The unholy trinity: taxonomy, species delimitation and DNA barcoding
Abstract
Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this ‘DNA barcoding’ initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the ‘DNA barcoding’ initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the ‘DNA barcoding’ initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings—Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of ‘DNA barcoding’.
References
-
Agosti D . 2003 Encyclopedia of life: should species description equal gene sequence?. Trends Ecol. Evol. 18, 273 doi:10.1016/S0169-5347(03)00099-5. . Crossref, ISI, Google Scholar -
Altschul S.F, Gish W, Miller W, Meyers E.W& Lipman D.J . 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403–410.doi:10.1006/jmbi.1990.9999. . Crossref, PubMed, ISI, Google Scholar -
Amato G, Egan M.G, Schaller G.B, Baker R.H, Rosenbaum H.C, Robichaud W.G& DeSalle R . 1999 The rediscovery of Roosevelt's barking deer (Muntiacus rooseveltorum). J. Mamm. 80, 639–643. Crossref, ISI, Google Scholar -
Avise J.C . 1989 A role for molecular genetic in the recognition and conservation of endangered species. Trends Ecol. Evol. 4, 279–281.doi:10.1016/0169-5347(89)90203-6. . Crossref, PubMed, ISI, Google Scholar -
Avise J.C& Ball R.M , Antonovics J& Futuyma D Oxford Surveys in Evolutionary Biology vol. 7 1990pp. 45–67. Eds. London:Oxford University Press. Google Scholar -
Avise J.C, Arnold J, Ball R.M, Bermingham E, Lamb T, Neigel J.E, Reeb C.A& Saunders N.C . 1987 Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18, 489–522. Crossref, Google Scholar -
Baker R.H& DeSalle R . 1997 Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst. Biol. 46, 654–673. Crossref, PubMed, ISI, Google Scholar -
Baker R.H, Yu X& DeSalle R . 1998 Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Mol. Phylogenet. Evol. 9, 427–436.doi:10.1006/mpev.1998.0519. . Crossref, PubMed, ISI, Google Scholar -
Baker C.S, Dalebout M.L, Lavery S& Ross H.A . 2003 www.DNA-surveillance: applied molecular taxonomy for species conservation and discovery. Trends Ecol. Evol. 18, 271 doi:10.1016/S0169-5347(03)00101-0. . Crossref, ISI, Google Scholar -
Baum D.A . 1992 Phylogenetic species concepts. Trends Ecol. Evol. 7, 2 doi:10.1016/0169-5347(92)90187-G. . Crossref, PubMed, ISI, Google Scholar -
Baum D.A& Donoghue M.J . 1995 Choosing among alternative ‘Phylogenetic’ species concepts. Syst. Bot. 20, 560–573. Crossref, ISI, Google Scholar -
Baum D.A& Shaw K.L Genealogical perspectives on the species problem. Experimental and molecular approaches to plant biosynthesis, Hoch P.C& Stephenson G.D . 1995pp. 289–303. Eds. St. Louis Missouri Botanical Garden:St. Louis. Google Scholar -
Birstein V.J, Doukakis P& DeSalle R . 2000 Polyphyly of mtDNA lineages in the Russian sturgeon, Acipenser gueldenstaedtii: forensic and evolutionary implications. Cons. Genet. 1, 81–88.doi:10.1023/A:1010141906100. . Crossref, Google Scholar -
Birstein V.J, Ruban G, Ludwig A, Doukakis P& DeSalle R . 2005 The enigmatic Caspian Sea Russian sturgeon: How many cryptic forms does it contain?. Systematics and Biodiversity. 3, 203–218.doi:10.1017/S1477200005001647. . Crossref, ISI, Google Scholar -
Black M.B, Halanych K.M, Maas P.A.Y, Hoeh W.R, Hashimoto J, Desbruyeres D, Lutz R.A& Vrijenhoek R.C . 1997 Molecular systematics of vestimentiferan tubeworms from hydrothermal vents and cold-water seeps. Mar. Biol. 130, 141–149.doi:10.1007/s002270050233. . Crossref, ISI, Google Scholar -
Blaxter M& Floyd R . 2003 Molecular taxonomics for biodiversity surveys: already a reality. Trends Ecol. Evol. 18, 268 doi:10.1016/S0169-5347(03)00102-2. . Crossref, ISI, Google Scholar -
Borda E& Siddall M.E . 2004 Arhynchobdellida (Annelida: Oligochaeta: Hirudinida): phylogenetic relationships and evolution. Mol. Phylogenet. Evol. 30, 213–225.doi:10.1016/j.ympev.2003.09.002. . Crossref, PubMed, ISI, Google Scholar -
Brower A.V.Z . 1999 A critique of Davis and Nixon's population aggregation analysis. Syst. Biol. 48, 199–213.doi:10.1080/106351599260535. . Crossref, PubMed, ISI, Google Scholar -
Cracraft J Species concepts and speciation analysis. Current Ornithology vol. 1 1983 New York:Plenum Press pp. 159–187. Google Scholar -
Cracraft J Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. Speciation and its consequences, Otte D& Endler J.A . 1989pp. 28–59. Eds. Sunderland, MA:Sinauer Associates, Inc.. Google Scholar -
Davis J.I& Nixon K.C . 1992 Populations, genetic variation, and the delimitation of phylogenetic species. Syst. Biol. 41, 421–435. Crossref, ISI, Google Scholar -
DeSalle R& Birstein V.J . 1996 PCR identification of black caviar. Nature. 381, 197–198.doi:10.1038/381197a0. . Crossref, ISI, Google Scholar -
Doukakis P, Birstein V.J, Ruban G.I& DeSalle R . 1999 Molecular genetic analysis among subspecies of two Eurasian sturgeon species, Acipenser baerii, and A. stellatus. Mol. Ecol. 8, 117–129.doi:10.1046/j.1365-294X.1999.00816.x. . Crossref, ISI, Google Scholar -
Dunn C.P . 2003 Keeping taxonomy based in morphology. Trends Ecol. Evol. 18, 270 doi:10.1016/S0169-5347(03)00094-6. . Crossref, ISI, Google Scholar -
Edmands S . 2001 Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes. Mol. Ecol. 10, 1743–1750.doi:10.1046/j.0962-1083.2001.01306.x. . Crossref, PubMed, ISI, Google Scholar -
Frost D.R& Kluge A.G . 1994 A consideration of epistemology in systematic biology, with special reference to species. Cladistics. 10, 259–294.doi:10.1111/j.1096-0031.1994.tb00178.x. . Crossref, ISI, Google Scholar -
Gatesy J, O'Grady P& Baker R.H . 1999 Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics. 15, 271–313.doi:10.1111/j.1096-0031.1999.tb00268.x. . Crossref, PubMed, ISI, Google Scholar -
Gatesy J, Matthee C, DeSalle R& Hayashi C . 2002 Resolution of a supertree/supermatrix paradox. Syst. Biol. 51, 652–664.doi:10.1080/10635150290102311. . Crossref, PubMed, ISI, Google Scholar -
Gatesy J, Amato G, Norell M, DeSalle R& Hayashi C . 2003 Combined support for wholesale taxic atavism in gavialine crocodylians. Syst. Biol. 52, 403–422. Crossref, PubMed, ISI, Google Scholar -
Gatesy J, Baker R.H& Hayashi C . 2004 Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53, 342–355.doi:10.1080/10635150490423971. . Crossref, PubMed, ISI, Google Scholar -
Godfray H.C.J . 2002 Challenges for taxonomy. Nature. 417, 17–19.doi:10.1038/417017a. . Crossref, PubMed, ISI, Google Scholar -
Goetze E . 2003 Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae. Proc. R. Soc. B. 270, 2321–2331.doi:10.1098/rspb.2003.2505. . Link, ISI, Google Scholar -
Goldstein P.Z& DeSalle R . 2000 Phylogenetic species, nested hierarchies, and character fixation. Cladistics. 16, 364–384.doi:10.1111/j.1096-0031.2000.tb00356.x. . Crossref, ISI, Google Scholar -
Goldstein P.Z& DeSalle R . 2003 Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Mol. Ecol. 12, 1993–1998.doi:10.1046/j.1365-294X.2003.01860.x. . Crossref, PubMed, ISI, Google Scholar -
Goldstein P.Z, DeSalle R, Amato G& Vogler A.P . 2000 Conservation genetics at the species boundary. Conserv. Biol. 14, 120–131.doi:10.1046/j.1523-1739.2000.98122.x. . Crossref, ISI, Google Scholar -
Govedich F.R& Davies R.W . 1998 The first record of the genus Helobdella (Hirudinoidea: Glossiphoniidae) from Australia, with a description of a new species, Helobdella papillornata. Hydrobiologia. 389, 45–49.doi:10.1023/A:1003543314841. . Crossref, ISI, Google Scholar -
Hebert P.D.N, Cywinska A, Ball S.L& deWaard J.R Biological identifications through DNA barcodes. Proc. R. Soc. B. 270, 2003a 313–321.doi:10.1098/rspb.2002.2218. . Link, ISI, Google Scholar -
Hebert P.D.N, Ratnasingham S& deWaard J.R Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. B. 270, Suppl. 2003b S96–S99. Link, ISI, Google Scholar -
Hebert P.D, Penton E.H, Burns J.M, Janzen D.H& Hallwachs W Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl Acad. Sci. USA. 101, 2004a 14812–14817.doi:10.1073/pnas.0406166101. . Crossref, PubMed, ISI, Google Scholar -
Hebert P.D.N, Stoeckle M.Y, Zemlak T.S& Francis C.M Identification of birds through DNA barcodes. PLoS Biol. 2, 2004b 1657–1663.doi:10.1371/journal.pbio.0020312. . Crossref, ISI, Google Scholar -
Kluge A.G . 1989 A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7–25. Crossref, Google Scholar -
Koski L.B& Golding G.B . 2001 The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540–542. Crossref, PubMed, ISI, Google Scholar -
Kutschera U . 1985 Beschreibung einer neuen Egelart, Helobdella striata nov. sp. (Hirudinea: Glossiphoniidae). Zool. Jb. Syst. 112, 469–476. Google Scholar -
Kutschera U . 1987 Notes on the taxonomy and biology of leeches of the genus Helobdella Blanchard 1896 (Hirudinea: Glossiphoniidae). Zool. Anz. 219, 321–323. ISI, Google Scholar -
Lipscomb D, Platnick N& Wheeler Q . 2003 The intellectual content of taxonomy: a comment on DNA taxonomy. Trends Ecol. Evol. 18, 65–66.doi:10.1016/S0169-5347(02)00060-5. . Crossref, ISI, Google Scholar -
Mallet J& Willmott K . 2003 Taxonomy: renaissance or Tower of Babel?. Trends Ecol. Evol. 18, 57 doi:10.1016/S0169-5347(02)00061-7. . Crossref, ISI, Google Scholar -
McKitrick M.C& Zink R.M . 1988 Species concepts in ornithology. Condor. 90, 1–14. Crossref, ISI, Google Scholar -
Nixon K.C& Wheeler Q.D . 1990 An amplification of the phylogenetic species concept. Cladistics. 6, 211–223. Crossref, ISI, Google Scholar -
Osgood W . 1932 Mammals of the Kelley-Roosevelts and Delacour Asiatic expeditions. Field Mus. Nat. Hist. Publ. 312, Zool. Ser. 18, 192–339. Google Scholar -
Prendini L . 2005 Comment on ‘Identifying spiders through DNA barcoding’. Can. J. Zool. 83, 498–504.doi:10.1139/z05-025. . Crossref, ISI, Google Scholar -
Proudlove G& Wood P.J . 2003 The blind leading the blind: cryptic subterranean species and DNA taxonomy. Trends Ecol. Evol. 18, 272 doi:10.1016/S0169-5347(03)00095-8. . Crossref, ISI, Google Scholar -
Ringuelet R . 1943 Sobre le morpfología y variabilidad de Helobdella triserialis (Em. Bl.) (Hirudinea, Glossiphoniidae). Notas del Museo de La Plata. 69, 215–240. Google Scholar -
Rokas A, Williams B.L, King N& Carroll S.B . 2003 Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425, 798–804.doi:10.1038/nature02053. . Crossref, PubMed, ISI, Google Scholar -
Ronquist F& Gardenfors U . 2003 Taxonomy and biodiversity inventories: time to deliver. Trends Ecol. Evol. 18, 269 doi:10.1016/S0169-5347(03)00098-3. . Crossref, ISI, Google Scholar -
Saitou N& Nei M . 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425. PubMed, ISI, Google Scholar -
Sarkar I.N, Thornton J.W, Planet P.J, Figurski D.H, Schierwater B& DeSalle R . 2002 An automated phylogenetic key for classifying homeoboxes. Mol. Phylogenet. Evol. 24, 388–399.doi:10.1016/S1055-7903(02)00259-2. . Crossref, PubMed, ISI, Google Scholar -
Seberg O, Humphries C.J, Knapp S, Stevenson D.W, Petersen G, Scharff N& Andersen N.M . 2003 Shortcuts in systematics? A commentary on DNA-based taxonomy. Trends. Ecol. Evol. 18, 63–65.doi:10.1016/S0169-5347(02)00059-9. . Crossref, ISI, Google Scholar -
Siddall M.E& Budinoff R.B . 2005 DNA-barcoding evidence for widespread introductions of a leech from the South American Helobdella triserialis complex. Conservation Genet. 6, 467–472.doi:10.1007/s10592-005-4986-y. . Crossref, ISI, Google Scholar -
Siddall M.E& Burreson E.M . 1998 Phylogeny of leeches (Hirudinea) based on mitochondrial cytochrome c oxidase subunit I. Mol. Phylogenet. Evol. 9, 156–162.doi:10.1006/mpev.1997.0455. . Crossref, PubMed, ISI, Google Scholar -
Siddall M.E, Apakupakul K, Burreson E.M, Coates K.A, Erséus C, Gelder S.R, Källersjö M& Trapido-Rosenthal H . 2001 Validating Livanow's hypothesis: molecular data agree that leeches, Branchiobdellidans and Acanthobdella peledina form a monophyletic group of oligochaetes. Mol. Phylogenet. Evol. 21, 346–351.doi:10.1006/mpev.2001.1021. . Crossref, PubMed, ISI, Google Scholar -
Tautz D, Arctander P, Minelli A, Thomas R.H& Vogler A.P . 2003 A plea for DNA taxonomy. Trends Ecol. Evol. 18, 70–74.doi:10.1016/S0169-5347(02)00041-1. . Crossref, ISI, Google Scholar -
Trontelj P& Utevsky S.Y . 2005 Celebrity with a neglected taxonomy: molecular systematics of the medicinal leech (genus Hirudo). Mol. Phylogenet. Evol. 34, 616–624.doi:10.1016/j.ympev.2004.10.012. . Crossref, PubMed, ISI, Google Scholar -
Verrill A.E . 1872 Descriptions of North American fresh-water leeches. Amer. J. Sci. 3, 126–139. Crossref, Google Scholar -
Walsh P . 2000 Sample size for the diagnosis of conservation units. Conserv. Biol. 14, 1533–1535.doi:10.1046/j.1523-1739.2000.98149.x. . Crossref, ISI, Google Scholar -
Wheeler Q.D, Raven P.H& Wilson E.O . 2004 Taxonomy: impediment or expedient?. Science. 303, 285 doi:10.1126/science.303.5656.285. . Crossref, PubMed, ISI, Google Scholar -
Wiens J.J& Penkrot T.A . 2002 Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51, 69–91.doi:10.1080/106351502753475880. . Crossref, PubMed, ISI, Google Scholar -
Wilson E.O . 2003 The encyclopedia of life. Trends Ecol. Evol. 18, 77 doi:10.1016/S0169-5347(02)00040-X. . Crossref, ISI, Google Scholar