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@article{cock2010sanger,
title={The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants},
author={Cock, Peter JA and Fields, Christopher J and Goto, Naohisa and Heuer, Michael L and Rice, Peter M},
journal={Nucleic acids research},
volume={38},
number={6},
pages={1767--1771},
year={2010},
publisher={Oxford University Press}
}
@ARTICLE{Boyer2016-gq,
title = "{obitools: a unix-inspired software package for DNA metabarcoding}",
author = "Boyer, Fr{\'e}d{\'e}ric and Mercier, C{\'e}line and Bonin,
Aur{\'e}lie and Le Bras, Yvan and Taberlet, Pierre and Coissac,
Eric",
abstract = "DNA metabarcoding offers new perspectives in biodiversity
research. This recently developed approach to ecosystem study
relies heavily on the use of next-generation sequencing (NGS)
and thus calls upon the ability to deal with huge sequence data
sets. The obitools package satisfies this requirement thanks to
a set of programs specifically designed for analysing NGS data
in a DNA metabarcoding context. Their capacity to filter and
edit sequences while taking into account taxonomic annotation
helps to set up tailor-made analysis pipelines for a broad range
of DNA metabarcoding applications, including biodiversity
surveys or diet analyses. The obitools package is distributed as
an open source software available on the following website:
http://metabarcoding.org/obitools. A Galaxy wrapper is available
on the GenOuest core facility toolshed:
http://toolshed.genouest.org.",
journal = "Molecular ecology resources",
publisher = "Wiley Online Library",
volume = 16,
number = 1,
pages = "176--182",
month = jan,
year = 2016,
url = "http://dx.doi.org/10.1111/1755-0998.12428",
keywords = "PCR errors; biodiversity; next-generation sequencing; sequence
analysis; taxonomic annotation",
language = "en",
issn = "1755-098X, 1755-0998",
pmid = "25959493",
doi = "10.1111/1755-0998.12428"
}
@article{Lipman1985-hw,
abstract = {An algorithm was developed which facilitates the search for
similarities between newly determined amino acid sequences and
sequences already available in databases. Because of the
algorithm's efficiency on many microcomputers, sensitive protein
database searches may now become a routine procedure for
molecular biologists. The method efficiently identifies regions
of similar sequence and then scores the aligned identical and
differing residues in those regions by means of an amino acid
replacability matrix. This matrix increases sensitivity by giving
high scores to those amino acid replacements which occur
frequently in evolution. The algorithm has been implemented in a
computer program designed to search protein databases very
rapidly. For example, comparison of a 200-amino-acid sequence to
the 500,000 residues in the National Biomedical Research
Foundation library would take less than 2 minutes on a
minicomputer, and less than 10 minutes on a microcomputer (IBM
PC).},
author = {Lipman, D J and Pearson, W R},
date-added = {2023-01-26 15:17:10 +0100},
date-modified = {2023-01-26 15:17:10 +0100},
issn = {0036-8075},
journal = {Science},
month = mar,
number = 4693,
pages = {1435--1441},
pmid = {2983426},
title = {{Rapid and sensitive protein similarity searches}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/2983426},
volume = 227,
year = 1985,
bdsk-url-1 = {http://www.ncbi.nlm.nih.gov/pubmed/2983426}}
@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{Riaz2011-gn,
title = "{ecoPrimers: inference of new DNA barcode markers from whole
genome sequence analysis}",
author = "Riaz, Tiayyba and Shehzad, Wasim and Viari, Alain and Pompanon,
Fran{\c c}ois and Taberlet, Pierre and Coissac, Eric",
abstract = "Using non-conventional markers, DNA metabarcoding allows
biodiversity assessment from complex substrates. In this article,
we present ecoPrimers, a software for identifying new barcode
markers and their associated PCR primers. ecoPrimers scans whole
genomes to find such markers without a priori knowledge.
ecoPrimers optimizes two quality indices measuring taxonomical
range and discrimination to select the most efficient markers
from a set of reference sequences, according to specific
experimental constraints such as marker length or specifically
targeted taxa. The key step of the algorithm is the
identification of conserved regions among reference sequences for
anchoring primers. We propose an efficient algorithm based on
data mining, that allows the analysis of huge sets of sequences.
We evaluate the efficiency of ecoPrimers by running it on three
different sequence sets: mitochondrial, chloroplast and bacterial
genomes. Identified barcode markers correspond either to barcode
regions already in use for plants or animals, or to new potential
barcodes. Results from empirical experiments carried out on a
promising new barcode for analyzing vertebrate diversity fully
agree with expectations based on bioinformatics analysis. These
tests demonstrate the efficiency of ecoPrimers for inferring new
barcodes fitting with diverse experimental contexts. ecoPrimers
is available as an open source project at:
http://www.grenoble.prabi.fr/trac/ecoPrimers.",
journal = "Nucleic acids research",
volume = 39,
number = 21,
pages = "e145",
month = nov,
year = 2011,
url = "http://dx.doi.org/10.1093/nar/gkr732",
language = "en",
issn = "0305-1048, 1362-4962",
pmid = "21930509",
doi = "10.1093/nar/gkr732",
pmc = "PMC3241669"
}
@ARTICLE{Seguritan2001-tg,
title = "{FastGroup: a program to dereplicate libraries of 16S rDNA
sequences}",
author = "Seguritan, V and Rohwer, F",
abstract = "BACKGROUND: Ribosomal 16S DNA sequences are an essential tool for
identifying and classifying microbes. High-throughput DNA
sequencing now makes it economically possible to produce very
large datasets of 16S rDNA sequences in short time periods,
necessitating new computer tools for analyses. Here we describe
FastGroup, a Java program designed to dereplicate libraries of
16S rDNA sequences. By dereplication we mean to: 1) compare all
the sequences in a data set to each other, 2) group similar
sequences together, and 3) output a representative sequence from
each group. In this way, duplicate sequences are removed from a
library. RESULTS: FastGroup was tested using a library of
single-pass, bacterial 16S rDNA sequences cloned from
coral-associated bacteria. We found that the optimal strategy for
dereplicating these sequences was to: 1) trim ambiguous bases
from the 5' end of the sequences and all sequence 3' of the
conserved Bact517 site, 2) match the sequences from the 3' end,
and 3) group sequences > or =97\% identical to each other.
CONCLUSIONS: The FastGroup program simplifies the dereplication
of 16S rDNA sequence libraries and prepares the raw sequences for
subsequent analyses.",
journal = "BMC bioinformatics",
volume = 2,
pages = "9",
month = oct,
year = 2001,
url = "http://dx.doi.org/10.1186/1471-2105-2-9",
language = "en",
issn = "1471-2105",
pmid = "11707150",
doi = "10.1186/1471-2105-2-9",
pmc = "PMC59723"
}
@ARTICLE{Taberlet2012-pf,
title = "{Environmental DNA}",
author = "Taberlet, Pierre and Coissac, Eric and Hajibabaei, Mehrdad and
Rieseberg, Loren H",
journal = "Molecular ecology",
volume = 21,
number = 8,
pages = "1789--1793",
month = apr,
year = 2012,
url = "http://dx.doi.org/10.1111/j.1365-294X.2012.05542.x",
language = "en",
issn = "0962-1083, 1365-294X",
pmid = "22486819",
doi = "10.1111/j.1365-294X.2012.05542.x"
}
@ARTICLE{Sogin2006-ab,
title = "{Microbial diversity in the deep sea and the underexplored "rare
biosphere"}",
author = "Sogin, Mitchell L and Morrison, Hilary G and Huber, Julie A and
Mark Welch, David and Huse, Susan M and Neal, Phillip R and
Arrieta, Jesus M and Herndl, Gerhard J",
abstract = "The evolution of marine microbes over billions of years predicts
that the composition of microbial communities should be much
greater than the published estimates of a few thousand distinct
kinds of microbes per liter of seawater. By adopting a massively
parallel tag sequencing strategy, we show that bacterial
communities of deep water masses of the North Atlantic and
diffuse flow hydrothermal vents are one to two orders of
magnitude more complex than previously reported for any microbial
environment. A relatively small number of different populations
dominate all samples, but thousands of low-abundance populations
account for most of the observed phylogenetic diversity. This
``rare biosphere'' is very ancient and may represent a nearly
inexhaustible source of genomic innovation. Members of the rare
biosphere are highly divergent from each other and, at different
times in earth's history, may have had a profound impact on
shaping planetary processes.",
journal = "Proceedings of the National Academy of Sciences of the United
States of America",
volume = 103,
number = 32,
pages = "12115--12120",
month = aug,
year = 2006,
url = "http://dx.doi.org/10.1073/pnas.0605127103",
issn = "0027-8424",
pmid = "16880384",
doi = "10.1073/pnas.0605127103",
pmc = "PMC1524930"
}
@ARTICLE{Sonstebo2010-vv,
title = "{Using next-generation sequencing for molecular reconstruction of
past Arctic vegetation and climate}",
author = "S{\o}nsteb{\o}, J H and Gielly, L and Brysting, A K and Elven, R
and Edwards, M and Haile, J and Willerslev, E and Coissac, E and
Rioux, D and Sannier, J and Taberlet, P and Brochmann, C",
abstract = "Palaeoenvironments and former climates are typically inferred
from pollen and macrofossil records. This approach is
time-consuming and suffers from low taxonomic resolution and
biased taxon sampling. Here, we test an alternative DNA-based
approach utilizing the P6 loop in the chloroplast trnL (UAA)
intron; a short (13-158 bp) and variable region with highly
conserved flanking sequences. For taxonomic reference, a whole
trnL intron sequence database was constructed from recently
collected material of 842 species, representing all widespread
and/or ecologically important taxa of the species-poor arctic
flora. The P6 loop alone allowed identification of all families,
most genera (>75\%) and one-third of the species, thus providing
much higher taxonomic resolution than pollen records. The
suitability of the P6 loop for analysis of samples containing
degraded ancient DNA from a mixture of species is demonstrated by
high-throughput parallel pyrosequencing of permafrost-preserved
DNA and reconstruction of two plant communities from the last
glacial period. Our approach opens new possibilities for
DNA-based assessment of ancient as well as modern biodiversity of
many groups of organisms using environmental samples.",
journal = "Molecular ecology resources",
volume = 10,
number = 6,
pages = "1009--1018",
month = nov,
year = 2010,
url = "http://dx.doi.org/10.1111/j.1755-0998.2010.02855.x",
language = "en",
issn = "1755-098X, 1755-0998",
pmid = "21565110",
doi = "10.1111/j.1755-0998.2010.02855.x"
}
@ARTICLE{Yoccoz2012-ix,
title = "{DNA from soil mirrors plant taxonomic and growth form diversity}",
author = "Yoccoz, N G and Br{\aa}then, K A and Gielly, L and Haile, J and
Edwards, M E and Goslar, T and Von Stedingk, H and Brysting, A K
and Coissac, E and Pompanon, F and S{\o}nsteb{\o}, J H and
Miquel, C and Valentini, A and De Bello, F and Chave, J and
Thuiller, W and Wincker, P and Cruaud, C and Gavory, F and
Rasmussen, M and Gilbert, M T P and Orlando, L and Brochmann, C
and Willerslev, E and Taberlet, P",
abstract = "Ecosystems across the globe are threatened by climate change and
human activities. New rapid survey approaches for monitoring
biodiversity would greatly advance assessment and understanding
of these threats. Taking advantage of next-generation DNA
sequencing, we tested an approach we call metabarcoding:
high-throughput and simultaneous taxa identification based on a
very short (usually <100 base pairs) but informative DNA
fragment. Short DNA fragments allow the use of degraded DNA from
environmental samples. All analyses included amplification using
plant-specific versatile primers, sequencing and estimation of
taxonomic diversity. We tested in three steps whether degraded
DNA from dead material in soil has the potential of efficiently
assessing biodiversity in different biomes. First, soil DNA from
eight boreal plant communities located in two different
vegetation types (meadow and heath) was amplified. Plant
diversity detected from boreal soil was highly consistent with
plant taxonomic and growth form diversity estimated from
conventional above-ground surveys. Second, we assessed DNA
persistence using samples from formerly cultivated soils in
temperate environments. We found that the number of crop DNA
sequences retrieved strongly varied with years since last
cultivation, and crop sequences were absent from nearby,
uncultivated plots. Third, we assessed the universal
applicability of DNA metabarcoding using soil samples from
tropical environments: a large proportion of species and families
from the study site were efficiently recovered. The results open
unprecedented opportunities for large-scale DNA-based
biodiversity studies across a range of taxonomic groups using
standardized metabarcoding approaches.",
journal = "Molecular ecology",
volume = 21,
number = 15,
pages = "3647--3655",
month = aug,
year = 2012,
url = "http://dx.doi.org/10.1111/j.1365-294X.2012.05545.x",
language = "en",
issn = "0962-1083, 1365-294X",
pmid = "22507540",
doi = "10.1111/j.1365-294X.2012.05545.x"
}
@ARTICLE{Parducci2012-rn,
title = "{Glacial survival of boreal trees in northern Scandinavia}",
author = "Parducci, Laura and J{\o}rgensen, Tina and Tollefsrud, Mari Mette
and Elverland, Ellen and Alm, Torbj{\o}rn and Fontana, Sonia L
and Bennett, K D and Haile, James and Matetovici, Irina and
Suyama, Yoshihisa and Edwards, Mary E and Andersen, Kenneth and
Rasmussen, Morten and Boessenkool, Sanne and Coissac, Eric and
Brochmann, Christian and Taberlet, Pierre and Houmark-Nielsen,
Michael and Larsen, Nicolaj Krog and Orlando, Ludovic and
Gilbert, M Thomas P and Kj{\ae}r, Kurt H and Alsos, Inger Greve
and Willerslev, Eske",
abstract = "It is commonly believed that trees were absent in Scandinavia
during the last glaciation and first recolonized the Scandinavian
Peninsula with the retreat of its ice sheet some 9000 years ago.
Here, we show the presence of a rare mitochondrial DNA haplotype
of spruce that appears unique to Scandinavia and with its highest
frequency to the west-an area believed to sustain ice-free
refugia during most of the last ice age. We further show the
survival of DNA from this haplotype in lake sediments and pollen
of Tr{\o}ndelag in central Norway dating back ~10,300 years and
chloroplast DNA of pine and spruce in lake sediments adjacent to
the ice-free And{\o}ya refugium in northwestern Norway as early
as ~22,000 and 17,700 years ago, respectively. Our findings imply
that conifer trees survived in ice-free refugia of Scandinavia
during the last glaciation, challenging current views on survival
and spread of trees as a response to climate changes.",
journal = "Science",
volume = 335,
number = 6072,
pages = "1083--1086",
month = mar,
year = 2012,
url = "http://dx.doi.org/10.1126/science.1216043",
language = "en",
issn = "0036-8075, 1095-9203",
pmid = "22383845",
doi = "10.1126/science.1216043"
}
@MISC{Chariton2010-cz,
title = "{Influence of the choice of physical and chemistry variables on
interpreting patterns of sediment contaminants and their
relationships with estuarine macrobenthic communities}",
author = "Chariton, Anthony A and Roach, Anthony C and Simpson, Stuart L and
Batley, Graeme E",
journal = "Marine and Freshwater Research",
volume = 61,
number = 10,
pages = "1109",
year = 2010,
url = "http://dx.doi.org/10.1071/mf09263",
doi = "10.1071/mf09263"
}
@ARTICLE{Baldwin2013-yc,
title = "{Impacts of inundation and drought on eukaryote biodiversity in
semi-arid floodplain soils}",
author = "Baldwin, Darren S and Colloff, Matthew J and Rees, Gavin N and
Chariton, Anthony A and Watson, Garth O and Court, Leon N and
Hartley, Diana M and Morgan, Matthew J and King, Andrew J and
Wilson, Jessica S and Hodda, Michael and Hardy, Christopher M",
abstract = "Floodplain ecosystems are characterized by alternating wet and
dry phases and periodic inundation defines their ecological
character. Climate change, river regulation and the construction
of levees have substantially altered natural flooding and drying
regimes worldwide with uncertain effects on key biotic groups.
In southern Australia, we hypothesized that soil eukaryotic
communities in climate change affected areas of a semi-arid
floodplain would transition towards comprising mainly dry-soil
specialist species with increasing drought severity. Here, we
used 18S rRNA amplicon pyrosequencing to measure the eukaryote
community composition in soils that had been depleted of water
to varying degrees to confirm that reproducible transitional
changes occur in eukaryotic biodiversity on this floodplain.
Interflood community structures (3 years post-flood) were
dominated by persistent rather than either aquatic or
dry-specialist organisms. Only 2\% of taxa were unique to dry
locations by 8 years post-flood, and 10\% were restricted to wet
locations (inundated a year to 2 weeks post-flood). Almost half
(48\%) of the total soil biota were detected in both these
environments. The discovery of a large suite of organisms able
to survive nearly a decade of drought, and up to a year
submerged supports the concept of inherent resilience of
Australian semi-arid floodplain soil communities under
increasing pressure from climatic induced changes in water
availability.",
journal = "Molecular ecology",
publisher = "Wiley Online Library",
volume = 22,
number = 6,
pages = "1746--1758",
month = mar,
year = 2013,
url = "http://dx.doi.org/10.1111/mec.12190",
issn = "0962-1083, 1365-294X",
pmid = "23379967",
doi = "10.1111/mec.12190"
}
@ARTICLE{Andersen2012-gj,
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"
}