A Glossary of DNA Barcoding Terms.


Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2024
Historique:
medline: 29 4 2024
pubmed: 29 4 2024
entrez: 29 4 2024
Statut: ppublish

Résumé

This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.

Identifiants

pubmed: 38683343
doi: 10.1007/978-1-0716-3581-0_35
doi:

Substances chimiques

DNA 9007-49-2

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

561-572

Informations de copyright

© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Références

Ronquist F, Huelsenbeck JP (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574
doi: 10.1093/bioinformatics/btg180 pubmed: 12912839
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci 107(20):9264–9269
doi: 10.1073/pnas.0913022107 pubmed: 20439743 pmcid: 2889046
Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C (2012) Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol 27(9):480–488
doi: 10.1016/j.tree.2012.04.012 pubmed: 22633974
Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8(7):e66213
doi: 10.1371/journal.pone.0066213 pubmed: 23861743 pmcid: 3704603
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791
doi: 10.2307/2408678 pubmed: 28561359
Vieites DR, Wollenberg KC, Andreone F, Köhler J, Glaw F, Vences M (2009) Vast underestimation of Madagascar’s biodiversity evidenced by an integrative amphibian inventory. Proc Natl Acad Sci 106(20):8267–8272
doi: 10.1073/pnas.0810821106 pubmed: 19416818 pmcid: 2688882
Sarkar IN, Planet PJ, Desalle ROB (2008) CAOS software for use in character-based DNA barcoding. Mol Ecol Resour 8(6):1256–1259
doi: 10.1111/j.1755-0998.2008.02235.x pubmed: 21586014
Jörger KM, Schrödl M (2013) How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 10(1):1–27
doi: 10.1186/1742-9994-10-59
Davis JI, Nixon KC (1992) Populations, genetic variation, and the delimitation of phylogenetic species. Syst Biol 41(4):421–435
doi: 10.1093/sysbio/41.4.421
Jombart T, Balloux F, Dray S (2010) Adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics 26(15):1907–1909
doi: 10.1093/bioinformatics/btq292 pubmed: 20525823
Tautz D, Arctander P, Minelli A et al (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74. https://doi.org/10.1016/S0169-5347(02)00041-1
doi: 10.1016/S0169-5347(02)00041-1
de Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879–886. https://doi.org/10.1080/10635150701701083
doi: 10.1080/10635150701701083 pubmed: 18027281
Collins RA, Cruickshank RH (2013) The seven deadly sins of DNA barcoding. Mol Ecol Res 13:969–975. https://doi.org/10.1111/1755-0998.12046
Miralles A, Ducasse J, Brouillet S et al (2022) SPART: a versatile and standardized data exchange format for species partition information. Mol Ecol Resour 22:430–438. https://doi.org/10.1111/1755-0998.13470
doi: 10.1111/1755-0998.13470 pubmed: 34288531
Dayrat B (2005) Toward integrative taxonomy. Biol J Linn Soc 85:407–415. https://doi.org/10.1111/j.1095-8312.2005.00503.x
doi: 10.1111/j.1095-8312.2005.00503.x
Will KP, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–851. https://doi.org/10.1080/10635150500354878
doi: 10.1080/10635150500354878 pubmed: 16243769
Avise JC, Jonathan Arnold R, Ball M, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18(1):489–522
doi: 10.1146/annurev.es.18.110187.002421
Brower AVZ (1999) Delimitation of phylogenetic species with DNA sequences: a critique of Davis and Nixon’s population aggregation analysis. Syst Biol 48:199–213
doi: 10.1080/106351599260535 pubmed: 12078641
Doyle JJ (1995) The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Syst Bot 20:574–588
doi: 10.2307/2419811
Puillandre N, Modica MV, Zhang Y et al (2012) Large-scale species delimitation method for hyperdiverse groups. Mol Ecol 21:2671–2691. https://doi.org/10.1111/j.1365-294X.2012.05559.x
doi: 10.1111/j.1365-294X.2012.05559.x pubmed: 22494453
Galtier N (2019) Delineating species in the speciation continuum: a proposal. Evol Appl 12:657–663. https://doi.org/10.1111/eva.12748
doi: 10.1111/eva.12748 pubmed: 30976300 pmcid: 6439491
DeSalle R (2006) Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv Biol 20(5):1545–1547
doi: 10.1111/j.1523-1739.2006.00543.x pubmed: 17002772
Rubinoff D (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20(4):1026–1033
doi: 10.1111/j.1523-1739.2006.00372.x pubmed: 16922219
Rubinoff D, Barcodes I (2006) DNA barcoding evolves into the familiar. Conserv Biol 20(5):1548–1549
doi: 10.1111/j.1523-1739.2006.00542.x pubmed: 17002773
Goldstein PZ, DeSalle R (2011) Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. BioEssays 33(2):135–147
doi: 10.1002/bies.201000036 pubmed: 21184470
Padial JM, Miralles A, De la Riva I, Vences M (2010) The integrative future of taxonomy. Front Zool 7:16. https://doi.org/10.1186/1742-9994-7-16
doi: 10.1186/1742-9994-7-16 pubmed: 20500846 pmcid: 2890416
Miralles A, Vences M (2013) New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One 8:e68242. https://doi.org/10.1371/journal.pone.0068242
doi: 10.1371/journal.pone.0068242 pubmed: 23874561 pmcid: 3710018
Ducasse J, Ung V, Lecointre G, Miralles A (2020) LIMES: a tool for comparing species partition. Bioinformatics 36:2282–2283. https://doi.org/10.1093/bioinformatics/btz911
doi: 10.1093/bioinformatics/btz911 pubmed: 31804675
Miralles A, Puillandre N, Vences M (2023) DNA barcoding in species delimitation: from genetic distances to integrative taxonomy. Chapter 4 in this book
DeSalle R, Goldstein P (2019) Review and interpretation of trends in DNA barcoding. Front Ecol Evol 7:302
doi: 10.3389/fevo.2019.00302

Auteurs

Miguel Vences (M)

Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.

Aurélien Miralles (A)

Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France.

Robert DeSalle (R)

Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA. desalle@amnh.org.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH