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710 lines
36 KiB
BibTeX
710 lines
36 KiB
BibTeX
@article{cock2010sanger,
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title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
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author={Cock, Peter JA and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
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journal={Nucleic acids research},
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volume={38},
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number={6},
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pages={1767--1771},
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year={2010},
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publisher={Oxford University Press}
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}
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@ARTICLE{Boyer2016-gq,
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title = "{obitools: a unix-inspired software package for DNA metabarcoding}",
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author = "Boyer, Fr{\'e}d{\'e}ric and Mercier, C{\'e}line and Bonin,
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Aur{\'e}lie and Le Bras, Yvan and Taberlet, Pierre and Coissac,
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Eric",
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abstract = "DNA metabarcoding offers new perspectives in biodiversity
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research. This recently developed approach to ecosystem study
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relies heavily on the use of next-generation sequencing (NGS)
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and thus calls upon the ability to deal with huge sequence data
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sets. The obitools package satisfies this requirement thanks to
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a set of programs specifically designed for analysing NGS data
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in a DNA metabarcoding context. Their capacity to filter and
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edit sequences while taking into account taxonomic annotation
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helps to set up tailor-made analysis pipelines for a broad range
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of DNA metabarcoding applications, including biodiversity
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surveys or diet analyses. The obitools package is distributed as
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an open source software available on the following website:
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http://metabarcoding.org/obitools. A Galaxy wrapper is available
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on the GenOuest core facility toolshed:
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http://toolshed.genouest.org.",
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journal = "Molecular ecology resources",
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publisher = "Wiley Online Library",
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volume = 16,
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number = 1,
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pages = "176--182",
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month = jan,
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year = 2016,
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url = "http://dx.doi.org/10.1111/1755-0998.12428",
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keywords = "PCR errors; biodiversity; next-generation sequencing; sequence
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analysis; taxonomic annotation",
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language = "en",
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issn = "1755-098X, 1755-0998",
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pmid = "25959493",
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doi = "10.1111/1755-0998.12428"
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}
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@article{Lipman1985-hw,
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abstract = {An algorithm was developed which facilitates the search for
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similarities between newly determined amino acid sequences and
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sequences already available in databases. Because of the
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algorithm's efficiency on many microcomputers, sensitive protein
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database searches may now become a routine procedure for
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molecular biologists. The method efficiently identifies regions
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of similar sequence and then scores the aligned identical and
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differing residues in those regions by means of an amino acid
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replacability matrix. This matrix increases sensitivity by giving
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high scores to those amino acid replacements which occur
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frequently in evolution. The algorithm has been implemented in a
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computer program designed to search protein databases very
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rapidly. For example, comparison of a 200-amino-acid sequence to
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the 500,000 residues in the National Biomedical Research
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Foundation library would take less than 2 minutes on a
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minicomputer, and less than 10 minutes on a microcomputer (IBM
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PC).},
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author = {Lipman, D J and Pearson, W R},
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date-added = {2023-01-26 15:17:10 +0100},
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date-modified = {2023-01-26 15:17:10 +0100},
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issn = {0036-8075},
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journal = {Science},
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month = mar,
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number = 4693,
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pages = {1435--1441},
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pmid = {2983426},
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title = {{Rapid and sensitive protein similarity searches}},
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url = {http://www.ncbi.nlm.nih.gov/pubmed/2983426},
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volume = 227,
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year = 1985,
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bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/2983426}}
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@ARTICLE{Shehzad2012-pn,
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title = "{Carnivore diet analysis based on next-generation sequencing:
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Application to the leopard cat (Prionailurus bengalensis) in
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Pakistan}",
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author = "Shehzad, Wasim and Riaz, Tiayyba and Nawaz, Muhammad A and
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Miquel, Christian and Poillot, Carole and Shah, Safdar A and
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Pompanon, Francois and Coissac, Eric and Taberlet, Pierre",
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journal = "Molecular ecology",
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publisher = "Wiley Online Library",
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volume = 21,
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number = 8,
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pages = "1951--1965",
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year = 2012,
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url = "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x",
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issn = "0962-1083"
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}
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@ARTICLE{Riaz2011-gn,
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title = "{ecoPrimers: inference of new DNA barcode markers from whole
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genome sequence analysis}",
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author = "Riaz, Tiayyba and Shehzad, Wasim and Viari, Alain and Pompanon,
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Fran{\c c}ois and Taberlet, Pierre and Coissac, Eric",
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abstract = "Using non-conventional markers, DNA metabarcoding allows
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biodiversity assessment from complex substrates. In this article,
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we present ecoPrimers, a software for identifying new barcode
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markers and their associated PCR primers. ecoPrimers scans whole
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genomes to find such markers without a priori knowledge.
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ecoPrimers optimizes two quality indices measuring taxonomical
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range and discrimination to select the most efficient markers
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from a set of reference sequences, according to specific
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experimental constraints such as marker length or specifically
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targeted taxa. The key step of the algorithm is the
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identification of conserved regions among reference sequences for
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anchoring primers. We propose an efficient algorithm based on
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data mining, that allows the analysis of huge sets of sequences.
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We evaluate the efficiency of ecoPrimers by running it on three
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different sequence sets: mitochondrial, chloroplast and bacterial
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genomes. Identified barcode markers correspond either to barcode
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regions already in use for plants or animals, or to new potential
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barcodes. Results from empirical experiments carried out on a
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promising new barcode for analyzing vertebrate diversity fully
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agree with expectations based on bioinformatics analysis. These
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tests demonstrate the efficiency of ecoPrimers for inferring new
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barcodes fitting with diverse experimental contexts. ecoPrimers
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is available as an open source project at:
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http://www.grenoble.prabi.fr/trac/ecoPrimers.",
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journal = "Nucleic acids research",
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volume = 39,
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number = 21,
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pages = "e145",
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month = nov,
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year = 2011,
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url = "http://dx.doi.org/10.1093/nar/gkr732",
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language = "en",
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issn = "0305-1048, 1362-4962",
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pmid = "21930509",
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doi = "10.1093/nar/gkr732",
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pmc = "PMC3241669"
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}
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@ARTICLE{Seguritan2001-tg,
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title = "{FastGroup: a program to dereplicate libraries of 16S rDNA
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sequences}",
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author = "Seguritan, V and Rohwer, F",
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abstract = "BACKGROUND: Ribosomal 16S DNA sequences are an essential tool for
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identifying and classifying microbes. High-throughput DNA
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sequencing now makes it economically possible to produce very
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large datasets of 16S rDNA sequences in short time periods,
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necessitating new computer tools for analyses. Here we describe
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FastGroup, a Java program designed to dereplicate libraries of
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16S rDNA sequences. By dereplication we mean to: 1) compare all
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the sequences in a data set to each other, 2) group similar
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sequences together, and 3) output a representative sequence from
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each group. In this way, duplicate sequences are removed from a
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library. RESULTS: FastGroup was tested using a library of
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single-pass, bacterial 16S rDNA sequences cloned from
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coral-associated bacteria. We found that the optimal strategy for
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dereplicating these sequences was to: 1) trim ambiguous bases
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from the 5' end of the sequences and all sequence 3' of the
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conserved Bact517 site, 2) match the sequences from the 3' end,
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and 3) group sequences > or =97\% identical to each other.
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CONCLUSIONS: The FastGroup program simplifies the dereplication
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of 16S rDNA sequence libraries and prepares the raw sequences for
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subsequent analyses.",
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journal = "BMC bioinformatics",
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volume = 2,
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pages = "9",
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month = oct,
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year = 2001,
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url = "http://dx.doi.org/10.1186/1471-2105-2-9",
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language = "en",
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issn = "1471-2105",
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pmid = "11707150",
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doi = "10.1186/1471-2105-2-9",
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pmc = "PMC59723"
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}
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@ARTICLE{Taberlet2012-pf,
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title = "{Environmental DNA}",
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author = "Taberlet, Pierre and Coissac, Eric and Hajibabaei, Mehrdad and
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Rieseberg, Loren H",
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journal = "Molecular ecology",
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volume = 21,
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number = 8,
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pages = "1789--1793",
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month = apr,
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year = 2012,
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url = "http://dx.doi.org/10.1111/j.1365-294X.2012.05542.x",
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language = "en",
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issn = "0962-1083, 1365-294X",
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pmid = "22486819",
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doi = "10.1111/j.1365-294X.2012.05542.x"
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}
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@ARTICLE{Sogin2006-ab,
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title = "{Microbial diversity in the deep sea and the underexplored "rare
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biosphere"}",
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author = "Sogin, Mitchell L and Morrison, Hilary G and Huber, Julie A and
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Mark Welch, David and Huse, Susan M and Neal, Phillip R and
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Arrieta, Jesus M and Herndl, Gerhard J",
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abstract = "The evolution of marine microbes over billions of years predicts
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that the composition of microbial communities should be much
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greater than the published estimates of a few thousand distinct
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kinds of microbes per liter of seawater. By adopting a massively
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parallel tag sequencing strategy, we show that bacterial
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communities of deep water masses of the North Atlantic and
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diffuse flow hydrothermal vents are one to two orders of
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magnitude more complex than previously reported for any microbial
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environment. A relatively small number of different populations
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dominate all samples, but thousands of low-abundance populations
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account for most of the observed phylogenetic diversity. This
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``rare biosphere'' is very ancient and may represent a nearly
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inexhaustible source of genomic innovation. Members of the rare
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biosphere are highly divergent from each other and, at different
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times in earth's history, may have had a profound impact on
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shaping planetary processes.",
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journal = "Proceedings of the National Academy of Sciences of the United
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States of America",
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volume = 103,
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number = 32,
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pages = "12115--12120",
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month = aug,
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year = 2006,
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url = "http://dx.doi.org/10.1073/pnas.0605127103",
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issn = "0027-8424",
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pmid = "16880384",
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doi = "10.1073/pnas.0605127103",
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pmc = "PMC1524930"
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}
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@ARTICLE{Sonstebo2010-vv,
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title = "{Using next-generation sequencing for molecular reconstruction of
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past Arctic vegetation and climate}",
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author = "S{\o}nsteb{\o}, J H and Gielly, L and Brysting, A K and Elven, R
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and Edwards, M and Haile, J and Willerslev, E and Coissac, E and
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Rioux, D and Sannier, J and Taberlet, P and Brochmann, C",
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abstract = "Palaeoenvironments and former climates are typically inferred
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from pollen and macrofossil records. This approach is
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time-consuming and suffers from low taxonomic resolution and
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biased taxon sampling. Here, we test an alternative DNA-based
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approach utilizing the P6 loop in the chloroplast trnL (UAA)
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intron; a short (13-158 bp) and variable region with highly
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conserved flanking sequences. For taxonomic reference, a whole
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trnL intron sequence database was constructed from recently
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collected material of 842 species, representing all widespread
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and/or ecologically important taxa of the species-poor arctic
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flora. The P6 loop alone allowed identification of all families,
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most genera (>75\%) and one-third of the species, thus providing
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much higher taxonomic resolution than pollen records. The
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suitability of the P6 loop for analysis of samples containing
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degraded ancient DNA from a mixture of species is demonstrated by
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high-throughput parallel pyrosequencing of permafrost-preserved
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DNA and reconstruction of two plant communities from the last
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glacial period. Our approach opens new possibilities for
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DNA-based assessment of ancient as well as modern biodiversity of
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many groups of organisms using environmental samples.",
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journal = "Molecular ecology resources",
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volume = 10,
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number = 6,
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pages = "1009--1018",
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month = nov,
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year = 2010,
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url = "http://dx.doi.org/10.1111/j.1755-0998.2010.02855.x",
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language = "en",
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issn = "1755-098X, 1755-0998",
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pmid = "21565110",
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doi = "10.1111/j.1755-0998.2010.02855.x"
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}
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@ARTICLE{Yoccoz2012-ix,
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title = "{DNA from soil mirrors plant taxonomic and growth form diversity}",
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author = "Yoccoz, N G and Br{\aa}then, K A and Gielly, L and Haile, J and
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Edwards, M E and Goslar, T and Von Stedingk, H and Brysting, A K
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and Coissac, E and Pompanon, F and S{\o}nsteb{\o}, J H and
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Miquel, C and Valentini, A and De Bello, F and Chave, J and
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Thuiller, W and Wincker, P and Cruaud, C and Gavory, F and
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Rasmussen, M and Gilbert, M T P and Orlando, L and Brochmann, C
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and Willerslev, E and Taberlet, P",
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abstract = "Ecosystems across the globe are threatened by climate change and
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human activities. New rapid survey approaches for monitoring
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biodiversity would greatly advance assessment and understanding
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of these threats. Taking advantage of next-generation DNA
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sequencing, we tested an approach we call metabarcoding:
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high-throughput and simultaneous taxa identification based on a
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very short (usually <100 base pairs) but informative DNA
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fragment. Short DNA fragments allow the use of degraded DNA from
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environmental samples. All analyses included amplification using
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plant-specific versatile primers, sequencing and estimation of
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taxonomic diversity. We tested in three steps whether degraded
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DNA from dead material in soil has the potential of efficiently
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assessing biodiversity in different biomes. First, soil DNA from
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eight boreal plant communities located in two different
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vegetation types (meadow and heath) was amplified. Plant
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diversity detected from boreal soil was highly consistent with
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plant taxonomic and growth form diversity estimated from
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conventional above-ground surveys. Second, we assessed DNA
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persistence using samples from formerly cultivated soils in
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temperate environments. We found that the number of crop DNA
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sequences retrieved strongly varied with years since last
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cultivation, and crop sequences were absent from nearby,
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uncultivated plots. Third, we assessed the universal
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applicability of DNA metabarcoding using soil samples from
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tropical environments: a large proportion of species and families
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from the study site were efficiently recovered. The results open
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unprecedented opportunities for large-scale DNA-based
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biodiversity studies across a range of taxonomic groups using
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standardized metabarcoding approaches.",
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journal = "Molecular ecology",
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volume = 21,
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number = 15,
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pages = "3647--3655",
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month = aug,
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year = 2012,
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url = "http://dx.doi.org/10.1111/j.1365-294X.2012.05545.x",
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language = "en",
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issn = "0962-1083, 1365-294X",
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pmid = "22507540",
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doi = "10.1111/j.1365-294X.2012.05545.x"
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}
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@ARTICLE{Parducci2012-rn,
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title = "{Glacial survival of boreal trees in northern Scandinavia}",
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author = "Parducci, Laura and J{\o}rgensen, Tina and Tollefsrud, Mari Mette
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and Elverland, Ellen and Alm, Torbj{\o}rn and Fontana, Sonia L
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and Bennett, K D and Haile, James and Matetovici, Irina and
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Suyama, Yoshihisa and Edwards, Mary E and Andersen, Kenneth and
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Rasmussen, Morten and Boessenkool, Sanne and Coissac, Eric and
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Brochmann, Christian and Taberlet, Pierre and Houmark-Nielsen,
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Michael and Larsen, Nicolaj Krog and Orlando, Ludovic and
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Gilbert, M Thomas P and Kj{\ae}r, Kurt H and Alsos, Inger Greve
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and Willerslev, Eske",
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abstract = "It is commonly believed that trees were absent in Scandinavia
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during the last glaciation and first recolonized the Scandinavian
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Peninsula with the retreat of its ice sheet some 9000 years ago.
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Here, we show the presence of a rare mitochondrial DNA haplotype
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of spruce that appears unique to Scandinavia and with its highest
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frequency to the west-an area believed to sustain ice-free
|
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refugia during most of the last ice age. We further show the
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survival of DNA from this haplotype in lake sediments and pollen
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of Tr{\o}ndelag in central Norway dating back ~10,300 years and
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chloroplast DNA of pine and spruce in lake sediments adjacent to
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the ice-free And{\o}ya refugium in northwestern Norway as early
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as ~22,000 and 17,700 years ago, respectively. Our findings imply
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that conifer trees survived in ice-free refugia of Scandinavia
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during the last glaciation, challenging current views on survival
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and spread of trees as a response to climate changes.",
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journal = "Science",
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volume = 335,
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number = 6072,
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pages = "1083--1086",
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month = mar,
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year = 2012,
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url = "http://dx.doi.org/10.1126/science.1216043",
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language = "en",
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issn = "0036-8075, 1095-9203",
|
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pmid = "22383845",
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doi = "10.1126/science.1216043"
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}
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@MISC{Chariton2010-cz,
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title = "{Influence of the choice of physical and chemistry variables on
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interpreting patterns of sediment contaminants and their
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relationships with estuarine macrobenthic communities}",
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author = "Chariton, Anthony A and Roach, Anthony C and Simpson, Stuart L and
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Batley, Graeme E",
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journal = "Marine and Freshwater Research",
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volume = 61,
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number = 10,
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pages = "1109",
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year = 2010,
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url = "http://dx.doi.org/10.1071/mf09263",
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doi = "10.1071/mf09263"
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}
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@ARTICLE{Baldwin2013-yc,
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title = "{Impacts of inundation and drought on eukaryote biodiversity in
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semi-arid floodplain soils}",
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author = "Baldwin, Darren S and Colloff, Matthew J and Rees, Gavin N and
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Chariton, Anthony A and Watson, Garth O and Court, Leon N and
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Hartley, Diana M and Morgan, Matthew J and King, Andrew J and
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Wilson, Jessica S and Hodda, Michael and Hardy, Christopher M",
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abstract = "Floodplain ecosystems are characterized by alternating wet and
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dry phases and periodic inundation defines their ecological
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character. Climate change, river regulation and the construction
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of levees have substantially altered natural flooding and drying
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regimes worldwide with uncertain effects on key biotic groups.
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In southern Australia, we hypothesized that soil eukaryotic
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communities in climate change affected areas of a semi-arid
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floodplain would transition towards comprising mainly dry-soil
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specialist species with increasing drought severity. Here, we
|
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used 18S rRNA amplicon pyrosequencing to measure the eukaryote
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community composition in soils that had been depleted of water
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to varying degrees to confirm that reproducible transitional
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changes occur in eukaryotic biodiversity on this floodplain.
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Interflood community structures (3 years post-flood) were
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dominated by persistent rather than either aquatic or
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dry-specialist organisms. Only 2\% of taxa were unique to dry
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locations by 8 years post-flood, and 10\% were restricted to wet
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locations (inundated a year to 2 weeks post-flood). Almost half
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(48\%) of the total soil biota were detected in both these
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environments. The discovery of a large suite of organisms able
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to survive nearly a decade of drought, and up to a year
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submerged supports the concept of inherent resilience of
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Australian semi-arid floodplain soil communities under
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increasing pressure from climatic induced changes in water
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availability.",
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journal = "Molecular ecology",
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publisher = "Wiley Online Library",
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volume = 22,
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number = 6,
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pages = "1746--1758",
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month = mar,
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year = 2013,
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url = "http://dx.doi.org/10.1111/mec.12190",
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issn = "0962-1083, 1365-294X",
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pmid = "23379967",
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doi = "10.1111/mec.12190"
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}
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@ARTICLE{Andersen2012-gj,
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title = "{Meta-barcoding of {\"e}dirt{\'\i}DNA from soil reflects
|
|
vertebrate biodiversity}",
|
|
author = "Andersen, Kenneth and Bird, Karen Lise and Rasmussen, Morten and
|
|
Haile, James and Breuning-Madsen, Henrik and Kjaer, Kurt H and
|
|
Orlando, Ludovic and Gilbert, M Thomas P and Willerslev, Eske",
|
|
journal = "Molecular ecology",
|
|
publisher = "Wiley Online Library",
|
|
volume = 21,
|
|
number = 8,
|
|
pages = "1966--1979",
|
|
year = 2012,
|
|
issn = "0962-1083"
|
|
}
|
|
|
|
|
|
@ARTICLE{Thomsen2012-au,
|
|
title = "{Monitoring endangered freshwater biodiversity using environmental
|
|
DNA}",
|
|
author = "Thomsen, Philip Francis and Kielgast, Jos and Iversen, Lars L and
|
|
Wiuf, Carsten and Rasmussen, Morten and Gilbert, M Thomas P and
|
|
Orlando, Ludovic and Willerslev, Eske",
|
|
abstract = "Freshwater ecosystems are among the most endangered habitats on
|
|
Earth, with thousands of animal species known to be threatened or
|
|
already extinct. Reliable monitoring of threatened organisms is
|
|
crucial for data-driven conservation actions but remains a
|
|
challenge owing to nonstandardized methods that depend on
|
|
practical and taxonomic expertise, which is rapidly declining.
|
|
Here, we show that a diversity of rare and threatened freshwater
|
|
animals--representing amphibians, fish, mammals, insects and
|
|
crustaceans--can be detected and quantified based on DNA obtained
|
|
directly from small water samples of lakes, ponds and streams. We
|
|
successfully validate our findings in a controlled mesocosm
|
|
experiment and show that DNA becomes undetectable within 2 weeks
|
|
after removal of animals, indicating that DNA traces are near
|
|
contemporary with presence of the species. We further demonstrate
|
|
that entire faunas of amphibians and fish can be detected by
|
|
high-throughput sequencing of DNA extracted from pond water. Our
|
|
findings underpin the ubiquitous nature of DNA traces in the
|
|
environment and establish environmental DNA as a tool for
|
|
monitoring rare and threatened species across a wide range of
|
|
taxonomic groups.",
|
|
journal = "Molecular ecology",
|
|
volume = 21,
|
|
number = 11,
|
|
pages = "2565--2573",
|
|
month = jun,
|
|
year = 2012,
|
|
url = "http://dx.doi.org/10.1111/j.1365-294X.2011.05418.x",
|
|
issn = "0962-1083, 1365-294X",
|
|
pmid = "22151771",
|
|
doi = "10.1111/j.1365-294X.2011.05418.x"
|
|
}
|
|
|
|
|
|
@ARTICLE{Valentini2009-ay,
|
|
title = "{New perspectives in diet analysis based on DNA barcoding and
|
|
parallel pyrosequencing: the trnL approach}",
|
|
author = "Valentini, Alice and Miquel, Christian and Nawaz, Muhammad Ali
|
|
and Bellemain, Eva and Coissac, Eric and Pompanon, Fran{\c c}ois
|
|
and Gielly, Ludovic and Cruaud, Corinne and Nascetti, Giuseppe
|
|
and Wincker, Patrick and Swenson, Jon E and Taberlet, Pierre",
|
|
abstract = "The development of DNA barcoding (species identification using a
|
|
standardized DNA sequence), and the availability of recent DNA
|
|
sequencing techniques offer new possibilities in diet analysis.
|
|
DNA fragments shorter than 100-150 bp remain in a much higher
|
|
proportion in degraded DNA samples and can be recovered from
|
|
faeces. As a consequence, by using universal primers that
|
|
amplify a very short but informative DNA fragment, it is
|
|
possible to reliably identify the plant taxon that has been
|
|
eaten. According to our experience and using this identification
|
|
system, about 50\% of the taxa can be identified to species
|
|
using the trnL approach, that is, using the P6 loop of the
|
|
chloroplast trnL (UAA) intron. We demonstrated that this new
|
|
method is fast, simple to implement, and very robust. It can be
|
|
applied for diet analyses of a wide range of phytophagous
|
|
species at large scales. We also demonstrated that our approach
|
|
is efficient for mammals, birds, insects and molluscs. This
|
|
method opens new perspectives in ecology, not only by allowing
|
|
large-scale studies on diet, but also by enhancing studies on
|
|
resource partitioning among competing species, and describing
|
|
food webs in ecosystems.",
|
|
journal = "Molecular ecology resources",
|
|
publisher = "WILEY-BLACKWELL PUBLISHING, INC",
|
|
volume = 9,
|
|
number = 1,
|
|
pages = "51--60",
|
|
month = jan,
|
|
year = 2009,
|
|
url = "http://dx.doi.org/10.1111/j.1755-0998.2008.02352.x",
|
|
address = "COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA",
|
|
keywords = "chloroplast DNA; diet analysis; DNA barcoding; faeces;
|
|
pyrosequencing; trnL (UAA) intron; universal primers",
|
|
language = "en",
|
|
issn = "1755-098X",
|
|
pmid = "21564566",
|
|
doi = "10.1111/j.1755-0998.2008.02352.x"
|
|
}
|
|
|
|
|
|
@ARTICLE{Kowalczyk2011-kg,
|
|
title = "{Influence of management practices on large herbivore diet---Case
|
|
of European bison in Bia{\l}owie{\.z}a Primeval Forest (Poland)}",
|
|
author = "Kowalczyk, Rafa{\l} and Taberlet, Pierre and Coissac, Eric and
|
|
Valentini, Alice and Miquel, Christian and Kami{\'n}ski, Tomasz
|
|
and W{\'o}jcik, Jan M",
|
|
abstract = "Large herbivores are keystone species in many forest areas, as
|
|
they shape the structure, species diversity and functioning of
|
|
those ecosystems. The European bison Bison bonasus has been
|
|
successfully restored after extinction in the wild at the
|
|
beginning of 20th century. As free-ranging populations of the
|
|
species were re-established mainly in forest habitats, knowledge
|
|
of the impact by the largest European terrestrial mammal on tree
|
|
stands is essential. This helps to make management and
|
|
conservation decisions for viable population maintenance of the
|
|
species in the wild. Using a novel DNA-based method of herbivore
|
|
diet analysis, the trnL approach (DNA-barcoding), we
|
|
investigated the influence of different foraging conditions
|
|
(access to supplementary fodder) on bison diet in winter and its
|
|
potential impact on woody species. Faecal samples were collected
|
|
from different bison treatment groups: (1) intensively fed; (2)
|
|
less intensively fed; (3) non-fed utilising forest habitats; and
|
|
(4) non-fed utilising agricultural areas surrounding the Forest.
|
|
These were analysed to estimate the proportion of different
|
|
plant groups consumed by bison. Bison groups differed
|
|
significantly in their diet. The amount of woody materials
|
|
(trees and shrubs) consumed by bison increased with decreasing
|
|
access to supplementary fodder, ranging from 16\% in intensively
|
|
fed bison to 65\% in non-fed bison utilising forest habitats.
|
|
Inversely, the amount of herbs, grasses and sedges decreased
|
|
from 82\% in intensively fed bison to 32\% in non fed bison
|
|
utilising forest habitats. The species of trees mainly browsed
|
|
by bison, Carpinus/Corylus, Betula sp. and Salix sp., were of
|
|
lower economic importance for forest management. The impact of
|
|
bison on tree species needs further investigation, however, we
|
|
can predict that browsing by bison, mainly on Carpinus/Corylus,
|
|
makes an insignificant impact on forestry due to the high and
|
|
increasing representation of this species in the forest
|
|
understory. Supplementary feeding has several negative effects
|
|
on bison ecology and health, therefore reduced and distributed
|
|
supplementary feeding should be applied as the management
|
|
practice in the Bia{\l}owie{\.z}a Forest.",
|
|
journal = "Forest ecology and management",
|
|
publisher = "ELSEVIER SCIENCE BV",
|
|
volume = 261,
|
|
number = 4,
|
|
pages = "821--828",
|
|
month = feb,
|
|
year = 2011,
|
|
url = "http://www.sciencedirect.com/science/article/pii/S0378112710006961",
|
|
annote = "di",
|
|
address = "PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS",
|
|
keywords = "Bison bonasus; trnL approach; DNA barcoding; Diet analysis;
|
|
Large ungulates; Wildlife management; L approach",
|
|
language = "English",
|
|
issn = "0378-1127",
|
|
doi = "10.1016/j.foreco.2010.11.026"
|
|
}
|
|
|
|
|
|
@ARTICLE{Deagle2009-yh,
|
|
title = "{Analysis of Australian fur seal diet by pyrosequencing prey DNA
|
|
in faeces}",
|
|
author = "Deagle, Bruce E and Kirkwood, Roger and Jarman, Simon N",
|
|
abstract = "DNA-based techniques have proven useful for defining trophic
|
|
links in a variety of ecosystems and recently developed
|
|
sequencing technologies provide new opportunities for dietary
|
|
studies. We investigated the diet of Australian fur seals
|
|
(Arctocephalus pusillus doriferus) by pyrosequencing prey DNA
|
|
from faeces collected at three breeding colonies across the
|
|
seals' range. DNA from 270 faecal samples was amplified with four
|
|
polymerase chain reaction primer sets and a blocking primer was
|
|
used to limit amplification of fur seal DNA. Pooled amplicons
|
|
from each colony were sequenced using the Roche GS-FLX platform,
|
|
generating > 20,000 sequences. Software was developed to sort and
|
|
group similar sequences. A total of 54 bony fish, 4 cartilaginous
|
|
fish and 4 cephalopods were identified based on the most
|
|
taxonomically informative amplicons sequenced (mitochondrial
|
|
16S). The prevalence of sequences from redbait (Emmelichthys
|
|
nitidus) and jack mackerel (Trachurus declivis) confirm the
|
|
importance of these species in the seals' diet. A third fish
|
|
species, blue mackerel (Scomber australasicus), may be a more
|
|
important prey species than previously recognised. There were
|
|
major differences in the proportions of prey DNA recovered in
|
|
faeces from different colonies, probably reflecting differences
|
|
in prey availability. Parallel hard-part analysis identified
|
|
largely the same main prey species as did the DNA-based
|
|
technique, but with lower species diversity and no remains from
|
|
cartilaginous prey. The pyrosequencing approach presented
|
|
significantly expands the capabilities of DNA-based methods of
|
|
dietary analysis and is suitable for large-scale diet
|
|
investigations on a broad range of animals.",
|
|
journal = "Molecular ecology",
|
|
volume = 18,
|
|
number = 9,
|
|
pages = "2022--2038",
|
|
month = may,
|
|
year = 2009,
|
|
url = "http://dx.doi.org/10.1111/j.1365-294X.2009.04158.x",
|
|
issn = "0962-1083, 1365-294X",
|
|
pmid = "19317847",
|
|
doi = "10.1111/j.1365-294X.2009.04158.x"
|
|
}
|
|
|
|
|
|
@ARTICLE{Shehzad2012-pn,
|
|
title = "{Carnivore diet analysis based on next-generation sequencing:
|
|
Application to the leopard cat (Prionailurus bengalensis) in
|
|
Pakistan}",
|
|
author = "Shehzad, Wasim and Riaz, Tiayyba and Nawaz, Muhammad A and
|
|
Miquel, Christian and Poillot, Carole and Shah, Safdar A and
|
|
Pompanon, Francois and Coissac, Eric and Taberlet, Pierre",
|
|
journal = "Molecular ecology",
|
|
publisher = "Wiley Online Library",
|
|
volume = 21,
|
|
number = 8,
|
|
pages = "1951--1965",
|
|
year = 2012,
|
|
url = "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x",
|
|
issn = "0962-1083"
|
|
}
|
|
|
|
|
|
@ARTICLE{Schloss2009-qy,
|
|
title = "{Introducing mothur: open-source, platform-independent,
|
|
community-supported software for describing and comparing
|
|
microbial communities}",
|
|
author = "Schloss, Patrick D and Westcott, Sarah L and Ryabin, Thomas and
|
|
Hall, Justine R and Hartmann, Martin and Hollister, Emily B and
|
|
Lesniewski, Ryan A and Oakley, Brian B and Parks, Donovan H and
|
|
Robinson, Courtney J and Sahl, Jason W and Stres, Blaz and
|
|
Thallinger, Gerhard G and Van Horn, David J and Weber, Carolyn F",
|
|
abstract = "mothur aims to be a comprehensive software package that allows
|
|
users to use a single piece of software to analyze community
|
|
sequence data. It builds upon previous tools to provide a
|
|
flexible and powerful software package for analyzing sequencing
|
|
data. As a case study, we used mothur to trim, screen, and align
|
|
sequences; calculate distances; assign sequences to operational
|
|
taxonomic units; and describe the alpha and beta diversity of
|
|
eight marine samples previously characterized by pyrosequencing
|
|
of 16S rRNA gene fragments. This analysis of more than 222,000
|
|
sequences was completed in less than 2 h with a laptop computer.",
|
|
journal = "Applied and environmental microbiology",
|
|
volume = 75,
|
|
number = 23,
|
|
pages = "7537--7541",
|
|
month = dec,
|
|
year = 2009,
|
|
url = "http://dx.doi.org/10.1128/AEM.01541-09",
|
|
issn = "0099-2240, 1098-5336",
|
|
pmid = "19801464",
|
|
doi = "10.1128/AEM.01541-09",
|
|
pmc = "PMC2786419"
|
|
}
|
|
|
|
|
|
@ARTICLE{Caporaso2010-ii,
|
|
title = "{QIIME allows analysis of high-throughput community sequencing data}",
|
|
author = "Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and
|
|
Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K
|
|
and Fierer, Noah and Pe{\~n}a, Antonio Gonzalez and Goodrich,
|
|
Julia K and Gordon, Jeffrey I and Huttley, Gavin A and Kelley,
|
|
Scott T and Knights, Dan and Koenig, Jeremy E and Ley, Ruth E and
|
|
Lozupone, Catherine A and McDonald, Daniel and Muegge, Brian D and
|
|
Pirrung, Meg and Reeder, Jens and Sevinsky, Joel R and Turnbaugh,
|
|
Peter J and Walters, William A and Widmann, Jeremy and Yatsunenko,
|
|
Tanya and Zaneveld, Jesse and Knight, Rob",
|
|
journal = "Nature methods",
|
|
volume = 7,
|
|
number = 5,
|
|
pages = "335--336",
|
|
month = may,
|
|
year = 2010,
|
|
url = "http://dx.doi.org/10.1038/nmeth.f.303",
|
|
issn = "1548-7091, 1548-7105",
|
|
pmid = "20383131",
|
|
doi = "10.1038/nmeth.f.303",
|
|
pmc = "PMC3156573"
|
|
}
|