Inconsistent estimates of diversity between traditional and DNA taxonomy in bdelloid rotifers

Organisms Diversity and Evolution

Volumn 9, Issue 1, 2009, Pages 3-12

  Kaya, Murat ^a,b   Herniou, Elisabeth A ^a,c   Barraclough, Timothy G ^a   Fontaneto, Diego ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b ANKARA UNIVERSITY   (Turkey)

^c UNIVERSITÉ DE TOURS   (France)

Author keywords

Alpha beta gamma diversity; Everything is everywhere hypothesis; Molecular phylogeny; Phylogeography; Rotifera Bdelloidea; Species richness

Indexed keywords

COMPARATIVE STUDY; DNA; INVERTEBRATE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DISTRIBUTION; SPECIES DIVERSITY; SPECIES RICHNESS; TAXONOMY;

ANIMALIA; BDELLOIDA; BDELLOIDEA (ROTIFERA); BRYOPHYTA; ROTIFERA;

EID: 64149132458     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1016/j.ode.2008.10.002     Document Type: Article

References (44)

1. Abell R., Thieme M.L., Revenga C., Bryer M., Kottelat M., Bogutskaya N., Coad B., Mandrak N., Contreras Balderas S., Bussing W., Stiassny M.L.J., Skelton P., Allen G.E., Unmack P., Naseka A., Ng R., Sindorf N., Robertson J., Armijo E., Higgins J.V., Heibel T.J., Wikramanayake E., Olson D., López H.L., Reis R.E., Lundberg J.G., Sabaj Pérez M.H., and Petry P. Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation. BioScience 58 (2008) 403-413
2. Ahrens D., Monaghan M.T., and Vogler A.P. DNA-based taxonomy for associating adults and larvae in multi-species assemblages of chafers (Coleoptera: Scarabaeidae). Mol. Phylogenet. Evol. 44 (2007) 436-449
3. Boyer S.L., Baker J.M., and Giribet G. Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread 'mite harvestman' defies DNA taxonomy. Mol. Ecol. 16 (2007) 4999-5016
4. Brown J.H. Macroecology: progress and prospect. Oikos 87 (1999) 3-14
5. Casu M., and Curini-Galletti M. Genetic evidence for the existence of cryptic species in the mesopsammic flatworm Pseudomonocelis ophiocephala (Rhabditophora: Proseriata). Biol. J. Linn. Soc. 87 (2006) 553-576
6. Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43 (1987) 783-791
7. Ciros-Pérez J., Gómez A., and Serra M. On the taxonomy of three sympatric sibling species of the Brachionus plicatilis (Rotifera) complex from Spain, with the description of B. ibericus n. sp. J. Plankton Res. 23 (2001) 1311-1328
8. Clare E.L., Lim B.K., Engstrom M.D., Eger J.L., and Hebert P.D.N. DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Mol. Ecol. Notes 7 (2007) 184-190
9. De Meester L., Gómez A., Okamura B., and Schwenk K. The monopolization hypothesis and the dispersal-gene flow paradox in aquatic organisms. Acta Oecol. 23 (2002) 121-135
10. Derycke S., Backeljau T., Vlaeminck C., Vierstraete A., Vanfleteren J., Vincx M., and Moens T. Spatiotemporal analysis of population genetic structure in Geomonhystera disjuncta (Nematoda, Monhysteridae) reveals high levels of molecular diversity. Mar. Biol. 151 (2007) 1799-1812
11. Donner J. Ordnung Bdelloidea. Bestimmungsbücher zur Bodenfauna Europas 6 (1965), Akademie Verlag, Berlin
12. Elias M., Hill R.I., Willmott K.R., Dasmahapatra K.K., Brower A.V.Z., Mallet J., and Jiggins C.D. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proc. R. Soc. B 274 (2007) 2881-2889
13. Fenchel T., and Finlay B.J. The ubiquity of small species: patterns of local and global diversity. BioScience 54 (2004) 777-784
14. Folmer O., Black M., Hoeh W., Lutz R., and Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3 (1994) 294-299
15. Fontaneto D., Ficetola G.F., Ambrosini R., and Ricci C. Patterns of diversity in microscopic animals: comparable to protists or to larger animals?. Global Ecol. Biogeogr. 15 (2006) 153-162
16. Fontaneto D., Herniou E.A., Boschetti C., Caprioli M., Melone G., Ricci C., and Barraclough T.G. Evidence for independently evolving species in bdelloid rotifers. PLoS Biol. 5 (2007) 914-921
17. Fontaneto D., Barraclough T.G., Chen K., Ricci C., and Herniou E.A. Molecular evidence for broad-scale distributions in bdelloid rotifers: everything is not everywhere but most things are very widespread. Mol. Ecol. 17 (2008) 3136-3146
18. Fontaneto D., Boschetti C., and Ricci C. Cryptic diversification in ancient asexuals: evidence from the bdelloid rotifer Philodina flaviceps. J. Evol. Biol. 21 (2008) 580-587
19. de Guia A.P.O., and Saitoh T. The gap between the concept and definitions in the evolutionarily significant unit: the need to integrate neutral genetic variation and adaptive variation. Ecol. Res. 22 (2007) 604-612
20. Guil, N., Hortal, J., Sánchez-Moreno, S., Machordom, A., in press. Effects of macro-environmental factors on the species richness of terrestrial tardigrade assemblages in an Iberian mountain environment. Landscape Ecol.
21. Hawkins B.A., Albuquerque F.S., Araujo M.B., Beck J., Bini L.M., Cabrero-Sanudo F.J., Castro-Parga I., Diniz J.A.F., Ferrer-Castan D., Field R., Gomez J.F., Hortal J., Kerr J.T., Kitching I.J., Leon-Cortes J.L., Lobo J.M., Montoya D., Moreno J.C., Olalla-Tarraga M.A., Pausas J.G., Qian H., Rahbek C., Rodriguez M.A., Sanders N.J., and Williams P. A global evaluation of metabolic theory as an explanation for terrestrial species richness gradients. Ecology 88 (2007) 1877-1888
22. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. PLoS Biol. 2 (2004) 1657-1663
23. Heethoff M., Domes K., Laumann M., Maraun M., Norton R.A., and Scheu S. High genetic divergences indicate ancient separation of parthenogenetic lineages of the oribatid mite Platynothrus peltifer (Acari, Oribatida). J. Evol. Biol. 20 (2007) 392-402
24. Highton R. Speciation in eastern North-American salamanders of the genus Plethodon. Annu. Rev. Ecol. Syst. 26 (1995) 579-600
25. Janzen D.H., Hajibabaei M., Burns J.M., Hallwachs W., Remigio E., and Hebert P.D. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005) 1835-1845
26. Kent M. Biogeography and macroecology. Prog. Phys. Geogr. 29 (2005) 256-264
27. Lahaye R., Van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S., Barraclough T.G., and Savolainen V. DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA 105 (2008) 2923-2928
28. Maddison D.R., and Maddison W.P. MacClade (2005), Sinauer Associates, Sunderland, MA
29. Nicholls B., and Racey P.A. Habitat selection as a mechanism of resource partitioning in two cryptic bat species Pipistrellus pipistrellus and Pipistrellus pygmaeus. Ecography 29 (2006) 697-708
30. Nylander J.A.A. MrModeltest v2. Program distributed by the author (2004), Evolutionary Biology Centre, Uppsala University
31. Orme C.D.L., Davies R.G., Olson V.A., Thomas G.H., Ding T.S., Rasmussen P.C., Ridgely R.S., Stattersfield A.J., Bennett P.M., Owens I.P.F., Blackburn T.M., and Gaston K.J. Global patterns of geographic range size in birds. PLoS Biol. 4 (2006) 1276-1283
32. Padial J.M., and De la Riva I. Taxonomic inflation and the stability of species lists: the perils of ostrich's behavior. Syst. Biol. 55 (2006) 859-867
33. Pfenninger M., Nowak C., Kley C., Steinke D., and Streit B. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Mol. Ecol. 16 (2007) 1957-1968
34. Pons J., Barraclough T.G., Gomez-Zurita J., Cardoso A., Duran D.P., Hazell S., Kamoun S., Sumlin W.D., and Vogler A.P. Sequence based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55 (2006) 595-609
35. R Development Core Team, 2007. R: A Language and Environment for Statistical Computing. Available at: 〈http://www.R-project.org〉.
36. Ricci C. A reconsideration of the taxonomic status of Macrotrachela quadricornifera (Rotifera, Bdelloidea). J. Zool. 255 (2001) 273-277
37. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
38. Rozas J., Sánchez-Del Barrio J.C., Messeguer X., and Rozas R. DNASP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
39. Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D.Y., Eisen J.A., Hoffman J.M., Remington K., Beeson K., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F., Utterback T., Rogers Y.H., Falcon L.I., Souza V., Bonilla-Rosso G., Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K., Friedman R., Frazier M., and Venter J.C. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5 (2007) 398-431
40. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
41. Strom S.L. Microbial ecology of ocean biogeochemistry: a community perspective. Science 320 (2008) 1043-1045
42. Suatoni E., Vicario S., Rice S., Snell T., and Caccone A. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer Brachionus plicatilis. Mol. Phyl. Evol. 41 (2006) 86-98
43. Vogler A.P., and Monaghan M.T. Recent advances in DNA taxonomy. J. Zool. Syst. Evol. Res. 45 (2007) 1-10
44. Whitworth T.L., Dawson R.D., Magalon H., and Baudry E. DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proc. R. Soc. B 274 (2007) 1731-1739