common-bib_01.bib

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@ARTICLE{Eaton2017-gx,
  title    = "Misconceptions on missing data in {RAD-seq} phylogenetics with a
              deep-scale example from flowering plants",
  author   = "Eaton, Deren A R and Spriggs, Elizabeth L and Park, Brian and
              Donoghue, Michael J",
  journal  = "Syst. Biol.",
  volume   =  66,
  number   =  3,
  pages    = "399--412",
  month    =  may,
  year     =  2017,
  language = "en",
  issn     = "1063-5157, 1076-836X",
  pmid     = "27798402",
  doi      = "10.1093/sysbio/syw092"
}


@ARTICLE{Tripp2017-cp,
  title    = "{RADseq} dataset with 90\% missing data fully resolves recent
              radiation of Petalidium (Acanthaceae) in the ultra-arid deserts
              of Namibia",
  author   = "Tripp, Erin A and Tsai, Yi-Hsin Erica and Zhuang, Yongbin and
              Dexter, Kyle G",
  journal  = "Ecol. Evol.",
  volume   =  7,
  number   =  19,
  pages    = "7920--7936",
  month    =  oct,
  year     =  2017,
  language = "en",
  issn     = "2045-7758",
  pmid     = "29043045",
  doi      = "10.1002/ece3.3274",
  pmc      = "PMC5632676"
}


@ARTICLE{Gautier2013-vj,
  title    = "The effect of {RAD} allele dropout on the estimation of genetic
              variation within and between populations",
  author   = "Gautier, Mathieu and Gharbi, Karim and Cezard, Timothee and
              Foucaud, Julien and Kerdelhu{\'e}, Carole and Pudlo, Pierre and
              Cornuet, Jean-Marie and Estoup, Arnaud",
  journal  = "Mol. Ecol.",
  volume   =  22,
  number   =  11,
  pages    = "3165--3178",
  month    =  jun,
  year     =  2013,
  language = "en",
  issn     = "0962-1083, 1365-294X",
  pmid     = "23110526",
  doi      = "10.1111/mec.12089"
}


@ARTICLE{Leache2015-eg,
  title    = "Phylogenomics of phrynosomatid lizards: conflicting signals from
              sequence capture versus restriction site associated {DNA}
              sequencing",
  author   = "Leach{\'e}, Adam D and Chavez, Andreas S and Jones, Leonard N and
              Grummer, Jared A and Gottscho, Andrew D and Linkem, Charles W",
  journal  = "Genome Biol. Evol.",
  volume   =  7,
  number   =  3,
  pages    = "706--719",
  month    =  feb,
  year     =  2015,
  language = "en",
  issn     = "1759-6653",
  pmid     = "25663487",
  doi      = "10.1093/gbe/evv026",
  pmc      = "PMC5322549"
}


@ARTICLE{Huang2016-na,
  title    = "Unforeseen consequences of excluding missing data from
              next-generation sequences: Simulation study of {RAD} sequences",
  author   = "Huang, Huateng and Knowles, L Lacey",
  journal  = "Syst. Biol.",
  volume   =  65,
  number   =  3,
  pages    = "357--365",
  month    =  may,
  year     =  2016,
  language = "en",
  issn     = "1063-5157, 1076-836X",
  pmid     = "24996413",
  doi      = "10.1093/sysbio/syu046"
}


@ARTICLE{Martin-Hernanz2019-bu,
  title    = "Maximize Resolution or Minimize Error? Using
              {Genotyping-By-Sequencing} to Investigate the Recent
              Diversification of Helianthemum (Cistaceae)",
  author   = "Mart{\'\i}n-Hernanz, Sara and Aparicio, Abelardo and
              Fern{\'a}ndez-Mazuecos, Mario and Rubio, Encarnaci{\'o}n and
              Reyes-Betancort, J Alfredo and Santos-Guerra, Arnoldo and
              Olangua-Corral, Mar{\'\i}a and Albaladejo, Rafael G",
  journal  = "Front. Plant Sci.",
  volume   =  10,
  pages    = "1416",
  month    =  nov,
  year     =  2019,
  language = "en",
  issn     = "1664-462X",
  pmid     = "31781140",
  doi      = "10.3389/fpls.2019.01416",
  pmc      = "PMC6859804"
}


@ARTICLE{Silliman2021-oo,
  title    = "Base-substitution mutation rate across the nuclear genome of
              Alpheus snapping shrimp and the timing of isolation by the
              Isthmus of Panama",
  author   = "Silliman, Katherine and Indorf, Jane L and Knowlton, Nancy and
              Browne, William E and Hurt, Carla",
  journal  = "BMC Ecol Evol",
  volume   =  21,
  number   =  1,
  pages    = "104",
  month    =  may,
  year     =  2021,
  language = "en",
  issn     = "2730-7182",
  pmid     = "34049492",
  doi      = "10.1186/s12862-021-01836-3",
  pmc      = "PMC8164322"
}


@ARTICLE{Diaz-Arce2019-nh,
  title    = "Selecting {RAD-Seq} Data Analysis Parameters for Population
              Genetics: The More the Better?",
  author   = "D{\'\i}az-Arce, Natalia and Rodr{\'\i}guez-Ezpeleta, Naiara",
  journal  = "Front. Genet.",
  volume   =  10,
  pages    = "533",
  month    =  may,
  year     =  2019,
  language = "en",
  issn     = "1664-8021",
  pmid     = "31191624",
  doi      = "10.3389/fgene.2019.00533",
  pmc      = "PMC6549478"
}



@ARTICLE{Peterson2012-tr,
  title    = "Double digest {RADseq}: an inexpensive method for de novo {SNP}
              discovery and genotyping in model and non-model species",
  author   = "Peterson, Brant K and Weber, Jesse N and Kay, Emily H and Fisher,
              Heidi S and Hoekstra, Hopi E",
  journal  = "PLoS One",
  volume   =  7,
  number   =  5,
  pages    = "e37135",
  month    =  may,
  year     =  2012,
  language = "en",
  issn     = "1932-6203",
  pmid     = "22675423",
  doi      = "10.1371/journal.pone.0037135",
  pmc      = "PMC3365034"
}



@ARTICLE{Lou2021-ew,
  title     = "Batch effects in population genomic studies with low-coverage
               whole genome sequencing data: causes, detection, and mitigation",
  author    = "Lou, Runyang Nicolas and Therkildsen, Nina Overgaard",
  journal   = "Authorea Preprints",
  publisher = "Authorea",
  month     =  aug,
  year      =  2021,
  doi       = "10.22541/au.162791857.78788821/v2"
}


@ARTICLE{Davies2016-rq,
  title    = "Rapid genotype imputation from sequence without reference panels",
  author   = "Davies, Robert W and Flint, Jonathan and Myers, Simon and Mott,
              Richard",
  journal  = "Nat. Genet.",
  volume   =  48,
  number   =  8,
  pages    = "965--969",
  month    =  aug,
  year     =  2016,
  language = "en",
  issn     = "1061-4036, 1546-1718",
  pmid     = "27376236",
  doi      = "10.1038/ng.3594",
  pmc      = "PMC4966640"
}


@ARTICLE{Rubinacci2021-dm,
  title    = "Efficient phasing and imputation of low-coverage sequencing data
              using large reference panels",
  author   = "Rubinacci, Simone and Ribeiro, Diogo M and Hofmeister, Robin J
              and Delaneau, Olivier",
  journal  = "Nat. Genet.",
  volume   =  53,
  number   =  1,
  pages    = "120--126",
  month    =  jan,
  year     =  2021,
  language = "en",
  issn     = "1061-4036, 1546-1718",
  pmid     = "33414550",
  doi      = "10.1038/s41588-020-00756-0"
}


@article{Fuller2020,
author = {Zachary L. Fuller  and Veronique J. L. Mocellin  and Luke A. Morris  and Neal Cantin  and Jihanne Shepherd  and Luke Sarre  and Julie Peng  and Yi Liao  and Joseph Pickrell  and Peter Andolfatto  and Mikhail Matz  and Line K. Bay  and Molly Przeworski },
title = {Population genetics of the coral <i>Acropora millepora</i>: Toward genomic prediction of bleaching},
journal = {Science},
volume = {369},
number = {6501},
pages = {eaba4674},
year = {2020},
doi = {10.1126/science.aba4674},

URL = {https://www.science.org/doi/abs/10.1126/science.aba4674},
eprint = {https://www.science.org/doi/pdf/10.1126/science.aba4674}
,
    abstract = { Corals worldwide are under threat from rising sea temperatures and pollution. One response to heat stress is coral bleaching—the loss of photosynthetic endosymbionts that provide energy for the coral. Fuller et al. present a high-resolution genome of the coral Acropora millepora (see the Perspective by Bay and Guerrero). They were able to perform population genetic analyses with samples sequenced at lower coverage and conduct genome-wide association studies. These data were combined to generate a polygenic risk score for bleaching that can be used in coral conservation. Science this issue p. eaba4674; see also p. 249 A high-quality genome analysis of a branching stony coral helps elucidate the genetics of coral bleaching. Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies. }
}

@ARTICLE{Lou2021-me,
  title    = "A beginner's guide to low-coverage whole genome sequencing for
              population genomics",
  author   = "Lou, Runyang Nicolas and Jacobs, Arne and Wilder, Aryn P and
              Therkildsen, Nina Overgaard",
  journal  = "Mol. Ecol.",
  month    =  jul,
  year     =  2021,
  language = "en",
  issn     = "0962-1083, 1365-294X",
  pmid     = "34250668",
  doi      = "10.1111/mec.16077"
}


@ARTICLE{Rivera-Colon2021-en,
  title    = "Simulation with {RADinitio} improves {RADseq} experimental design
              and sheds light on sources of missing data",
  author   = "Rivera-Col{\'o}n, Angel G and Rochette, Nicolas C and Catchen,
              Julian M",
  journal  = "Mol. Ecol. Resour.",
  volume   =  21,
  number   =  2,
  pages    = "363--378",
  month    =  feb,
  year     =  2021,
  language = "en",
  issn     = "1755-098X, 1755-0998",
  pmid     = "32275349",
  doi      = "10.1111/1755-0998.13163"
}


@ARTICLE{Dorant2019-fb,
  title    = "Comparing Pool-seq, Rapture, and {GBS} genotyping for inferring
              weak population structure: The American lobster (Homarus
              americanus) as a case study",
  author   = "Dorant, Yann and Benestan, Laura and Rougemont, Quentin and
              Normandeau, Eric and Boyle, Brian and Rochette, R{\'e}my and
              Bernatchez, Louis",
  journal  = "Ecol. Evol.",
  volume   =  9,
  number   =  11,
  pages    = "6606--6623",
  month    =  jun,
  year     =  2019,
  language = "en",
  issn     = "2045-7758",
  pmid     = "31236247",
  doi      = "10.1002/ece3.5240",
  pmc      = "PMC6580275"
}

@ARTICLE{Fuentes-Pardo2017-nu,
  title    = "Whole-genome sequencing approaches for conservation biology:
              Advantages, limitations and practical recommendations",
  author   = "Fuentes-Pardo, Angela P and Ruzzante, Daniel E",
  journal  = "Mol. Ecol.",
  volume   =  26,
  number   =  20,
  pages    = "5369--5406",
  month    =  oct,
  year     =  2017,
  language = "en",
  issn     = "0962-1083, 1365-294X",
  pmid     = "28746784",
  doi      = "10.1111/mec.14264"
}


@ARTICLE{Dorant2019-fb,
  title    = "Comparing Pool-seq, Rapture, and {GBS} genotyping for inferring
              weak population structure: The American lobster (Homarus
              americanus) as a case study",
  author   = "Dorant, Yann and Benestan, Laura and Rougemont, Quentin and
              Normandeau, Eric and Boyle, Brian and Rochette, R{\'e}my and
              Bernatchez, Louis",
  journal  = "Ecol. Evol.",
  volume   =  9,
  number   =  11,
  pages    = "6606--6623",
  month    =  jun,
  year     =  2019,
  language = "en",
  issn     = "2045-7758",
  pmid     = "31236247",
  doi      = "10.1002/ece3.5240",
  pmc      = "PMC6580275"
}

@ARTICLE{Benjelloun2019-dq,
  title    = "An evaluation of sequencing coverage and genotyping strategies to
              assess neutral and adaptive diversity",
  author   = "Benjelloun, Badr and Boyer, Fr{\'e}d{\'e}ric and Streeter, Ian
              and Zamani, Wahid and Engelen, Stefan and Alberti, Adriana and
              Alberto, Florian J and BenBati, Mohamed and Ibnelbachyr, Mustapha
              and Chentouf, Mouad and Bechchari, Abdelmajid and Rezaei, Hamid R
              and Naderi, Saeid and Stella, Alessandra and Chikhi, Abdelkader
              and Clarke, Laura and Kijas, James and Flicek, Paul and Taberlet,
              Pierre and Pompanon, Fran{\c c}ois",
  journal  = "Mol. Ecol. Resour.",
  volume   =  19,
  number   =  6,
  pages    = "1497--1515",
  month    =  nov,
  year     =  2019,
  language = "en",
  issn     = "1755-098X, 1755-0998",
  pmid     = "31359622",
  doi      = "10.1111/1755-0998.13070",
  pmc      = "PMC7115901"
}


@ARTICLE{Zheng2017-pl,
  title    = "{SeqArray-a} storage-efficient high-performance data format for
              {WGS} variant calls",
  author   = "Zheng, Xiuwen and Gogarten, Stephanie M and Lawrence, Michael and
              Stilp, Adrienne and Conomos, Matthew P and Weir, Bruce S and
              Laurie, Cathy and Levine, David",
  journal  = "Bioinformatics",
  volume   =  33,
  number   =  15,
  pages    = "2251--2257",
  month    =  aug,
  year     =  2017,
  language = "en",
  issn     = "1367-4803, 1367-4811",
  pmid     = "28334390",
  doi      = "10.1093/bioinformatics/btx145",
  pmc      = "PMC5860110"
}

@ARTICLE{Mastretta-Yanes2015-jb,
  title    = "Restriction site-associated {DNA} sequencing, genotyping error
              estimation and de novo assembly optimization for population
              genetic inference",
  author   = "Mastretta-Yanes, A and Arrigo, N and Alvarez, N and Jorgensen, T
              H and Pi{\~n}ero, D and Emerson, B C",
  journal  = "Mol. Ecol. Resour.",
  volume   =  15,
  number   =  1,
  pages    = "28--41",
  month    =  jan,
  year     =  2015,
  language = "en",
  issn     = "1755-098X, 1755-0998",
  pmid     = "24916682",
  doi      = "10.1111/1755-0998.12291"
}

@ARTICLE{LaCava2020-bg,
  title    = "Accuracy of de novo assembly of {DNA} sequences from
              double-digest libraries varies substantially among software",
  author   = "LaCava, Melanie E F and Aikens, Ellen O and Megna, Libby C and
              Randolph, Gregg and Hubbard, Charley and Buerkle, C Alex",
  journal  = "Mol. Ecol. Resour.",
  volume   =  20,
  number   =  2,
  pages    = "360--370",
  month    =  mar,
  year     =  2020,
  language = "en",
  issn     = "1755-098X, 1755-0998",
  pmid     = "31665547",
  doi      = "10.1111/1755-0998.13108"
}

@ARTICLE{McCartney-Melstad2019-ac,
  title    = "An empirical pipeline for choosing the optimal clustering
              threshold in {RADseq} studies",
  author   = "McCartney-Melstad, Evan and Gidi{\c s}, M{\"u}ge and Shaffer, H
              Bradley",
  journal  = "Mol. Ecol. Resour.",
  volume   =  19,
  number   =  5,
  pages    = "1195--1204",
  month    =  sep,
  year     =  2019,
  language = "en",
  issn     = "1755-098X, 1755-0998",
  pmid     = "31058458",
  doi      = "10.1111/1755-0998.13029"
}

@ARTICLE{OLeary2018-iy,
  title    = "These aren't the loci you'e looking for: Principles of effective
              {SNP} filtering for molecular ecologists",
  author   = "O'Leary, Shannon J and Puritz, Jonathan B and Willis, Stuart C
              and Hollenbeck, Christopher M and Portnoy, David S",
  journal  = "Mol. Ecol.",
  month    =  jul,
  year     =  2018,
  language = "en",
  issn     = "0962-1083, 1365-294X",
  pmid     = "29987880",
  doi      = "10.1111/mec.14792"
}

@ARTICLE{Matz2018-vl,
  title    = "Fantastic Beasts and How To Sequence Them: Ecological Genomics
              for Obscure Model Organisms",
  author   = "Matz, Mikhail V",
  journal  = "Trends Genet.",
  volume   =  34,
  number   =  2,
  pages    = "121--132",
  month    =  feb,
  year     =  2018,
  language = "en",
  issn     = "0168-9525",
  pmid     = "29198378",
  doi      = "10.1016/j.tig.2017.11.002"
}

@ARTICLE{Elshire2011-or,
  title    = "A robust, simple genotyping-by-sequencing ({{GBS}}) approach for
              high diversity species",
  author   = "Elshire, Robert J and Glaubitz, Jeffrey C and Sun, Qi and Poland,
              Jesse A and Kawamoto, Ken and Buckler, Edward S and Mitchell,
              Sharon E",
  journal  = "PLoS One",
  volume   =  6,
  number   =  5,
  pages    = "e19379",
  month    =  may,
  year     =  2011,
  language = "en",
  issn     = "1932-6203",
  pmid     = "21573248",
  doi      = "10.1371/journal.pone.0019379",
  pmc      = "PMC3087801"
}

}


@ARTICLE{Andrews2016-ay,
  title    = "Harnessing the power of {RADseq} for ecological and evolutionary
              genomics",
  author   = "Andrews, Kimberly R and Good, Jeffrey M and Miller, Michael R and
              Luikart, Gordon and Hohenlohe, Paul A",
  journal  = "Nat. Rev. Genet.",
  volume   =  17,
  number   =  2,
  pages    = "81--92",
  month    =  feb,
  year     =  2016,
  language = "en",
  issn     = "1471-0056, 1471-0064",
  pmid     = "26729255",
  doi      = "10.1038/nrg.2015.28",
  pmc      = "PMC4823021"
}


@ARTICLE{Wagner2013-ff,
  title    = "Genome-wide {RAD} sequence data provide unprecedented resolution
              of species boundaries and relationships in the Lake Victoria
              cichlid adaptive radiation",
  author   = "Wagner, Catherine E and Keller, Irene and Wittwer, Samuel and
              Selz, Oliver M and Mwaiko, Salome and Greuter, Lucie and
              Sivasundar, Arjun and Seehausen, Ole",
  journal  = "Mol. Ecol.",
  volume   =  22,
  number   =  3,
  pages    = "787--798",
  month    =  feb,
  year     =  2013,
  language = "en",
  issn     = "0962-1083, 1365-294X",
  pmid     = "23057853",
  doi      = "10.1111/mec.12023"
}


@ARTICLE{Rubin2012-hw,
  title    = "Inferring phylogenies from {RAD} sequence data",
  author   = "Rubin, Benjamin E R and Ree, Richard H and Moreau, Corrie S",
  journal  = "PLoS One",
  volume   =  7,
  number   =  4,
  pages    = "e33394",
  month    =  apr,
  year     =  2012,
  language = "en",
  issn     = "1932-6203",
  pmid     = "22493668",
  doi      = "10.1371/journal.pone.0033394",
  pmc      = "PMC3320897"
}


@ARTICLE{Harvey2015-vh,
  title    = "Similarity thresholds used in {DNA} sequence assembly from short
              reads can reduce the comparability of population histories across
              species",
  author   = "Harvey, Michael G and Judy, Caroline Duffie and Seeholzer, Glenn
              F and Maley, James M and Graves, Gary R and Brumfield, Robb T",
  journal  = "PeerJ",
  volume   =  3,
  pages    = "e895",
  month    =  apr,
  year     =  2015,
  language = "en",
  issn     = "2167-8359",
  pmid     = "25922792",
  doi      = "10.7717/peerj.895",
  pmc      = "PMC4411482"
}


@ARTICLE{Ilut2014-ja,
  title    = "Defining loci in restriction-based reduced representation genomic
              data from nonmodel species: sources of bias and diagnostics for
              optimal clustering",
  author   = "Ilut, Daniel C and Nydam, Marie L and Hare, Matthew P",
  journal  = "Biomed Res. Int.",
  volume   =  2014,
  pages    = "675158",
  month    =  jun,
  year     =  2014,
  language = "en",
  issn     = "2314-6133, 2314-6141",
  pmid     = "25057498",
  doi      = "10.1155/2014/675158",
  pmc      = "PMC4095725"
}
@article{sims2014sequencing,
  title={Sequencing depth and coverage: key considerations in genomic analyses},
  author={Sims, David and Sudbery, Ian and Ilott, Nicholas E and Heger, Andreas and Ponting, Chris P},
  journal={Nature Reviews Genetics},
  volume={15},
  number={2},
  pages={121--132},
  year={2014},
  publisher={Nature Publishing Group}
}
@article{korneliussen2014angsd,
  title={ANGSD: analysis of next generation sequencing data},
  author={Korneliussen, Thorfinn Sand and Albrechtsen, Anders and Nielsen, Rasmus},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={1--13},
  year={2014},
  publisher={BioMed Central}
}
@article{jones2016targeted,
  title={Targeted capture in evolutionary and ecological genomics},
  author={Jones, Matthew R and Good, Jeffrey M},
  journal={Molecular ecology},
  volume={25},
  number={1},
  pages={185--202},
  year={2016},
  publisher={Wiley Online Library}
}
@article{futschik2010next,
  title={The next generation of molecular markers from massively parallel sequencing of pooled DNA samples},
  author={Futschik, Andreas and Schlötterer, Christian},
  journal={Genetics},
  volume={186},
  number={1},
  pages={207--218},
  year={2010},
  publisher={Oxford University Press}
}

@article{nielsen2011genotype,
  title={Genotype and SNP calling from next-generation sequencing data},
  author={Nielsen, Rasmus and Paul, Joshua S and Albrechtsen, Anders and Song, Yun S},
  journal={Nature Reviews Genetics},
  volume={12},
  number={6},
  pages={443--451},
  year={2011},
  publisher={Nature Publishing Group}
}
@article{puritz2018expressed,
  title={Expressed exome capture sequencing: A method for cost-effective exome sequencing for all organisms},
  author={Puritz, Jonathan B and Lotterhos, Katie E},
  journal={Molecular ecology resources},
  volume={18},
  number={6},
  pages={1209--1222},
  year={2018},
  publisher={Wiley Online Library}
}


@article{Schlotterer2014,
author = {Schl{\"{o}}tterer, Christian and Tobler, Raymond and Kofler, Robert and Nolte, Viola},
doi = {10.1038/nrg3803},
eprint = {NIHMS150003},
isbn = {1471-0056},
issn = {14710064},
journal = {Nature Reviews Genetics},
mendeley-groups = {Copepods/pool-seq},
number = {11},
pages = {749--763},
pmid = {25246196},
publisher = {Nature Publishing Group},
title = {{Sequencing pools of individuals-mining genome-wide polymorphism data without big funding}},
url = {http://dx.doi.org/10.1038/nrg3803},
volume = {15},
year = {2014}
}


@article{Griffiths2020,
author = {Griffiths, Joanna S and Kawji, Yasmeen and Kelly, Morgan W},
doi = {10.1093/molbev/msaa289},
issn = {0737-4038},
journal = {Molecular Biology and Evolution},
mendeley-groups = {Evolution in Conservation,Mine},
month = {nov},
number = {4},
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