메뉴 건너뛰기




Volumn 10, Issue 4, 2010, Pages 287-296

Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)

Author keywords

Compensatory base change; Cryptic species; Eutardigrada; ITS2; Species identification; Tardigrada

Indexed keywords

BIOCHEMICAL COMPOSITION; BIOPHYSICS; DEVELOPMENTAL BIOLOGY; FUNCTIONAL MORPHOLOGY; GENETIC ANALYSIS; IDENTIFICATION METHOD; INVERTEBRATE; MATRIX; NEW RECORD; NEW SPECIES; POPULATION STRUCTURE; SECONDARY STRUCTURE; TAXONOMY; TOPOLOGY;

EID: 78649634393     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1007/s13127-010-0025-z     Document Type: Article
Times cited : (73)

References (54)
  • 2
    • 0034084748 scopus 로고    scopus 로고
    • The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence
    • Coleman, A. W. (2000). The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist, 151, 1-9.
    • (2000) Protist , vol.151 , pp. 1-9
    • Coleman, A.W.1
  • 3
    • 0037677692 scopus 로고    scopus 로고
    • ITS2 is a double-edged tool for eukaryote evolutionary comparisons
    • Coleman, A. W. (2003). ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics, 19, 370-375.
    • (2003) Trends in Genetics , vol.19 , pp. 370-375
    • Coleman, A.W.1
  • 4
    • 34250821680 scopus 로고    scopus 로고
    • Pan-eukaryote ITS2 homologies revealed by RNA secondary structure
    • Coleman, A. W. (2007). Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35, 3322-3329.
    • (2007) Nucleic Acids Research , vol.35 , pp. 3322-3329
    • Coleman, A.W.1
  • 5
    • 57649155508 scopus 로고    scopus 로고
    • Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide
    • Coleman, A. W. (2009). Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution, 50, 197-203.
    • (2009) Molecular Phylogenetics and Evolution , vol.50 , pp. 197-203
    • Coleman, A.W.1
  • 6
    • 0036148914 scopus 로고    scopus 로고
    • Exploring the phylogenetic utility of ITS sequences for animals: A test case for abalone (Haliotis)
    • Coleman, A. W., & Vacquier, V. D. (2002). Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). Journal of Molecular Evolution, 54, 246-257.
    • (2002) Journal of Molecular Evolution , vol.54 , pp. 246-257
    • Coleman, A.W.1    Vacquier, V.D.2
  • 7
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 8
    • 4043087606 scopus 로고    scopus 로고
    • The ubiquity of small species: Patterns of local and global diversity
    • Fenchel, T., & Finlay, B. J. (2004). The ubiquity of small species: patterns of local and global diversity. Bioscience Biotechnology and Biochemistry, 54, 777-784.
    • (2004) Bioscience Biotechnology and Biochemistry , vol.54 , pp. 777-784
    • Fenchel, T.1    Finlay, B.J.2
  • 9
    • 18744401646 scopus 로고    scopus 로고
    • Prof Dist: A tool for the construction of large phylogenetic trees based on profile distances
    • Friedrich, J., Dandekar, T., Wolf, M., & Müller, T. (2005). Prof Dist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics, 21, 2108-2109.
    • (2005) Bioinformatics , vol.21 , pp. 2108-2109
    • Friedrich, J.1    Dandekar, T.2    Wolf, M.3    Müller, T.4
  • 10
    • 0001351490 scopus 로고    scopus 로고
    • Tardigrade phylogeny: Congruency of morphological and molecular evidence
    • Garey, J. R., Nelson, D. R., Mackey, L. Y., & Li, J. (1999). Tardigrade phylogeny: congruency of morphological and molecular evidence. Zoologischer Anzeiger, 238, 205-210.
    • (1999) Zoologischer Anzeiger , vol.238 , pp. 205-210
    • Garey, J.R.1    Nelson, D.R.2    Mackey, L.Y.3    Li, J.4
  • 11
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel, O. (1997). BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14, 685-695.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 12
    • 78649630361 scopus 로고
    • Herrn Karl Bonnets Abhandlungen aus der Insektologie aus d. Franz. übers. u. mit einigen Zusätzen hrsg. ν. Joh
    • Halle: Gebauer
    • Goeze, J. A. E. (1773). Herrn Karl Bonnets Abhandlungen aus der Insektologie aus d. Franz. übers. u. mit einigen Zusätzen hrsg. ν. Joh. August Ephraim Goeze. Halle: Gebauer.
    • (1773) August Ephraim Goeze
    • Goeze, J.A.E.1
  • 13
    • 0035711828 scopus 로고    scopus 로고
    • Phylogenetic relationships in the Macrobiotidae (Tardigrada: Eutardigrada: Parachela)
    • Guidetti, R., & Bertolani, R. (2001). Phylogenetic relationships in the Macrobiotidae (Tardigrada: Eutardigrada: Parachela). Zoologischer Anzeiger, 240, 371-376.
    • (2001) Zoologischer Anzeiger , vol.240 , pp. 371-376
    • Guidetti, R.1    Bertolani, R.2
  • 14
    • 33646591460 scopus 로고    scopus 로고
    • Tardigrade taxonomy: An updated check list of the taxa and a list of characters for their identification
    • 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.
    • (2005) Zootaxa , vol.845 , pp. 1-46
    • Guidetti, R.1    Bertolani, R.2
  • 15
    • 18544371829 scopus 로고    scopus 로고
    • Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela) : A combined morphological and molecular approach
    • Guidetti, R., Gandolfi, A., Rossi, V., & Bertolani, R. (2005). Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela) : a combined morphological and molecular approach. Zoologica Scripta, 34, 235-244.
    • (2005) Zoologica Scripta , vol.34 , pp. 235-244
    • Guidetti, R.1    Gandolfi, A.2    Rossi, V.3    Bertolani, R.4
  • 18
    • 67349265506 scopus 로고    scopus 로고
    • Fine scale population structure in the Echiniscus blumi-canadensis series (Heterotardigrada, Tardigrada) in an Iberian mountain range-when morphology fails to explain genetic structure
    • 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.
    • (2009) Molecular Phylogenetics and Evolution , vol.51 , pp. 606-613
    • Guil, N.1    Giribet, G.2
  • 19
    • 0028261409 scopus 로고
    • Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective
    • Gutell, R. R., Larsen, N., & Woese, C. R. (1994). Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiological Reviews, 58, 10-26.
    • (1994) Microbiological Reviews , vol.58 , pp. 10-26
    • Gutell, R.R.1    Larsen, N.2    Woese, C.R.3
  • 20
    • 37849009975 scopus 로고    scopus 로고
    • Trehalose and anhydrobiosis in tardigrades-evidence for divergence in responses to dehydration
    • Hengherr, S., Heyer, A. G., Kohler, H. R., & Schill, R. O. (2008). Trehalose and anhydrobiosis in tardigrades-evidence for divergence in responses to dehydration. FEBS Journal, 275, 281-288.
    • (2008) FEBS Journal , vol.275 , pp. 281-288
    • Hengherr, S.1    Heyer, A.G.2    Kohler, H.R.3    Schill, R.O.4
  • 22
    • 63049125195 scopus 로고    scopus 로고
    • Freeze tolerance, supercooling points and ice formation: Comparative studies on the subzero temperature survival of limno-terrestrial tardigrades
    • Hengherr, S., Worland, M. R., Reuner, A., Brümmer, F., & Schill, R. O. (2009b). Freeze tolerance, supercooling points and ice formation: comparative studies on the subzero temperature survival of limno-terrestrial tardigrades. Journal of Experimental Biology, 212, 802.
    • (2009) Journal of Experimental Biology , vol.212 , pp. 802
    • Hengherr, S.1    Worland, M.R.2    Reuner, A.3    Brümmer, F.4    Schill, R.O.5
  • 23
    • 14544276399 scopus 로고    scopus 로고
    • Retention of embryonated eggs in parthenogenetic Macrobiotus richtersi Murray, 1911 (Eutardigrada)
    • Hohberg, K., & Greven, H. (2005). Retention of embryonated eggs in parthenogenetic Macrobiotus richtersi Murray, 1911 (Eutardigrada). Zoologischer Anzeiger, 243, 211-213.
    • (2005) Zoologischer Anzeiger , vol.243 , pp. 211-213
    • Hohberg, K.1    Greven, H.2
  • 24
    • 0348014716 scopus 로고    scopus 로고
    • Cladistic analysis of the Echiniscidae Thulin, 1928 (Tardigrada: Heterotardigrada: Echiniscoidea)
    • Jørgensen, A. (2000). Cladistic analysis of the Echiniscidae Thulin, 1928 (Tardigrada: Heterotardigrada: Echiniscoidea). Steenstrupia, 25, 11-23.
    • (2000) Steenstrupia , vol.25 , pp. 11-23
    • Jørgensen, A.1
  • 25
    • 3042551480 scopus 로고    scopus 로고
    • Molecular phylogeny of Tardigrada-investigation of the monophyly of Heterotardigrada
    • Jørgensen, A., & Kristensen, R. M. (2004). Molecular phylogeny of Tardigrada-investigation of the monophyly of Heterotardigrada. Molecular Phylogenetics and Evolution, 32, 666-670.
    • (2004) Molecular Phylogenetics and Evolution , vol.32 , pp. 666-670
    • Jørgensen, A.1    Kristensen, R.M.2
  • 26
    • 34547680386 scopus 로고    scopus 로고
    • Molecular study of the tardigrade Echiniscus testudo (Echiniscidae) reveals low DNA sequence diversity over a large geographical area
    • Jørgensen, A., Møbjerg, N., & Kristensen, R. M. (2007). Molecular study of the tardigrade Echiniscus testudo (Echiniscidae) reveals low DNA sequence diversity over a large geographical area. Journal of Limnology, 66 (Supplement 1), 77-83.
    • (2007) Journal of Limnology , vol.66 , Issue.1 SUPPL. , pp. 77-83
    • Jørgensen, A.1    Møbjerg, N.2    Kristensen, R.M.3
  • 28
    • 76749097624 scopus 로고    scopus 로고
    • Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
    • Keller, A., Förster, F., Müller, T., Dandekar, T., Schultz, J., & Wolf, M. (2010). Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct, 5, 4.
    • (2010) Biology Direct , vol.5 , pp. 4
    • Keller, A.1    Förster, F.2    Müller, T.3    Dandekar, T.4    Schultz, J.5    Wolf, M.6
  • 30
    • 0001234595 scopus 로고
    • Generic revision of the Echiniscidae (Heterotardigrada), with a discussion of the origin of the family
    • R Bertolani Ed., Modena: Mucchi
    • Kristensen, R M. (1987). Generic revision of the Echiniscidae (Heterotardigrada), with a discussion of the origin of the family. In R Bertolani (Ed.), Biology of tardigrades, selected symposia and monographs U. Z. I (Vol. 1, pp. 261-335). Modena: Mucchi.
    • (1987) Biology of Tardigrades, Selected Symposia and Monographs U. Z. I , vol.1 , pp. 261-335
    • Kristensen, R.M.1
  • 33
    • 34547660580 scopus 로고    scopus 로고
    • An attempt to revisit the global biogeography of limno-terrestrial Tardigrada
    • McInnes, S. J., & Pugh, P. J. A. (2007). An attempt to revisit the global biogeography of limno-terrestrial Tardigrada. Journal of Limnology, 66 (Supplement 1), 90-96.
    • (2007) Journal of Limnology , vol.66 , Issue.1 SUPPL. , pp. 90-96
    • McInnes, S.J.1    Pugh, P.J.A.2
  • 34
    • 34547691525 scopus 로고    scopus 로고
    • New records on cyclomorphosis in the marine eutardigrade Halobiotus crispae (Eutardigrada: Hypsibiidae)
    • Møbjerg, N., Jørgensen, A., Eibye-Jacobsen, J., Agerlin Halberg, K., Persson, D., & Kristensen, R M. (2007). New records on cyclomorphosis in the marine eutardigrade Halobiotus crispae (Eutardigrada: Hypsibiidae). Journal of Limnology, 66 (Supplement 1), 132-140.
    • (2007) Journal of Limnology , vol.66 , Issue.1 SUPPL. , pp. 132-140
    • Møbjerg, N.1    Jørgensen, A.2    Eibye-Jacobsen, J.3    Halberg, A.K.4    Persson, D.5    Kristensen, R.M.6
  • 36
    • 0036625891 scopus 로고    scopus 로고
    • Current status of the Tardigrada: Evolution and ecology
    • Nelson, D. R (2002). Current status of the Tardigrada: evolution and ecology. Integrative and Comparative Biology, 42, 652-659.
    • (2002) Integrative and Comparative Biology , vol.42 , pp. 652-659
    • Nelson, D.R.1
  • 37
    • 29844440287 scopus 로고    scopus 로고
    • A family level analysis of tardigrade phylogeny
    • Nichols, P. B., Nelson, D. R, & Garey, J. R. (2006). A family level analysis of tardigrade phylogeny. Hydrobiologia, 558, 53-60.
    • (2006) Hydrobiologia , vol.558 , pp. 53-60
    • Nichols, P.B.1    Nelson, D.R.2    Garey, J.R.3
  • 38
    • 0002220916 scopus 로고
    • Analisi di nuovi caratteri nello studio degli Eutardigradi
    • Pilato, G (1981). Analisi di nuovi caratteri nello studio degli Eutardigradi. Animalia, 8, 51-57.
    • (1981) Animalia , vol.8 , pp. 51-57
    • Pilato, G.1
  • 40
    • 3242690512 scopus 로고    scopus 로고
    • Robust support for tardigrade clades and their ages from three protein-coding nuclear genes
    • Regier, J. C., Shultz, J. W., Kambic, R. E., & Nelson, D. R (2004). Robust support for tardigrade clades and their ages from three protein-coding nuclear genes. Invertebrate Biology, 123, 93-100.
    • (2004) Invertebrate Biology , vol.123 , pp. 93-100
    • Regier, J.C.1    Shultz, J.W.2    Kambic, R.E.3    Nelson, D.R.4
  • 41
    • 34547702670 scopus 로고    scopus 로고
    • Comparison of different protocols for DNA preparation and PCR amplification of mitochondrial genes of tardigrades
    • Schill, R. O. (2007). Comparison of different protocols for DNA preparation and PCR amplification of mitochondrial genes of tardigrades. Journal of Limnology, 66 (Supplement 1), 164-170.
    • (2007) Journal of Limnology , vol.66 , Issue.1 SUPPL. , pp. 164-170
    • Schill, R.O.1
  • 43
    • 67349271005 scopus 로고    scopus 로고
    • ITS2 sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics
    • Schultz, J., & Wolf, M. (2009). ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Molecular Phylogenetics and Evolution, 52, 520-523.
    • (2009) Molecular Phylogenetics and Evolution , vol.52 , pp. 520-523
    • Schultz, J.1    Wolf, M.2
  • 44
    • 15444361843 scopus 로고    scopus 로고
    • A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota
    • Schultz, J., Maisel, S., Gerlach, D., Müller, T, & Wolf, M. (2005). A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA, 11, 361-364.
    • (2005) RNA , vol.11 , pp. 361-364
    • Schultz, J.1    Maisel, S.2    Gerlach, D.3    Müller, T.4    Wolf, M.5
  • 45
    • 33747844305 scopus 로고    scopus 로고
    • The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses
    • Schultz, J., Müller, T., Achtziger, M., Seibel, P. N., Dandekar, T, & Wolf, M. (2006). The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research, 34 (Web Server issue), W704-707.
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB SERVER ISSUE
    • Schultz, J.1    Müller, T.2    Achtziger, M.3    Seibel, P.N.4    Dandekar, T.5    Wolf, M.6
  • 46
    • 33751213606 scopus 로고    scopus 로고
    • 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing
    • Seibel, P. N., Müller, T., Dandekar, T., Schultz, J., & Wolf, M. (2006). 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics, 7, 498.
    • (2006) BMC Bioinformatics , vol.7 , pp. 498
    • Seibel, P.N.1    Müller, T.2    Dandekar, T.3    Schultz, J.4    Wolf, M.5
  • 47
    • 58049121167 scopus 로고    scopus 로고
    • Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
    • Seibel, P. N., Müller, T., Dandekar, T., & Wolf, M. (2008). Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes, 1, 91.
    • (2008) BMC Research Notes , vol.1 , pp. 91
    • Seibel, P.N.1    Müller, T.2    Dandekar, T.3    Wolf, M.4
  • 48
    • 38549087890 scopus 로고    scopus 로고
    • The ITS2 Database II: Homology modelling RNA structure for molecular systematics
    • Selig, C., Wolf, M., Müller, T., Dandekar, T., & Schultz, J. (2008). The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research, 36 (Database issue), D377-380.
    • (2008) Nucleic Acids Research , vol.36 , Issue.DATABASE ISSUE
    • Selig, C.1    Wolf, M.2    Müller, T.3    Dandekar, T.4    Schultz, J.5
  • 50
    • 0000432452 scopus 로고
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
    • M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White Eds., San Diego: Academic
    • White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols: A guide to methods and applications (pp. 315-322). San Diego: Academic.
    • (1990) PCR Protocols: A Guide to Methods and Applications , pp. 315-322
    • White, T.J.1    Bruns, T.2    Lee, S.3    Taylor, J.4
  • 51
    • 27144461969 scopus 로고    scopus 로고
    • Homology modeling revealed more than 20, 000 rRNA internal transcribed spacer 2 (ITS2) secondary structures
    • Wolf, M., Achtziger, M., Schultz, J., Dandekar, T., & Müller, T. (2005a). Homology modeling revealed more than 20, 000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA, 11, 1616-1623.
    • (2005) RNA , vol.11 , pp. 1616-1623
    • Wolf, M.1    Achtziger, M.2    Schultz, J.3    Dandekar, T.4    Müller, T.5
  • 52
    • 23744457850 scopus 로고    scopus 로고
    • CBCAnalyzer: Inferring phylogenies based on compensatory base changes in RNA secondary structures
    • Wolf, M., Friedrich, J., Dandekar, T., & Müller, T. (2005b). CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biology, 5, 291-294.
    • (2005) Silico Biology , vol.5 , pp. 291-294
    • Wolf, M.1    Friedrich, J.2    Dandekar, T.3    Müller, T.4
  • 54
    • 53849098418 scopus 로고    scopus 로고
    • Prof DistS: (profile-) distance based phylogeny on sequence-structure alignments
    • Wolf, M., Ruderisch, B., Dandekar, T., Schultz, J., & Müller, T. (2008). Prof DistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics, 24, 2401-2402.
    • (2008) Bioinformatics , vol.24 , pp. 2401-2402
    • Wolf, M.1    Ruderisch, B.2    Dandekar, T.3    Schultz, J.4    Müller, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.