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BioMed Research International
Volume 2014 (2014), Article ID 926342, 15 pages
http://dx.doi.org/10.1155/2014/926342
Research Article

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

1Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
2Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
3Dubna International University for Nature, Society and Man, Universitetskaya Street 19, Dubna 141980, Russia

Received 23 April 2014; Revised 8 July 2014; Accepted 8 July 2014; Published 18 August 2014

Academic Editor: Peter F. Stadler

Copyright © 2014 Maxim V. Zagoskin et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. G. A. Boxshall and D. Defaye, “Global diversity of copepods (Crustacea: Copepoda) in freshwater,” Hydrobiologia, vol. 595, no. 1, pp. 195–207, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. B. Dussart and D. Defaye, World Directory of Crustacea Copepoda of Inland Waters. II—Cyclopiformes, Backhuys, Leiden, The Netherlands, 2006.
  3. F. Kiefer, “Versuch eines Systems der Cyclopiden,” Zoologischer Anzeiger, vol. 73, no. 11-12, pp. 302–308, 1927. View at Google Scholar
  4. R. Gurney, British Fresh-Water Copepoda. III. Cyclopoida, Ray Society, London, UK, 1933.
  5. V. M. Rylov, Cyclopoida presnykh vod. Freshwater Cyclopoida V.3, Leningrad, Moscow, Russia, 1948.
  6. H. C. Yeatman, “Free-living Copepoda. Cyclopoida,” in Fresh-water Biology, W. T. Edmondson, Ed., pp. 795–815, John Wiley & Sons, New York, NY, USA, 1959. View at Google Scholar
  7. B. Dussart, Les Copépodes des Eaux Continentales de Europe Occidentals, Vol. 2. Cyclopoides et Biologie, N. Boubée, Paris, France, 1969.
  8. V. I. Monchenko, “Gnathostomata cyclopoida: cyclopidae,” The Fauna of Ukraina Naukova Dumka, Kiev, USSR, vol. 27, no. 3, pp. 1–452, 1974, http://scholar.google.ru/citations?view_op=view_citation&hl=ru&user=b97TEWUAAAAJ&citation_for_view=b97TEWUAAAAJ:hqOjcs7Dif8C. View at Google Scholar
  9. A. Bucklin, B. W. Frost, and T. D. Kocher, “DNA sequence variation of the mitochondrial 16S rRNA in Calanus (Copepoda: Calanoida): intraspecific and interspecific patterns,” Molecular Marine Biology and Biotechnology, vol. 1, no. 6, pp. 397–407, 1992. View at Google Scholar
  10. A. Bucklin, T. C. LaJeunesse, E. Curry, J. Wallinga, and K. Garrison, “Molecular diversity of the copepod, Nannocalanus minor: genetic evidence of species and population structure in the North Atlantic Ocean,” Journal of Marine Research, vol. 54, no. 2, pp. 285–310, 1996. View at Publisher · View at Google Scholar · View at Scopus
  11. R. S. Burton, “Intraspecific phylogeography across the point conception biogeographic boundary,” Evolution, vol. 52, no. 3, pp. 734–745, 1998. View at Publisher · View at Google Scholar · View at Scopus
  12. C. C. Caudill and A. Bucklin, “Molecular phylogeography and evolutionary history of the estuarine copepod, Acartia tonsa, on the Northwest Atlantic coast,” Hydrobiologia, vol. 511, pp. 91–102, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Edmands, “Phylogeography of the intertidal copepod Tigriopus californicus reveals substantially reduced population differentiation at northern latitudes,” Molecular Ecology, vol. 10, no. 7, pp. 1743–1750, 2001. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Eyun, Y. Lee, H. Suh, S. Kim, and Y. S. Ho, “Genetic identification and molecular phylogeny of Pseudodiaptomus species (Calanoida, Pseudodiaptomidae) in Korean waters,” Zoological Science, vol. 24, no. 3, pp. 265–271, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. E. Goetze, “Population differentiation in the open sea: insights from the pelagic copepod pleuromamma xiphias,” Integrative and Comparative Biology, vol. 51, no. 4, pp. 580–597, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Laakmann and S. Holst, “Emphasizing the diversity of North Sea hydromedusae by combined morphological and molecular methods,” Journal of Plankton Research, vol. 36, no. 1, pp. 64–76, 2014. View at Google Scholar
  17. P. K. Lindeque, R. P. Harris, M. B. Jones, and G. R. Smerdon, “Distribution of Calanus spp. as determined using a genetic identification system,” Scientia Marina, vol. 68, supplement 1, pp. 121–128, 2007. View at Google Scholar · View at Scopus
  18. W. Minxiao, S. Song, L. Chaolun, and S. Xin, “Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies,” BMC Genomics, vol. 12, no. 1, article 73, 2011. View at Publisher · View at Google Scholar · View at Scopus
  19. P. D. Rawson and R. S. Burton, “Molecular evolution at the cytochrome oxidase subunit 2 gene among divergent populations of the intertidal copepod, Tigriopus californicus,” Journal of Molecular Evolution, vol. 62, no. 6, pp. 753–764, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. H. Y. Soh, E. Ok Park, B. A. Venmathi Maran, and S. Yong Moon, “A new species of Acartia subgenus Euacartia (Copepoda: Calanoida: Acartiidae) from Korean estuaries based on morphological and molecular evidence,” Journal of Crustacean Biology, vol. 33, no. 5, pp. 718–729, 2013. View at Google Scholar
  21. C. S. Willett and J. T. Ladner, “Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence,” BMC Evolutionary Biology, vol. 9, no. 1, article 139, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. G. D. Cepeda, L. Blanco-Bercial, A. Bucklin, C. M. Berón, and M. D. Viñas, “Molecular systematic of three species of Oithona (Copepoda, Cyclopoida) from the Atlantic ocean: comparative analysis using 28S rDNA,” PLoS ONE, vol. 7, no. 4, Article ID e35861, 2012. View at Publisher · View at Google Scholar · View at Scopus
  23. J. Hirai, S. Shimode, and A. Tsuda, “Evaluation of ITS2-28S as a molecular marker for identification of calanoid copepods in the subtropical western North Pacific,” Journal of Plankton Research, vol. 35, no. 3, pp. 644–656, 2013. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Kim and W. Kim, “Molecular phylogeny of poecilostome copepods based on the 18S rDNA sequences,” Korean Journal of Biological Sciences, vol. 4, no. 3, pp. 257–261, 2000. View at Google Scholar
  25. A. P. Shinn, B. A. Banks, N. Tange et al., “Utility of 18S rDNA and ITS sequences as population markers for Lepeophtheirus salmonis (Copepoda: Caligidae) parasitising Atlantic salmon (Salmo salar) in Scotland,” Contributions to Zoology, vol. 69, no. 1-2, pp. 89–98, 2000. View at Google Scholar · View at Scopus
  26. S. J. Adamowicz, S. Menu-Marque, S. A. Halse et al., “The evolutionary diversification of the Centropagidae (Crustacea, Calanoida): a history of habitat shifts,” Molecular Phylogenetics and Evolution, vol. 55, no. 2, pp. 418–430, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. L. Blanco-Bercial, J. Bradford-Grieve, and A. Bucklin, “Molecular phylogeny of the Calanoida (Crustacea: Copepoda),” Molecular Phylogenetics and Evolution, vol. 59, no. 1, pp. 103–113, 2011. View at Publisher · View at Google Scholar · View at Scopus
  28. E. Braga, R. Zardoya, A. Meyer, and J. Yen, “Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida),” Marine Biology, vol. 133, no. 1, pp. 79–90, 1999. View at Publisher · View at Google Scholar · View at Scopus
  29. A. Bucklin, B. W. Frost, J. Bradford-Grieve, L. D. Allen, and N. J. Copley, “Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae,” Marine Biology, vol. 142, no. 2, pp. 333–343, 2003. View at Google Scholar · View at Scopus
  30. A. Bucklin and B. W. Frost, “Morphological and molecular Phylogenetic analysis of evolutionary lineages within Clausocalanus (Copepoda: Calanoida),” Journal of Crustacean Biology, vol. 29, no. 1, pp. 111–120, 2009. View at Publisher · View at Google Scholar · View at Scopus
  31. A. Cornils and L. Blanco-Bercial, “Phylogeny of the paracalanidae giesbrecht, 1888 (Crustacea: Copepoda: Calanoida),” Molecular Phylogenetics and Evolution, vol. 69, no. 3, pp. 861–872, 2013. View at Publisher · View at Google Scholar · View at Scopus
  32. S. M. Dippenaar, “Estimated molecular phylogenetic relationships of six siphonostomatoid families (Copepoda) symbiotic on elasmobranchs,” Crustaceana, vol. 82, no. 12, pp. 1547–1567, 2009. View at Publisher · View at Google Scholar · View at Scopus
  33. D. F. Figueroa, “Phylogenetic analysis of Ridgewayia (Copepoda: Calanoida) from the Galapagos and of a new species from the Florida keys with a reevaluation of the phylogeny of Calanoida,” Journal of Crustacean Biology, vol. 31, no. 1, pp. 153–165, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. E. Goetze, “Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae,” Proceedings of the Royal Society B: Biological Sciences, vol. 270, no. 1531, pp. 2321–2331, 2003. View at Publisher · View at Google Scholar · View at Scopus
  35. S. Laakmann, G. Gerdts, R. Erler, T. Knebelsberger, P. Martínez Arbizu, and M. J. Raupach, “Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences,” Molecular Ecology Resources, vol. 13, no. 5, pp. 862–876, 2013. View at Publisher · View at Google Scholar · View at Scopus
  36. R. J. Machida, M. U. Miya, M. Nishida, and S. Nishida, “Molecular phylogeny and evolution of the pelagic copepod genus Neocalanus (Crustacea: Copepoda),” Marine Biology, vol. 148, no. 5, pp. 1071–1079, 2006. View at Publisher · View at Google Scholar · View at Scopus
  37. M. Taniguchi, “Molecular phylogeny of Neocalanus copepods in the subarctic Pacific Ocean, with notes on non-geographical genetic variations for Neocalanus cristatus,” Journal of Plankton Research, vol. 26, no. 10, pp. 1249–1255, 2004. View at Publisher · View at Google Scholar · View at Scopus
  38. C. E. Lee, “Global phylogeography of a cryptic copepod species complex and reproductive isolation between genetically proximate ‘populations’,” Evolution, vol. 54, no. 6, pp. 2014–2027, 2000. View at Google Scholar · View at Scopus
  39. S. J. Adamowicz, S. Menu-Marque, P. D. N. Hebert, and A. Purvis, “Molecular systematics and patterns of morphological evolution in the Centropagidae (Copepoda: Calanoida) of Argentina,” Biological Journal of the Linnean Society, vol. 90, no. 2, pp. 279–292, 2007. View at Publisher · View at Google Scholar · View at Scopus
  40. E. Goetze, “Global population genetic structure and biogeography of the oceanic copepods Eucalanus hyalinus and E. spinifer,” Evolution, vol. 59, no. 11, pp. 2378–2398, 2005. View at Google Scholar · View at Scopus
  41. R. J. Machida and A. Tsuda, “Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences,” PLoS ONE, vol. 5, no. 4, Article ID e10278, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. G. A. Wyngaard, M. Hołyńska, and J. A. Schulte, “Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography,” Molecular Phylogenetics and Evolution, vol. 55, no. 3, pp. 753–764, 2010. View at Publisher · View at Google Scholar · View at Scopus
  43. V. Alekseev, H. J. Dumont, J. Pensaert, D. Baribwegure, and J. R. Vanfleteren, “A redescription of Eucyclops serrulatus (Fischer, 1851) (Crustacea: Copepoda: Cyclopoida) and some related taxa, with a phylogeny of the E. serrulatus-group,” Zoologica Scripta, vol. 35, no. 2, pp. 123–147, 2006. View at Publisher · View at Google Scholar · View at Scopus
  44. M. R. Miracle, V. Alekseev, V. Monchenko, V. Sentandreu, and E. Vicente, “Molecular-genetic-based contribution to the taxonomy of the Acanthocyclops robustus group,” Journal of Natural History, vol. 47, no. 5–12, pp. 863–888, 2013. View at Publisher · View at Google Scholar · View at Scopus
  45. M. Bláha, M. Hulák, J. Slouková, and J. Těšitel, “Molecular and morphological patterns across Acanthocyclops vernalis-robustus species complex (Copepoda, Cyclopoida),” Zoologica Scripta, vol. 39, no. 3, pp. 259–268, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. T. Karanovic and M. Krajicek, “When anthropogenic translocation meets cryptic speciation globalized bouillon originates; molecular variability of the cosmopolitan freshwater cyclopoid Macrocyclops albidus (Crustacea: Copepoda),” Annales de Limnologie, vol. 48, no. 1, pp. 63–80, 2012. View at Publisher · View at Google Scholar · View at Scopus
  47. T. Karanovic and M. Krajicek, “First molecular data on the Western Australian Diacyclops (Copepoda, Cyclopoida) confirm morpho-species but question size differentiation and monophyly of the Alticola-group,” Crustaceana, vol. 85, no. 12-13, pp. 1549–1569, 2012. View at Publisher · View at Google Scholar · View at Scopus
  48. T. Y. Mayor, N. G. Sheveleva, L. V. Sukhanova, O. A. Timoshkin, and S. V. Kiril'chik, “Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin,” Russian Journal of Genetics, vol. 46, no. 11, pp. 1373–1380, 2010. View at Publisher · View at Google Scholar · View at Scopus
  49. T. Karanovic and S. J. B. Cooper, “Molecular and morphological evidence for short range endemism in the Kinnecaris solitaria complex (Copepoda: Parastenocarididae), with descriptions of seven new species,” Zootaxa, no. 3026, pp. 1–64, 2011. View at Google Scholar · View at Scopus
  50. F. Marrone, S. L. Brutto, and M. Arculeo, “Molecular evidence for the presence of cryptic evolutionary lineages in the freshwater copepod genus Hemidiaptomus G.O. Sars, 1903 (Calanoida, Diaptomidae),” Hydrobiologia, vol. 644, no. 1, pp. 115–125, 2010. View at Publisher · View at Google Scholar · View at Scopus
  51. R. Scheihing, L. Cardenas, R. F. Nespolo et al., “Morphological and molecular analysis of centropagids from the high Andean plateau (Copepoda: Calanoidea),” Hydrobiologia, vol. 637, no. 1, pp. 45–52, 2010. View at Publisher · View at Google Scholar · View at Scopus
  52. R. A. Thum and R. G. Harrison, “Deep genetic divergences among morphologically similar and parapatric Skistodiaptomus (Copepoda: Calanoida: Diaptomidae) challenge the hypothesis of Pleistocene speciation,” Biological Journal of the Linnean Society, vol. 96, no. 1, pp. 150–165, 2009. View at Publisher · View at Google Scholar · View at Scopus
  53. H. Y. Soh, S. W. Kwon, W. Lee, and Y. H. Yoon, “A new Pseudodiaptomus (Copepoda, Calanoida) from Korea supported by molecular data,” Zootaxa, no. 3368, pp. 229–244, 2012. View at Google Scholar · View at Scopus
  54. M. A. Marszalek, S. Dayanandan, and E. J. Maly, “Phylogeny of the genus Hesperodiaptomus (Copepoda) based on nucleotide sequence data of the nuclear ribosomal gene,” Hydrobiologia, vol. 624, no. 1, pp. 61–69, 2009. View at Publisher · View at Google Scholar · View at Scopus
  55. R. A. Thum, “Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera,” Hydrobiologia, vol. 519, no. 1–3, pp. 135–141, 2004. View at Publisher · View at Google Scholar · View at Scopus
  56. R. Huys, J. Llewellyn-Hughes, P. D. Olson, and K. Nagasawa, “Small subunit rDNA and Bayesian inference reveal Pectenophilus ornatus (Copepoda incertae sedis) as highly transformed Mytilicolidae, and support assignment of Chondracanthidae and Xarifiidae to Lichomolgoidea (Cyclopoida),” Biological Journal of the Linnean Society, vol. 87, no. 3, pp. 403–425, 2006. View at Publisher · View at Google Scholar · View at Scopus
  57. R. Huys, J. Llewellyn-Hughes, S. Conroy-Dalton, P. D. Olson, J. N. Spinks, and D. A. Johnston, “Extraordinary host switching in siphonostomatoid copepods and the demise of the Monstrilloida: integrating molecular data, ontogeny and antennulary morphology,” Molecular Phylogenetics and Evolution, vol. 43, no. 2, pp. 368–378, 2007. View at Publisher · View at Google Scholar · View at Scopus
  58. J. Ki, K. Lee, H. G. Park, S. Chullasorn, H. Dahms, and J. Lee, “Phylogeography of the copepod Tigriopus japonicus along the Northwest Pacific rim,” Journal of Plankton Research, vol. 31, no. 2, pp. 209–221, 2009. View at Publisher · View at Google Scholar · View at Scopus
  59. P. D. N. Hebert, A. Cywinska, S. L. Ball, and J. R. DeWaard, “Biological identifications through DNA barcodes,” Proceedings of the Royal Society B, vol. 270, no. 1512, pp. 313–321, 2003. View at Publisher · View at Google Scholar · View at Scopus
  60. R. J. Machida, M. U. Miya, M. Nishida, and S. Nishida, “Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda),” Marine Biotechnology, vol. 4, no. 4, pp. 406–417, 2002. View at Google Scholar
  61. R. S. Burton, R. J. Byrne, and P. D. Rawson, “Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus,” Gene, vol. 403, no. 1-2, pp. 53–59, 2007. View at Publisher · View at Google Scholar · View at Scopus
  62. S. A. Gerbi, “Evolution of ribosomal DNA,” in Molecular Evolutionary Genetics, pp. 419–517, Plenum, New York, NY, USA, 1985. View at Google Scholar
  63. U. W. Hwang and W. Kim, “General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics.,” Korean Journal of Parasitology, vol. 37, no. 4, pp. 215–228, 1999. View at Publisher · View at Google Scholar · View at Scopus
  64. D. M. Hillis and M. T. Dixon, “Ribosomal DNA: molecular evolution and phylogenetic inference,” Quarterly Review of Biology, vol. 66, no. 4, pp. 411–453, 1991. View at Publisher · View at Google Scholar · View at Scopus
  65. D. H. Huson and D. Bryant, “Application of phylogenetic networks in evolutionary studies,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 254–267, 2006. View at Publisher · View at Google Scholar · View at Scopus
  66. D. M. Hillis, C. Moritz, and B. K. Mable, Eds., Molecular Systematics, Sinauer Associates, Sunderland, Mass, USA, 1996.
  67. E. V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution, Pearson Education, FT Press, 2012.
  68. T. Sang, D. J. Crawford, and T. F. Stuessy, “Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 15, pp. 6813–6817, 1995. View at Publisher · View at Google Scholar · View at Scopus
  69. S. Giessler and C. C. Englbrecht, “Dynamic reticulate evolution in a Daphnia multispecies complex,” Journal of Experimental Zoology A, Ecological Genetics and Physiology, vol. 311, no. 7, pp. 530–548, 2009. View at Google Scholar · View at Scopus
  70. H. Kauserud and T. Schumacher, “Ribosomal DNA variation, recombination and inheritance in the basidiomycete Trichaptum abietinum: implications for reticulate evolution,” Heredity, vol. 91, no. 2, pp. 163–172, 2003. View at Publisher · View at Google Scholar · View at Scopus
  71. P. M. W. Wyatt, C. S. Pitts, and R. K. Butlin, “A molecular approach to detect hybridization between bream Abramis brama, roach Rutlius rutilus and rudd Scardinius erythrophthalmus,” Journal of Fish Biology, vol. 69, pp. 52–71, 2006. View at Publisher · View at Google Scholar · View at Scopus
  72. J. Fuertes Aguilar and G. Nieto Feliner, “Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae),” Molecular Phylogenetics and Evolution, vol. 28, no. 3, pp. 430–447, 2003. View at Publisher · View at Google Scholar · View at Scopus
  73. H. Yamaji, T. Fukuda, J. Yokoyama et al., “Reticulate evolution and phylogeography in Asarumsect. Asiasarum (Aristolochiaceae) documented in internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA,” Molecular Phylogenetics and Evolution, vol. 44, no. 2, pp. 863–884, 2007. View at Publisher · View at Google Scholar · View at Scopus
  74. M. A. Hershkovitz, C. C. Hernández-Pellicer, and M. T. K. Arroyo, “Ribosomal DNA evidence for the diversification of Tropaeolum sect. Chilensia (Tropaeolaceae),” Plant Systematics and Evolution, vol. 260, no. 1, pp. 1–24, 2006. View at Publisher · View at Google Scholar · View at Scopus
  75. A. Hugall, J. Stanton, and C. Moritz, “Reticulate evolution and the origins of ribosomal internal transcribed spacer diversity in apomictic Meloidogyne,” Molecular Biology and Evolution, vol. 16, no. 2, pp. 157–164, 1999. View at Publisher · View at Google Scholar · View at Scopus
  76. J. F. Wendel, A. Schnabel, and T. Seelanan, “Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium),” Proceedings of the National Academy of Sciences of the United States of America, vol. 92, no. 1, pp. 280–284, 1995. View at Publisher · View at Google Scholar · View at Scopus
  77. K. O'Donnell and E. Cigelnik, “Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous,” Molecular Phylogenetics and Evolution, vol. 7, no. 1, pp. 103–116, 1997. View at Publisher · View at Google Scholar · View at Scopus
  78. K. O'Donnell, E. Cigelnik, and H. I. Nirenberg, “Molecular systematics and phylogeography of the Gibberella fujikuroi species complex,” Mycologia, vol. 90, no. 3, pp. 465–493, 1998. View at Publisher · View at Google Scholar · View at Scopus
  79. C. M. Brasier, D. E. L. Cooke, and J. M. Duncan, “Origin of a new Phytophthora pathogen through interspecific hybridization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 10, pp. 5878–5883, 1999. View at Publisher · View at Google Scholar · View at Scopus
  80. K. W. Hughes and R. H. Petersen, “Apparent recombination or gene conversion in the ribosomal ITS region of a Flammulina (Fungi, Agaricales) hybrid,” Molecular Biology and Evolution, vol. 18, no. 1, pp. 94–96, 2001. View at Publisher · View at Google Scholar · View at Scopus
  81. G. Newcombe, B. Stirling, S. McDonald, and H. D. Bradshaw Jr., “Melampsora × columbiana, a natural hybrid of M. medusae and M. occidentalis,” Mycological Research, vol. 104, no. 3, pp. 261–274, 2000. View at Publisher · View at Google Scholar · View at Scopus
  82. K. H. Chu, C. P. Li, and H. Y. Ho, “The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in crustacea,” Marine Biotechnology, vol. 3, no. 4, pp. 355–361, 2001. View at Publisher · View at Google Scholar · View at Scopus
  83. L. H. Rieseberg, “Hybrid origins of plant species,” Annual Review of Ecology and Systematics, vol. 28, no. 1, pp. 359–389, 1997. View at Publisher · View at Google Scholar · View at Scopus
  84. R. Cui, M. Schumer, K. Kruesi, R. Walter, P. Andolfatto, and G. G. Rosenthal, “Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes,” Evolution, vol. 67, no. 8, pp. 2166–2179, 2013. View at Publisher · View at Google Scholar · View at Scopus
  85. L. Bullini, “Origin and evolution of animal hybrid species,” Trends in Ecology and Evolution, vol. 9, no. 11, pp. 422–426, 1994. View at Publisher · View at Google Scholar · View at Scopus
  86. T. E. Dowling and C. L. Secor, “The role of hybridization and introgression in the diversification of animals,” Annual Review of Ecology and Systematics, vol. 28, pp. 593–619, 1997. View at Publisher · View at Google Scholar · View at Scopus
  87. J. Mallet, “Hybridization as an invasion of the genome,” Trends in Ecology and Evolution, vol. 20, no. 5, pp. 229–237, 2005. View at Publisher · View at Google Scholar · View at Scopus
  88. U. Arnason, R. Spilliaert, A. Pálsdóttir, and A. Arnason, “Molecular identification of hybrids between the two largest whale species, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus),” Hereditas, vol. 115, no. 2, pp. 183–189, 1991. View at Publisher · View at Google Scholar · View at Scopus
  89. A. V. Z. Brower, “Introgression of wing pattern alleles and speciation via homoploid hybridization in Heliconius butterflies: a review of evidence from the genome.,” Proceedings Biological Sciences, vol. 280, no. 1752, Article ID 20122302, 2013. View at Publisher · View at Google Scholar · View at Scopus
  90. H. L. Carson, K. Y. Kaneshiro, and F. C. Val, “Natural hybridization between the sympatric Hawaiian species Drosophila silvestris and Drosophila heteroneura,” Evolution, vol. 43, no. 1, pp. 190–203, 1989. View at Publisher · View at Google Scholar
  91. S. Gießler and C. C. Englbrecht, “Dynamic reticulate evolution in a Daphnia multispecies complex,” Journal of Experimental Zoology A: Ecological Genetics and Physiology, vol. 311, no. 7, pp. 531–549, 2009. View at Publisher · View at Google Scholar · View at Scopus
  92. S. Gießler, E. Mader, and K. Schwenk, “Morphological evolution and genetic differentiation in Daphnia species complexes,” Journal of Evolutionary Biology, vol. 12, no. 4, pp. 710–723, 1999. View at Publisher · View at Google Scholar · View at Scopus
  93. D. J. Taylor, P. D. N. Hebert, and J. K. Colbourne, “Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation,” Molecular Phylogenetics and Evolution, vol. 5, no. 3, pp. 495–510, 1996. View at Publisher · View at Google Scholar · View at Scopus
  94. R. Vergilino, S. Markova, M. Ventura, M. Manca, and F. Dufresne, “Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers,” Molecular Ecology, vol. 20, no. 6, pp. 1191–1207, 2011. View at Publisher · View at Google Scholar
  95. D. V. Mukha and A. P. Sidorenko, “Detection and analysis of Tetrahymena pyriformis 26S ribosomal DNA domain sequences, differing in degree of evolutionary conservation,” Molekulyarnaya Biologiya, vol. 29, no. 3, pp. 529–537, 1995. View at Google Scholar · View at Scopus
  96. D. V. Mukha and A. P. Sidorenko, “Identification of highly conservative domains within the 17s ribosomal dna sequence from Tetrahymena pyriformis,” Genetika, vol. 32, no. 11, pp. 1494–1497, 1996. View at Google Scholar · View at Scopus
  97. D. V. Mukha, A. P. Sidorenko, I. V. Lazebnaya, B. M. Wiegmann, and C. Schal, “Analysis of intraspecies polymorphism in the ribosomal DNA cluster of the cockroach Blattella germanica,” Insect Molecular Biology, vol. 9, no. 2, pp. 217–222, 2000. View at Publisher · View at Google Scholar · View at Scopus
  98. D. Mukha, B. M. Wiegmann, and C. Schal, “Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta),” Insect Biochemistry and Molecular Biology, vol. 32, no. 9, pp. 951–960, 2002. View at Publisher · View at Google Scholar · View at Scopus
  99. F. Sanger, S. Nicklen, and A. R. Coulson, “DNA sequencing with chain-terminating inhibitors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 12, pp. 5463–5467, 1977. View at Publisher · View at Google Scholar · View at Scopus
  100. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  101. M. Goujon, H. McWilliam, W. Li et al., “A new bioinformatics analysis tools framework at EMBL-EBI,” Nucleic Acids Research, vol. 38, no. 2, Article ID gkq313, pp. W695–W699, 2010. View at Google Scholar · View at Scopus
  102. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar · View at Scopus
  103. X. Xia and Z. Xie, “DAMBE: software package for data analysis in molecular biology and evolution,” Journal of Heredity, vol. 92, no. 4, pp. 371–373, 2001. View at Publisher · View at Google Scholar · View at Scopus
  104. X. Xia, Data Analysis in Molecular Biology and Evolution, Kluwer Academic Publishers, Boston, Mass, USA, 2000.
  105. X. Xia, Z. Xie, M. Salemi, L. Chen, and Y. Wang, “An index of substitution saturation and its application,” Molecular Phylogenetics and Evolution, vol. 26, no. 1, pp. 1–7, 2003. View at Publisher · View at Google Scholar · View at Scopus
  106. P. Lemey, M. Salemi, and A.-M. Vandamme, Eds., The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, Cambridge, UK, 2009.
  107. W. M. Fitch, “Toward defining the course of evolution: minimum change for a specific tree topology,” Systematic Biology, vol. 20, no. 4, pp. 406–416, 1971. View at Google Scholar
  108. J. Felsenstein, “Evolutionary trees from DNA sequences: a maximum likelihood approach,” Journal of Molecular Evolution, vol. 17, no. 6, pp. 368–376, 1981. View at Publisher · View at Google Scholar · View at Scopus
  109. A. Rzhetsky and M. Nei, “A simple method for estimating and testing minimum-evolution trees,” Molecular Biology and Evolution, vol. 9, no. 5, pp. 945–967, 1992. View at Google Scholar · View at Scopus
  110. J. P. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback, “Bayesian inference of phylogeny and its impact on evolutionary biology,” Science, vol. 294, no. 5550, pp. 2310–2314, 2001. View at Publisher · View at Google Scholar · View at Scopus
  111. J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 39, no. 4, pp. 783–791, 1985. View at Google Scholar
  112. M. Hasegawa, H. Kishino, and T. Yano, “Dating of the human-ape splitting by a molecular clock of mitochondrial DNA,” Journal of Molecular Evolution, vol. 22, no. 2, pp. 160–174, 1985. View at Publisher · View at Google Scholar · View at Scopus
  113. K. Katoh, K. Kuma, H. Toh, and T. Miyata, “MAFFT version 5: improvement in accuracy of multiple sequence alignment,” Nucleic Acids Research, vol. 33, no. 2, pp. 511–518, 2005. View at Publisher · View at Google Scholar · View at Scopus
  114. A. Dereeper, S. Audic, J. Claverie, and G. Blanc, “BLAST-EXPLORER helps you building datasets for phylogenetic analysis,” BMC Evolutionary Biology, vol. 10, no. 1, article 8, 2010. View at Publisher · View at Google Scholar · View at Scopus
  115. A. Dereeper, V. Guignon, G. Blanc et al., “Phylogeny.fr: robust phylogenetic analysis for the non-specialist,” Nucleic Acids Research, vol. 36, pp. W465–W469, 2008. View at Publisher · View at Google Scholar · View at Scopus
  116. J. Castresana, “Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis,” Molecular Biology and Evolution, vol. 17, no. 4, pp. 540–552, 2000. View at Publisher · View at Google Scholar · View at Scopus
  117. K. Tamura, “Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases,” Molecular Biology and Evolution, vol. 9, no. 4, pp. 678–687, 1992. View at Google Scholar · View at Scopus
  118. J. P. Huelsenbeck and F. Ronquist, “MRBAYES: bayesian inference of phylogenetic trees,” Bioinformatics, vol. 17, no. 8, pp. 754–755, 2001. View at Publisher · View at Google Scholar · View at Scopus
  119. F. Ronquist and J. P. Huelsenbeck, “MrBayes 3: bayesian phylogenetic inference under mixed models,” Bioinformatics, vol. 19, no. 12, pp. 1572–1574, 2003. View at Publisher · View at Google Scholar · View at Scopus
  120. J. A. A. Nylander, MrModeltest v2. Program Distributed by the Author, Evolutionary Biology Centre, Uppsala University, 2004.
  121. P. Legendre and V. Makarenkov, “Reconstruction of biogeographic and evolutionary networks using reticulograms,” Systematic Biology, vol. 51, no. 2, pp. 199–216, 2002. View at Publisher · View at Google Scholar · View at Scopus
  122. V. Makarenkov, “T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks,” Bioinformatics, vol. 17, no. 7, pp. 664–668, 2001. View at Publisher · View at Google Scholar · View at Scopus
  123. V. Makarenkov, “An algorithm for the fitting of a tree metric according to a weighted least-squares criterion,” Journal of Classification, vol. 16, no. 1, pp. 3–26, 1999. View at Publisher · View at Google Scholar · View at MathSciNet · View at Scopus
  124. A. Rocha-Olivares, J. W. Fleeger, and D. W. Foltz, “Decoupling of molecular and morphological evolution in deep lineages of a meiobenthic harpacticoid copepod,” Molecular Biology and Evolution, vol. 18, no. 6, pp. 1088–1102, 2001. View at Publisher · View at Google Scholar · View at Scopus
  125. B. W. Frost and A. Bucklin, “Morphological and molecular phylogenetic analysis of evolutionary lineages within Clausocalanus (Copepoda: Calanoida),” Journal of Crustacean Biology, vol. 29, no. 1, pp. 111–120, 2009. View at Publisher · View at Google Scholar · View at Scopus
  126. T. A. Heath, S. M. Hedtke, and D. M. Hillis, “Taxon sampling and the accuracy of phylogenetic analyses,” Journal of Systematics and Evolution, vol. 46, no. 3, pp. 239–257, 2008. View at Publisher · View at Google Scholar · View at Scopus
  127. J. Bergsten, “A review of long-branch attraction,” Cladistics, vol. 21, no. 2, pp. 163–193, 2005. View at Publisher · View at Google Scholar · View at Scopus