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references.bib
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references.bib
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@article{yang1998improved,
title={Improved DNA extraction from ancient bones using silica-based spin columns},
author={Yang, Dongya Y and Eng, Barry and Waye, John S and Dudar, J Christopher and Saunders, Shelley R},
journal={American Journal of Physical Anthropology: The Official Publication of the American Association of Physical Anthropologists},
volume={105},
number={4},
pages={539--543},
year={1998},
publisher={Wiley Online Library}
}
@article{miya2015mifish,
title={MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species},
author={Miya, Masaki and Sato, Yukuto and Fukunaga, Tsukasa and Sado, Tetsuya and Poulsen, Jan Yde and Sato, Keiichi and Minamoto, Toshifumi and Yamamoto, Satoshi and Yamanaka, Hiroki and Araki, Hitoshi and others},
journal={Royal Society open science},
volume={2},
number={7},
pages={150088},
year={2015},
publisher={The Royal Society Publishing}
}
@article{riaz2011ecoprimers,
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},
journal={Nucleic acids research},
volume={39},
number={21},
pages={e145--e145},
year={2011},
publisher={Oxford University Press}
}
@article{altschul1990basic,
title={Basic local alignment search tool},
author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
journal={Journal of molecular biology},
volume={215},
number={3},
pages={403--410},
year={1990},
publisher={Elsevier}
}
@article{callahan2016dada2,
title={DADA2: high-resolution sample inference from Illumina amplicon data},
author={Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
journal={Nature methods},
volume={13},
number={7},
pages={581},
year={2016},
publisher={Nature Publishing Group}
}
@article{zieritz2012identifying,
title={Identifying freshwater mussels (Unionoida) and parasitic glochidia larvae from host fish gills: a molecular key to the North and Central European species},
author={Zieritz, Alexandra and Gum, Bernhard and Kuehn, Ralph and Geist, Juergen},
journal={Ecology and evolution},
volume={2},
number={4},
pages={740--750},
year={2012},
publisher={Wiley Online Library}
}
@article{sell2013identification,
title={Identification and characterization of the first microsatellite loci for the thick-shelled river mussel Unio crassus (Bivalvia: Unionidae)},
author={Sell, Jerzy and Mioduchowska, Monika and Kaczmarczyk, Agnieszka and Szyma{\'n}czak, Robert},
journal={Journal of Experimental Zoology Part A: Ecological Genetics and Physiology},
volume={319},
number={2},
pages={113--116},
year={2013},
publisher={Wiley Online Library}
}
@article{ivanova2007universal,
title={Universal primer cocktails for fish DNA barcoding},
author={Ivanova, Natalia V and Zemlak, Tyler S and Hanner, Robert H and Hebert, Paul DN},
journal={Molecular Ecology Resources},
volume={7},
number={4},
pages={544--548},
year={2007},
publisher={Wiley Online Library}
}
@Manual{bold,
title = {bold: Interface to Bold Systems API},
author = {Scott Chamberlain},
year = {2017},
note = {R package version 0.5.0},
url = {https://CRAN.R-project.org/package=bold}
}
@Article{decipher,
title = {Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R},
author = {Erik S. Wright},
journal = {The R Journal},
year = {2016},
volume = {8},
number = {1},
pages = {352-359}
}
@Article{sangerseqr,
title = {Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products},
author = {Jonathon T Hill and Bradley L Demarest and Brent W Bisgrove and Yi-chu Su and Megan Smith and H. Joseph Yost},
year = {2014},
journal = {Developmental Dynamics},
}
@Manual{sangeranalyser,
title = {sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R},
author = {Rob Lanfear},
year = {2015},
note = {R package version 0.1.0}
}
@article{atkinson2018quantitative,
title={A quantitative PCR-based environmental DNA assay for detecting Atlantic salmon (Salmo salar L.)},
author={Atkinson, Siobh{\'a}n and Carlsson, Jeanette EL and Ball, Bernard and Egan, Damian and Kelly-Quinn, Mary and Whelan, Ken and Carlsson, Jens},
journal={Aquatic Conservation: Marine and Freshwater Ecosystems},
volume={28},
number={5},
pages={1238--1243},
year={2018},
publisher={Wiley Online Library}
}
@article{carim2016environmental,
title={An environmental DNA marker for detecting nonnative brown trout (Salmo trutta)},
author={Carim, KJ and Wilcox, TM and Anderson, M and Lawrence, DJ and Young, MK and McKelvey, KS and Schwartz, MK},
journal={Conservation Genetics Resources},
volume={8},
number={3},
pages={259--261},
year={2016},
publisher={Springer}
}
@article{altschul1990basic,
title={Basic local alignment search tool},
author={Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
journal={Journal of molecular biology},
volume={215},
number={3},
pages={403--410},
year={1990},
publisher={Elsevier}
}
@Article{covarrubias2016fragman,
title = {Fragman: An R package for fragment analysis},
author = {Covarrubias-Pazaran G and Diaz-Garcia L and Schlautman B and Salazar W and Zalapa J},
journal = {BMC Genetics},
year = {2016},
volume = {17(62)},
pages = {1-8},
}
@Manual{goudet2015hierfstat,
title = {hierfstat: Estimation and Tests of Hierarchical F-Statistics},
author = {Jerome Goudet and Thibaut Jombart},
year = {2015},
note = {R package version 0.04-22},
url = {https://CRAN.R-project.org/package=hierfstat},
}
@Article{paradis2010pegas,
title = {pegas: an {R} package for population genetics with an integrated--modular approach},
author = {E. Paradis},
journal = {Bioinformatics},
year = {2010},
volume = {26},
pages = {419-420},
}
@Article{jombart2008adegenet,
title = {adegenet: a R package for the multivariate analysis of genetic markers},
journal = {Bioinformatics},
year = {2008},
author = {T. Jombart},
volume = {24},
pages = {1403-1405},
doi = {10.1093/bioinformatics/btn129},
}
@article{martin2011cutadapt,
title={Cutadapt removes adapter sequences from high-throughput sequencing reads},
author={Martin, Marcel},
journal={EMBnet. journal},
volume={17},
number={1},
pages={10--12},
year={2011}
}
@article{roy2018development,
title={Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada},
author={Roy, M{\'e}lanie and Belliveau, Val{\'e}rie and Mandrak, Nicholas E and Gagn{\'e}, Nellie},
journal={Biological invasions},
volume={20},
number={2},
pages={299--314},
year={2018},
publisher={Springer}
}
@article{hellstrom2018inventering,
title={Inventering av fiskf{\"o}rekomst med eDNA, i sj{\"o}n B{\aa}ven, S{\"o}rmlands l{\"a}n.},
author={Hellstr{\"o}m, Micaela and Spens, Johan},
year={2018}
}
@misc{jeuthe2018mal,
title={Mal i B{\aa}ven 2017--Inventeringsstudier i lekomr{\aa}den},
author={Jeuthe, Henrik and {\"O}stby, David and others},
year={2018},
publisher={L{\"a}nsstyrelsen i S{\"o}dermanlands l{\"a}n}
}