefsrud, Ellen Elverland, Torbjørn Alm, Sonia L Fontana, K D Bennett, et al. 2012. “Glacial survival of boreal trees in northern Scandinavia.” Science 335 (6072): 1083–86. https://doi.org/10.1126/science.1216043.
Riaz, Tiayyba, Wasim Shehzad, Alain Viari, François Pompanon, Pierre Taberlet, and Eric Coissac. 2011. “ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.” Nucleic Acids Research 39 (21): e145. https://doi.org/10.1093/nar/gkr732.
Schloss, Patrick D, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, et al. 2009. “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.” Applied and Environmental Microbiology 75 (23): 7537–41. https://doi.org/10.1128/AEM.01541-09.
Seguritan, V, and F Rohwer. 2001. “FastGroup: a program to dereplicate libraries of 16S rDNA sequences.” BMC Bioinformatics 2 (October): 9. https://doi.org/10.1186/1471-2105-2-9.
Shehzad, Wasim, Tiayyba Riaz, Muhammad A Nawaz, Christian Miquel, Carole Poillot, Safdar A Shah, Francois Pompanon, Eric Coissac, and Pierre Taberlet. 2012. “Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan.” Molecular Ecology 21 (8): 1951–65. https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x.
Sogin, Mitchell L, Hilary G Morrison, Julie A Huber, David Mark Welch, Susan M Huse, Phillip R Neal, Jesus M Arrieta, and Gerhard J Herndl. 2006. “Microbial diversity in the deep sea and the underexplored "rare biosphere".” Proceedings of the National Academy of Sciences of the United States of America 103 (32): 12115–20. https://doi.org/10.1073/pnas.0605127103.
Sønstebø, J H, L Gielly, A K Brysting, R Elven, M Edwards, J Haile, E Willerslev, et al. 2010. “Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.” Molecular Ecology Resources 10 (6): 1009–18. https://doi.org/10.1111/j.1755-0998.2010.02855.x.
Taberlet, Pierre, Eric Coissac, Mehrdad Hajibabaei, and Loren H Rieseberg. 2012. “Environmental DNA.” Molecular Ecology 21 (8): 1789–93. https://doi.org/10.1111/j.1365-294X.2012.05542.x.
Thomsen, Philip Francis, Jos Kielgast, Lars L Iversen, Carsten Wiuf, Morten Rasmussen, M Thomas P Gilbert, Ludovic Orlando, and Eske Willerslev. 2012. “Monitoring endangered freshwater biodiversity using environmental DNA.” Molecular Ecology 21 (11): 2565–73. https://doi.org/10.1111/j.1365-294X.2011.05418.x.
Valentini, Alice, Christian Miquel, Muhammad Ali Nawaz, Eva Bellemain, Eric Coissac, François Pompanon, Ludovic Gielly, et al. 2009. “New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach.” Molecular Ecology Resources 9 (1): 51–60. https://doi.org/10.1111/j.1755-0998.2008.02352.x.
Yoccoz, N G, K A Bråthen, L Gielly, J Haile, M E Edwards, T Goslar, H Von Stedingk, et al. 2012. “DNA from soil mirrors plant taxonomic and growth form diversity.” Molecular Ecology 21 (15): 3647–55. https://doi.org/10.1111/j.1365-294X.2012.05545.x.