-
1
-
-
84859590042
-
Environmental DNA
-
Taberlet, P., Coissac, E., Hajibabaei, M. & Rieseberg, L. H. Environmental DNA. Mol. Ecol. 21, 1789-1793 (2012).
-
(2012)
Mol. Ecol.
, vol.21
, pp. 1789-1793
-
-
Taberlet, P.1
Coissac, E.2
Hajibabaei, M.3
Rieseberg, L.H.4
-
2
-
-
33947238287
-
The sorcerer II global ocean sampling expedition: Northwest atlantic through eastern tropical pacific
-
Rusch, D. B. et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLOS Biol. 5, e77 (2007).
-
(2007)
PLOS Biol.
, vol.5
, pp. e77
-
-
Rusch, D.B.1
-
3
-
-
11144354360
-
Environmental genome shotgun sequencing of the sargasso sea
-
Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
-
4
-
-
84864319256
-
Surveillance of fish species composition using environmental DNA
-
Minamoto, T., Yamanaka, H., Takahara, T., Honjo, M. N. & Kawabata, Z. i. Surveillance of fish species composition using environmental DNA. Limnology 13, 193-197 (2011).
-
(2011)
Limnology
, vol.13
, pp. 193-197
-
-
Minamoto, T.1
Yamanaka, H.2
Takahara, T.3
Honjo, M.N.4
Kawabata, Z.I.5
-
5
-
-
79960795565
-
Molecular detection of vertebrates in stream water: A demonstration using rocky mountain tailed frogs and Idaho giant salamanders
-
Goldberg, C. S., Pilliod, D. S., Arkle, R. S. & Waits, L. P. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLOS One 6, e22746 (2011).
-
(2011)
PLOS One
, vol.6
, pp. e22746
-
-
Goldberg, C.S.1
Pilliod, D.S.2
Arkle, R.S.3
Waits, L.P.4
-
6
-
-
85028161389
-
Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)
-
Biggs, J. et al. Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biol. Conserv. 183, 19-28 (2015).
-
(2015)
Biol. Conserv.
, vol.183
, pp. 19-28
-
-
Biggs, J.1
-
7
-
-
84890168653
-
Factors influencing detection of eDNA from a stream-dwelling amphibian
-
Pilliod, D. S., Goldberg, C. S., Arkle, R. S. & Waits, L. P. Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol. Ecol. Resour. 14, 109-116 (2014).
-
(2014)
Mol. Ecol. Resour.
, vol.14
, pp. 109-116
-
-
Pilliod, D.S.1
Goldberg, C.S.2
Arkle, R.S.3
Waits, L.P.4
-
8
-
-
84904401917
-
Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to detect invasive crayfish procambarus clarkiiin freshwater ponds
-
Tréguier, A. et al. Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkiiin freshwater ponds. J. Appl. Ecol. 51, 871-879 (2014).
-
(2014)
J. Appl. Ecol.
, vol.51
, pp. 871-879
-
-
Tréguier, A.1
-
9
-
-
84874628573
-
Validation of eDNA surveillance sensitivity for detection of asian carps in controlled and field experiments
-
Mahon, A. R. et al. Validation of eDNA surveillance sensitivity for detection of Asian carps in controlled and field experiments. PLOS One 8, e58316 (2013).
-
(2013)
PLOS One
, vol.8
, pp. e58316
-
-
Mahon, A.R.1
-
10
-
-
77957672841
-
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
-
Kuczynski, J. et al. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Meth. 7, 813-819 (2010).
-
(2010)
Nat. Meth.
, vol.7
, pp. 813-819
-
-
Kuczynski, J.1
-
11
-
-
0029687530
-
Reproducibility of ancient DNA sequences from extinct pleistocene fauna
-
Taylor, P. G. Reproducibility of ancient DNA sequences from extinct Pleistocene fauna. Mol. Biol. Evol. 13, 283-285 (1996).
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 283-285
-
-
Taylor, P.G.1
-
12
-
-
84861563592
-
Monitoring endangered freshwater biodiversity using environmental DNA
-
Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565-2573 (2012).
-
(2012)
Mol. Ecol.
, vol.21
, pp. 2565-2573
-
-
Thomsen, P.F.1
-
13
-
-
84859621660
-
New environmental metabarcodes for analysing soil DNA: Potential for studying past and present ecosystems
-
Epp, L. S. et al. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol. Ecol. 21, 1821-1833 (2012).
-
(2012)
Mol. Ecol.
, vol.21
, pp. 1821-1833
-
-
Epp, L.S.1
-
14
-
-
79751508033
-
Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces
-
Zeale, M. R., Butlin, R. K., Barker, G. L., Lees, D. C. & Jones, G. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol. Ecol. Resour. 11, 236-244 (2011).
-
(2011)
Mol. Ecol. Resour.
, vol.11
, pp. 236-244
-
-
Zeale, M.R.1
Butlin, R.K.2
Barker, G.L.3
Lees, D.C.4
Jones, G.5
-
15
-
-
33646592870
-
Isolation, amplification, and identification of ancient copepod DNA from lake sediments
-
Bissett, A., Gibson, J. A. E., Jarman, S. N., Swadling, K. M. & Cromer, L. Isolation, amplification, and identification of ancient copepod DNA from lake sediments. Limnol. Oceanogr.-Meth. 3, 533-542 (2005).
-
(2005)
Limnol. Oceanogr.-Meth.
, vol.3
, pp. 533-542
-
-
Bissett, A.1
Gibson, J.A.E.2
Jarman, S.N.3
Swadling, K.M.4
Cromer, L.5
-
16
-
-
33847371187
-
Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding
-
Taberlet, P. et al. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35, e14 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. e14
-
-
Taberlet, P.1
-
17
-
-
0242384034
-
Review and re-analysis of domain-specific 16S primers
-
Baker, G. C., Smith, J. J. & Cowan, D. A. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Meth. 55, 541-555 (2003).
-
(2003)
J. Microbiol. Meth.
, vol.55
, pp. 541-555
-
-
Baker, G.C.1
Smith, J.J.2
Cowan, D.A.3
-
18
-
-
81355143738
-
Barcoding diatoms: Evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols
-
Zimmermann, J., Jahn, R. & Gemeinholzer, B. Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Org. Divers. Evol. 11, 173-192 (2011).
-
(2011)
Org. Divers. Evol.
, vol.11
, pp. 173-192
-
-
Zimmermann, J.1
Jahn, R.2
Gemeinholzer, B.3
-
19
-
-
84862245279
-
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
-
Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC bioinformatics 13, 134 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 134
-
-
Ye, J.1
-
20
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega
-
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 539
-
-
Sievers, F.1
-
21
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in R language
-
Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289-290 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
23
-
-
80053316194
-
A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data
-
Chan, E. R. et al. A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data. Genomics 98, 253-259 (2011).
-
(2011)
Genomics
, vol.98
, pp. 253-259
-
-
Chan, E.R.1
-
24
-
-
84921929059
-
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
-
Deiner, K., Walser, J.-C., Mächler, E. & Altermatt, F. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol. Conserv. 183, 53-63 (2015).
-
(2015)
Biol. Conserv.
, vol.183
, pp. 53-63
-
-
Deiner, K.1
Walser, J.-C.2
Mächler, E.3
Altermatt, F.4
-
25
-
-
34249089172
-
Universal primers amplify a 23s rDNA plastid marker in eukaryotic algae and cyanobacteria
-
Sherwood, A. R. & Presting, G. G. Universal primers amplify a 23s rDNA plastid marker in eukaryotic algae and cyanobacteria. J. Phycol. 43, 605-608 (2007).
-
(2007)
J. Phycol.
, vol.43
, pp. 605-608
-
-
Sherwood, A.R.1
Presting, G.G.2
-
26
-
-
84857011001
-
PANDAseq: Paired-end assembler for illumina sequences
-
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G. & Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 31
-
-
Masella, A.P.1
Bartram, A.K.2
Truszkowski, J.M.3
Brown, D.G.4
Neufeld, J.D.5
-
27
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
28
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Meth. 7, 335-336 (2010).
-
(2010)
Nat. Meth.
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
29
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
30
-
-
12744281935
-
The extraction and purification of microbial DNA from sediments
-
Ogram, A., Sayler, G. S. & Barkay, T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Meth. 7, 57-66 (1987).
-
(1987)
J. Microbiol. Meth.
, vol.7
, pp. 57-66
-
-
Ogram, A.1
Sayler, G.S.2
Barkay, T.3
-
31
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005).
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
-
32
-
-
46949088285
-
Species detection using environmental DNA from water samples
-
Ficetola, G. F., Miaud, C., Pompanon, F. & Taberlet, P. Species detection using environmental DNA from water samples. Biol. Lett. 4, 423-425 (2008).
-
(2008)
Biol. Lett.
, vol.4
, pp. 423-425
-
-
Ficetola, G.F.1
Miaud, C.2
Pompanon, F.3
Taberlet, P.4
-
33
-
-
84857508990
-
Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments
-
Bik, H. M. et al. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol. Ecol. 21, 1048-1059 (2012).
-
(2012)
Mol. Ecol.
, vol.21
, pp. 1048-1059
-
-
Bik, H.M.1
-
34
-
-
84928642033
-
A metagenetic approach for revealing community structure of marine planktonic copepods
-
Hirai, J., Kuriyama, M., Ichikawa, T., Hidaka, K. & Tsuda, A. A metagenetic approach for revealing community structure of marine planktonic copepods. Mol. Ecol. Resour. 15, 68-80 (2015).
-
(2015)
Mol. Ecol. Resour.
, vol.15
, pp. 68-80
-
-
Hirai, J.1
Kuriyama, M.2
Ichikawa, T.3
Hidaka, K.4
Tsuda, A.5
-
35
-
-
84859623044
-
Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity
-
Andersen, K. et al. Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity. Mol. Ecol. 21, 1966-1979 (2012).
-
(2012)
Mol. Ecol.
, vol.21
, pp. 1966-1979
-
-
Andersen, K.1
-
36
-
-
84898618580
-
Using environmental DNA to census marine fishes in a large mesocosm
-
Kelly, R. P., Port, J. A., Yamahara, K. M. & Crowder, L. B. Using environmental DNA to census marine fishes in a large mesocosm. PLOS One 9, e86175 (2014).
-
(2014)
PLOS One
, vol.9
, pp. e86175
-
-
Kelly, R.P.1
Port, J.A.2
Yamahara, K.M.3
Crowder, L.B.4
-
37
-
-
84908601386
-
Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species
-
Mächler, E., Deiner, K., Steinmann, P. & Altermatt, F. Utility of Environmental DNA for Monitoring Rare and Indicator Macroinvertebrate Species. Freshwater Science 33, 1174-1183 (2014).
-
(2014)
Freshwater Science
, vol.33
, pp. 1174-1183
-
-
Mächler, E.1
Deiner, K.2
Steinmann, P.3
Altermatt, F.4
-
38
-
-
84895765802
-
Transport distance of invertebrate environmental DNA in a natural river
-
Deiner, K. & Altermatt, F. Transport distance of invertebrate environmental DNA in a natural river. PLOS One 9, e88786 (2014).
-
(2014)
PLOS One
, vol.9
, pp. e88786
-
-
Deiner, K.1
Altermatt, F.2
-
39
-
-
77954554269
-
An in silico approach for the evaluation of DNA barcodes
-
Ficetola, G. F. et al. An in silico approach for the evaluation of DNA barcodes. BMC Genomics 11, 434 (2010).
-
(2010)
BMC Genomics
, vol.11
, pp. 434
-
-
Ficetola, G.F.1
-
40
-
-
84925340061
-
REVIEW: The detection of aquatic animal species using environmental DNA-A review of eDNA as a survey tool in ecology
-
Rees, H. C. et al. REVIEW: The detection of aquatic animal species using environmental DNA-a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51, 1450-1459 (2014).
-
(2014)
J. Appl. Ecol.
, vol.51
, pp. 1450-1459
-
-
Rees, H.C.1
-
41
-
-
84904345282
-
Particle size distribution and optimal capture of aqueous macrobial eDNA
-
Turner, C. R. et al. Particle size distribution and optimal capture of aqueous macrobial eDNA. Meth. Ecol. Evol. 5, 676-684 (2014).
-
(2014)
Meth. Ecol. Evol.
, vol.5
, pp. 676-684
-
-
Turner, C.R.1
-
42
-
-
84931956994
-
Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods
-
Pinol, J., Mir, G., Gomez-Polo, P. & Agusti, N. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol. Ecol. Resour. 15, 819-830 (2015).
-
(2015)
Mol. Ecol. Resour.
, vol.15
, pp. 819-830
-
-
Pinol, J.1
Mir, G.2
Gomez-Polo, P.3
Agusti, N.4
-
43
-
-
84941286809
-
Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass-sequence relationships with an innovative metabarcoding protocol
-
Elbrecht, V. & Leese, F. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass-Sequence Relationships with an Innovative Metabarcoding Protocol. PLOS One 10, e0130324 (2015).
-
(2015)
PLOS One
, vol.10
, pp. e0130324
-
-
Elbrecht, V.1
Leese, F.2
-
44
-
-
84872282833
-
Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol
-
Hajibabaei, M., Spall, J. L., Shokralla, S. & van Konynenburg, S. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecol. 12, 28 (2012).
-
(2012)
BMC Ecol.
, vol.12
, pp. 28
-
-
Hajibabaei, M.1
Spall, J.L.2
Shokralla, S.3
Van Konynenburg, S.4
-
45
-
-
84901823211
-
Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics
-
Gibson, J. et al. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc. Natl. Acad. Sci. USA 111, 8007-8012 (2014).
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 8007-8012
-
-
Gibson, J.1
-
46
-
-
84956702713
-
Metabarcoding is powerful yet still blind: A comparative analysis of morphological and molecular surveys of seagrass communities
-
Cowart, D. A. et al. Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities. PLOS One 10, e0117562 (2015).
-
(2015)
PLOS One
, vol.10
, pp. e0117562
-
-
Cowart, D.A.1
|