Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada, Heterotardigrada)

Zoological Journal of the Linnean Society

Volumn 169, Issue 4, 2013, Pages 713-736

  Guil, Noemí ^a   Jørgensen, Aslak ^b   Giribet, Gonzalo ^c   Kristensen, Reinhardt Møbjerg ^b  

^a MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c HARVARD UNIVERSITY   (United States)

Author keywords

18S rRNA; 28S rRNA; Bayesian; Cladistics; DNA taxonomy; Echiniscidae; Morphology; Parsimony network

Indexed keywords

ECHINISCIDAE; ECHINISCOIDEA; ECHINISCUS; HETEROTARDIGRADA; TARDIGRADA;

EID: 84888431909     PISSN: 00244082     EISSN: 10963642     Source Type: Journal    
DOI: 10.1111/zoj.12090     Document Type: Article

References (67)

1. Bertolani R, Biserov V, Rebecchi L, Cesari M. 2011. Taxonomy and biogeography of tardigrades using an integrated approach: new results on species of the Macrobiotus hufelandi group. Invertebrate Zoology 8: 23-36.
2. Bertolani R, Rebecchi L, Cesari M. 2010. A model study for tardigrade identification. In: Nimis PL, Vignes Lebbe R, eds. Tools for identifying biodiversity: progress and problems. Trieste: EUT Edizioni Università di Trieste, 333-339.
3. Binda MG, Kristensen RM. 1986. Notes on the genus Oreella (Oreellidae) and the systematic position of Carphania fluviatilis Binda, 1978 (Carphanidae fam nov., Heterotardigrada). Animalia 131: 9-20.
4. Bissett A, Gibson JAE, Jarman SN, Swadling KM, Cromer L. 2005. Isolation, amplification, and identification of ancient copepod DNA from lake sediments. Limnology and Oceanography: Methods 3: 533-542.
5. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552.
6. Cesari M, Bertolani R, Rebecchi L, Guidetti R. 2009. DNA barcoding in Tardigrada: the first case study on Macrobiotus macrocalix Bertolani and Rebecchi 1993 (Eutardigrada, Macrobiotidae). Molecular Ecology Resources 9: 699-706.
7. Cesari M, Giovannini I, Bertolani R, Rebecchi L. 2011a. An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens. Zootaxa 3104: 42-51.
8. Cesari M, Giovannini I, Bertolani R, Rebecchi L. 2011b. DNA barcoding an integrative taxonomy of Macrobiotus hufelandi C.A.S. Schultze 1834, the first tardigrade species to be described, and some related species. Zootaxa 2997: 19-36.
9. Cesari M, Guidetti R, Rebecchi L, Giovannini I, Bertolani R. 2013. A DNA barcoding approach in the study of tardigrades. Journal of Limnology 72: 182-198.
10. Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
11. Dastych H. 1984. Tardigrada from Antarctic with description of several new species. Acta Zoologica Cracoviensia 27: 377-436.
12. De Laet JE. 2005. Parsimony and the problem of inapplicables in sequence data. In: Albert VA, ed. Parsimony, phylogeny, and genomics. Oxford: Oxford University Press, 81-116.
13. Degma P, Bertolani R, Guidetti R. 2013. Actual checklist of Tardigrada species (2009-2013, Ver. 23: 15-07-2013). Available at: http://www.tardigrada.modena.unimo.it/miscellanea/Actual%20checklist%20of%20Tardigrada.pdf
14. Degma P, Guidetti R. 2007. Notes on current checklist of Tardigrada. Zootaxa 1579: 41-53.
15. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
16. Fenchel T, Finlay BJ. 2004. The ubiquity of small species: patterns of local and global diversity. Bioscience 54: 777-784.
17. Funk DJ, Omland KE. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution and Systematics 34: 397-423.
18. Garey JR, Krotec M, Nelson DR, Brooks J. 1996. Molecular analysis supports a tardigrade arthropod association. Invertebrate Biology 115: 79-88.
19. Garey JR, Nelson DR, Mackey LJ, Li J. 1999. Tardigrade phylogeny: congruency of morphological and molecular evidence. Zoologischer Anzeiger 238: 205-210.
20. Giribet G. 2005. Generating implied alignments under direct optimization using POY. Cladistics 21: 396-402.
21. Giribet G, Carranza S, Baguñà J, Riutort M, Ribera C. 1996. First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Molecular Biology and Evolution 13: 76-84.
22. Goloboff P. 1999. Analyzing large datasets in reasonable times: solutions for composite optima. Cladistics 15: 415-428.
23. Guidetti R, Bertolani R. 2005. Tardigrade taxonomy: an updated check list of the taxa and a list of characters for their identification. Zootaxa 845: 1-46.
24. Guidetti R, Schill RO, Bertolani R, Dankekar T, Wolf M. 2009. New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov. Journal of Zoological Systematics and Evolutionary Research 47: 315-332.
25. Guil N. 2008. New records and within-species variability of Iberian tardigrades (Tardigrada), with comments on the species from the Echiniscus blumi-canadensis series. Zootaxa 1757: 1-30.
26. Guil N, Giribet G. 2009. Fine scale population structure in the Echiniscus blumi-canadensis series (Heterotardigrada, Tardigrada) in an Iberian mountain range - when morphology fails to explain genetic structure. Molecular Phylogenetics and Evolution 51: 606-613.
27. Guil N, Giribet G. 2012. A comprehensive molecular phylogeny of tardigrades: adding genes and taxa to a poorly resolved phylum-level phylogeny. Cladistics 28: 21-49.
28. Guil N, Machordom A, Guidetti R. 2013. High level of phenotypic homoplasy amongst eutardigrades (Tardigrada) based on morphological and total evidence phylogenetic analyses. Zoological Journal of the Linnean Society 169: 1-26.
29. Guo SW, Thompson EA. 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
30. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
31. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics Applications Note 17: 754-755.
32. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.
33. Jørgensen A. 2000. Cladistic analysis of the Echiniscidae Thulin, 1928 (Tardigrada: Heterotardigrada: Echiniscoidea). Steenstrupia 25: 11-23.
34. Jørgensen A, Faurby S, Hansen JG, Møbjerg N, Kristensen RM. 2010. Molecular phylogeny of Arthrotardigrada (Tardigrada). Molecular Phylogenetics and Evolution 54: 1006-1015.
35. Jørgensen A, Kristensen RM. 2004. Molecular phylogeny of Tardigrada - investigation of the monophyly of Heterotardigrada. Molecular Phylogenetics and Evolution 32: 666-670.
36. Jørgensen A, Møbjerg N, Kristensen RM. 2011. Phylogeny and evolution of the Echiniscidae (Echiniscoidea, Tardigrada) - an investigation of the congruence between molecules and morphology. Journal of Zoological Systematics and Evolutionary Research 49: 6-16.
37. Kristensen RM. 1987. Generic revision of the Echiniscidae (Hetrotardigrada), with a discussion of the origin of the family. Selected Symposia and Monograph U. Z. I. 1: 261-335.
38. Losos JB, Hillis DM, Greene HW. 2012. Evolution. Who speaks with a forked tongue? Science 338: 1428-1429.
39. Marley NJ, McInnes SJ, Sands CJ. 2011. Phylum Tardigrada: a re-evaluation of the Parachela. Zootaxa 2819: 51-64.
40. Møbjerg N, Jorgensen A, Eibye-Jacobsen J, Halberg KA, Persson D, Kristensen RM. 2007. New records on cyclomorphosis in the marine eutardigrade Halobiotus crispae (Eutardigrada: Hypsibiidae). Journal of Limnology 66 (Suppl. 1): 132-140.
41. Near TJ. 2009. Conflict and resolution between phylogenies inferred from molecular and phenotypic data sets for hagfish, lampreys, and gnathostomes. Journal of Experimental Zoology 312B: 749-761.
42. Nixon KC. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
43. O'Leary MA, Kaufman SG. 2012. MorphoBank 3.0: web application for morphological phylogenetics and taxonomy. Available at: http://www.morphobank.org
44. Okamoto M, Urushima H, Hasegawa H. 2009. Phylogenetic relationships of rodent pinworms (genus Syphacia) in Japan inferred from 28S rDNA sequences. Parasitology International 58: 330-333.
45. Peluffo J, Moly de Peluffo MC, Rocha AM. 2002. Rediscovery of Echiniscus rufoviridis du Bois-Marcus 1944 (Heterotardigrada, Echiniscidae). New contributions to the knowledge of its morphology, bioecology and distribution. Gayana 66: 97-101.
46. Pilato G, Fontoura P, Lisi O. 2007. Remarks on the Echiniscus viridis group, with the description of a new species (Tardigrada, Echiniscidae). Journal of Limnology 66 (Suppl. 1): 33-39.
47. Pilato G, Fontoura P, Lisi O, Beasley C. 2008. New description of Echiniscus scabrospinosus Fontoura, 1982, and description of a new species of Echiniscus (Heterotardigrada) from China. Zootaxa 1856: 41-54.
48. Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M. 2008. Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48: 369-371.
49. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818.
50. Ramazzotti G, Maucci W. 1983. Il phylum Tardigrada. III edizione riveduta e aggiornata. Memorie dell'Istituto Italiano di Idrobiologia 'Dott. Marco de Marchi' 41: 1-1012.
51. Rheindt FE, Székely T, Edwards SV, Lee PLM, Burke T, Kennerley PR, Bakewell DN, Alrashidi M, Kozstolányi A, Weston MA, Liu WT, Llei WP, Shigeta Y, Javed S, Zefania S, Küpper C. 2011. Conflict between genetic and phenotypic differentiation: the evolutionary history of a 'lost and rediscovered' shorebird. PLoS ONE 6: e26995.
52. Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
53. Sands CJ, Convey P, Linse K, McInnes SJ. 2008a. Assessing meiofaunal variation among individuals utilising morphological and molecular approaches: an example using the Tardigrada. BMC Ecology 8: 7.
54. Sands CJ, McInnes SJ, Marley N, Goodall-Copestake WP, Convey P, Linse K. 2008b. Phylum Tardigrada: an 'individual' approach. Cladistics 24: 1-11.
55. Schill RO, Steinbrück G. 2007. Identification and differentiation of Heterotardigrada and Eutardigrada species by riboprinting. Journal of Zoological Systematics and Evolutionary Research 45: 184-190.
56. Schwendinger PJ, Giribet G. 2005. The systematics of the southeast Asian genus Fangensis Rambla (Opiliones: Cyphophthalmi: Stylocellidae). Invertebrate Systematics 19: 297-323.
57. Srivathsan A, Meier R. 2012. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28: 190-194.
58. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
59. Swofford DL. 1998. PAUP*: phylogenetic analysis using parsimony and other methods. Sunderland, MA: Sinauer Associates.
60. Varón A, Sy Vinh L, Wheeler WC. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26: 72-85.
61. Vicente F, Fontoura P, Cesari M, Rebecchi L, Guidetti R, Serrano A, Bertonali R. 2013. Integrative taxonomy allows identification of synonymous species and the erection of a new genus of Echiniscidae (Tardigrada, Heterotardigrada). Zootaxa 3613: 557-572.
62. Wheeler WC. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12: 1-9.
63. Wheeler WC. 2003. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19: 261-268.
64. Wheeler WC, Aagesen L, Arango CP, Faivovich J, Grant T, D'Haese CA, Janies D, Smith WL, Varón A, Giribet G. 2005. Dynamic homology and phylogenetic systematics: a unified approach using POY. New York: American Museum of Natural History.
65. Whiting MF, Carpenter JM, Wheeler QD, Wheeler WC. 1997. The Strepsiptera problem: phylogeny of the holometaboloous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Systematics Biology 46: 1-68.
66. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367-372.
67. Zhi-Huan X, Xiao-Dong J, Gui-Zhong W, Jian-Feng H, Ming-Hong C, Li-Sheng W, Jie-Lan J, Xue-Lei C. 2011. DNA extraction, amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake, Antarctica. Journal of Plankton Research 33: 917-925.