Direct optimization and multiple alignment of 28S D2-D3 rDNA sequences: Problems with indels on the way to a molecular phylogeny of the cryptine ichneumon waSPS (Insecta: Hymenoptera)

Cladistics

Volumn 22, Issue 5, 2006, Pages 442-473

  Laurenne, Nina M ^a,b   Broad, Gavin R ^c,e   Quicke, Donald L J ^d,e  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

^e DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE; OPTIMIZATION; PHYLOGENY; TAXONOMY; WASP;

AGRIOTYPINAE; ALOMYA; BRACHYCYRTINAE; CRYPTINAE; HYMENOPTERA; ICHNEUMONIDAE; ICHNEUMONINAE; INSECTA;

EID: 33748850565     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2006.00112.x     Document Type: Article

References (89)

1. Aagesen, L., 2005. Direct optimization, affine gap costs, and node stability. Mol. Phylogenet. Evol. 36, 641-653.
2. Aagesen, L., Petersen, G., Seberg, O., 2005. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics, 21, 15-30.
3. Ashmead, W.H., 1906. Descriptions of new Hymenoptera from Japan. Proc. US Natl. Mus. 30, 169-201.
4. Askew, R.R., Shaw, M.R., 1986. Parasitoid communities: their size, structure and development. In: Waage, J., Greathead, D. (Eds.), Insect Parasitoids. Academic Press, London, pp. 225-262.
5. Austin, A.D., 1985. The function of spider egg sacs in relation to parasitoids and predators, with special reference to the Australian Fauna. J. Nat. Hist. 19, 359-376.
6. Belshaw, R., Quicke, D.L.J., 1997. A molecular phylogeny of the Aphidiinae (Hymenoptera: Braconidae). Mol. Phylogenet. Evol. 7, 281-293.
7. Belshaw, R., Quicke, D.L.J., 2002. Robustness of ancestral state estimates: evolution of life history strategy in ichneumonoid parasitoids. Syst. Biol. 51, 450-477.
8. Belshaw, R., Fitton, M., Herniou, E., Gimeno, C., Quicke, D.L.J., 1998. A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28S ribosomal DNA. Syst. Entomol. 23, 109-123.
9. Belshaw, R., Grafen, A., Quicke, D.L.J., 2003. Inferring life history from ovipositor morphology in parasitoid wasps using phylogenetic regression and discriminant analysis. Zool. J. Linn. Soc. 139, 213-238.
10. Broad, G.R., Quicke, D.L.J., 2000. The adaptive significance of host location by vibrational sounding in parasitoid wasps. Proc. R. Soc. (Lond.) B. 267, 2403-2409.
11. DeSalle, R., Giribet, G., Wheeler, W., 2002. Molecular Systematics and Evolution: Theory and Practice. Birkhaeuser Verlag, Basel, Switzerland.
12. Diller, E., 1981. Bemerkungen zur Systematik der Phaeogenini mit einem vorläufigen Katalog der Gattungen (Hymenoptera, Ichneumonidae). Entomofauna, 2, 93-111.
13. Fitton, M.G., Gauld, I.D., Shaw, M.R., 1982. The taxonomy and biology of the British Adelognathinae (Hymenoptera: Ichneumonidae). J. Nat. Hist. 16, 275-283.
14. Fitton, M.G., Shaw, M.R., Austin, A.D., 1987. The Hymenoptera associated with spiders in Europe. Zool. J. Linn. Soc. 90, 65-93.
15. Gaston, K.J., Gauld, I.D., 1993. How many species of pimplines (Hymenoptera: Ichneumonidae) are there in Costa Rica? J. Trop. Ecol. 9, 491-499.
16. Gauld, I.D., 1983. The classification, evolution and distribution of the Labeninae, an ancient southern group of Ichneumonidae (Hymenoptera). Syst. Entomol. 8, 167-178.
17. Gauld, I.D., 1984. An Introduction to the Ichneumonidae of Australia. British Museum (Natural History), London.
18. Gauld, I.D., 1988. Evolutionary patterns of host utilization by ichneumonid parasitoids (Hymenoptera: Ichneumonidae and Braconidae). Biol. J. Linn. Soc. 35, 351-377.
19. Gauld, I.D., 1991. The Ichneumonidae of Costa Rica, 1. Mem. Am. Entomol. Inst. 47, 1-589.
20. Gauld, I.D., 1995. Ichneumonidae. In: Hanson, P.E., Gauld, I.D. (Eds.), The Hymenoptera of Costa Rica. Oxford University Press and The Natural History Museum, London, pp. 390-431.
21. Gauld, I.D., 1997. The Ichneumonidae of Costa Rica, 2. Mem. Am. Entomol. Inst. 57, 1-485.
22. Gauld, I.D., 2000. The Ichneumonidae of Costa Rica, 3. Mem. Am. Entomol. Inst. 63, 1-453.
23. Gauld, I.D., Mound, L.A., 1982. Homoplasy and the delineation of holophyletic genera in some insect groups. Syst. Entomol. 7, 73-86.
24. Gauld, I.D., Wahl, D.B., 2002. The Eucerotinae: a Gondwanan origin for a cosmopolitan group of Ichneumonidae? J. Nat. Hist. 36, 2229-2248.
25. Gauld, I.D., Ward, S., 2000. Subfamily Brachycyrtinae. In: Gauld, I.D. (Ed.), The Ichneumonidae of Costa Rica 3. Mem. Am. Entomol. Inst. 63, 1-453, 13-35.
26. Gauld, I.D., Wahl, D.B., Broad, G.R., 2002. The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study. Zool. J. Linn. Soc. 136, 421-485.
27. Gillespie, J.J., Yoder, M.J., Wharton, R.A., 2005. Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on sequence alignment and phylogeny estimation. J. Mol. Evol. 61, 114-137.
28. Giribet, G., 2001. Exploring the behaviour of POY, a program for direct optimization of molecular data. Cladistics, 17, 60-70.
29. Gladstein, D.S., Wheeler, W., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics, 12, 1-9.
30. Godfray, H.C.J., 1994. Parasitoids, Behavioural and Evolutionary Ecology. Princeton University Press, Princeton, NJ.
31. Gokhman, V.E., 1988. Ecological and morphological aspects of formation and evolution of the ichneumonid flies of the subfamily Ichneumoninae (Hymenoptera, Ichneumonidae). Entomol. Obozr. 67, 821-825. [in Russian with English summary.].
32. Gokhman, V.E., 1992. On the origin of endoparasitism in the subfamily Ichneumoninae (Hymenoptera, Ichneumonidae). Zh. Obshch. Biol. 53, 600-608.
33. Gokhman, V.E., 1995. Trends of biological evolution in the subfamily Ichneumoninae and related groups (Hymenoptera Ichneumonidae): an attempt of phylogenetic reconstruction. Russ. Entomol. J. 4, 91-103.
34. Goloboff, P.A., 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics, 15, 415-428.
35. Goloboff, P.A., Farris, J.S., 2000. Methods for quick consensus estimation. Cladistics, 17, 26-34.
36. Graybeal, A., 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47, 9-17.
37. Haeselbarth, E., 1979. Zur Parasitierung der Puppen von Forleule (Panolis flammea [Schiff.], Kiefernspanner (Bupalus piniarius [L.]) und Heidelbeerspanner (Boarmia bistortana [Goeze] in bayerischen Kiefernwäldern. Z. Angew. Entomol. 87, 311-322.
38. Hanson, P., Gauld, I.D., 1995. Hymenoptera of Costa Rica. Oxford University Press, New York.
39. He, J., 1991. Three new species of Megalomya Uchida from China (Hymenoptera: Ichneumonidae). Orient. Insects, 25, 145-153.
40. Hinz, R., Short, J., 1983. The biology of the European species of the genus Ichneumon and related species (Hymenoptera: Ichneumonidae). Contr. Am. Entomol. Inst. 20, 151-152.
41. Hinz, R., Short, J., 1983. Life-history and systematic position of the European Alomya species (Hymenoptera: Ichneumonidae). Entomol. Scand. 14, 462-466.
42. Horstmann, K., 1998. Revisionen einiger Gattungen und Arten der Phygadeuontini II (Hymenoptera, Ichneumonidae, Cryptinae). Entomofeuna. 19, 433-460.
43. ICZN, 1994. Opinion 1757. Cryptus Fabricius, 1804 and Cryptinae Kirby, 1837 (Insecta, Hymenoptera): conserved. Bull. Zool. Nom. 51, 74-75.
44. Janies, D., Wheeler, W., 2001. POY Documentation and Command Summary. American Museum of Natural History, New York. Program and documentation available at: ftp://ftp.amhn.org/pub/molecular/poy.
45. Kerrich, G.J., 1968. Description of an ichneumonid (Hym.) that preys on egg-masses of weevils harmful to tea culture in Kenya. Bull. Entomol. Res. 59, 469-472.
46. Lougheed, S.C., Freeland, J.R., Handford, P., Boag, P.T., 2000. A molecular phylogeny of warbling-finches (Poospiza): paraphyly in a Neotropical emberizid genus. Mol. Phylogenet. Evol. 17, 367-378.
47. Matsumoto, R., Saigusa, T., 2001. The biology and immature stages of Thrybius togashii Kusigemati (Hymenoptera: Ichneumonidae: Cryptinae), with a description of the male. J. Nat. Hist. 35, 1507-1516.
48. Momoi, S., Kishitani, Y., Iwata, K., 1965. Studies on an ichneumonid parasite (Hymenoptera) of Clania minuscula (Lepidoptera). Sci. Report Hyogo University Agric. 7, 25-31.
49. Morley, C., 1912. No. XII. - Hymenoptera, Ichneumonidae. Trans. Linn. Soc. Lond. 15, 169-179.
50. Nixon, K.C., 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407-414.
51. Olsson, U., Alström, P., Ericson, P.G.P., Sundberg, P., 2005. Non-monophyletic taxa and cryptic species - Evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves). Mol. Phylogenet. Evol. 36, 261-276.
52. Omland, K.E., Lanyon, S.M., Fritz, S.J., 1999. A molecular phylogeny of the New World orioles (Icterus): The importance of dense taxon sampling. Mol. Phylogenetic. Evol. 12, 224-239.
53. Perkins, J.F., 1959. Ichneumonidae, key to subfamilies and Ichneumoninae - 1. Handbk Ident. Br. Insects 7 (Part 2ai), 1-116.
54. Perkins, J.F., 1960. Ichneumonidae, Subfamilies Ichneumoninae II, Alomyinae, Agriotypinae and Lycorininae. Handbk Ident. Br. Insects 7 (Part 2aii), 117-213.
55. Petersen, G., Seberg, O., Aagesen, L., Frederiksen, S., 2004. An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae). Mol. Phylogent. Evol. 30, 733-742.
56. Porter, C.C., 1998. Guía de los géneros de Ichneumonidae en la región neantárctica del sur de Sudamérica. Op. Lilloana, 42, 1-234.
57. Purvis, A., Quicke, D.L.J., 1997. Phylogeny reconstruction: Are the big easy? Trends Ecol. Evol. 12, 49-50.
58. Quicke, D.L.J., 1997. Parasitic Wasps. Chapman & Hall, London, UK.
59. Quicke, D.L.J., Lopez-Vaamonde, C., Belshaw, R., 1999. The basal Ichneumonidae (Insecta, Hymenoptera): 28S, D2 rDNA considerations of the Brachycyrtinae, Labeninae, Paxylommatinae and Xoridinae. Zool. Scr. 28, 203-210.
60. Quicke, D.L.J., Fitton, M.G., Notton, D.G., Belshaw, R., Broad, G.R., Dolphin, K., 2000. Phylogeny of the Ichneumonidae (Hymenoptera). A simultaneous molecular and morphological analysis. In: Austin, A.D., Dowton, M. (Eds.), Hymenoptera: Evolution, Biodiversity and Biological Control. CSIRO, Canberra, Australia, pp. 74-83.
61. Quicke, D.L.J., Taylor, J., Purvis, A., 2001. Changing the landscape: a new strategy for estimating large phylogenies. Syst. Biol. 50, 60-66.
62. Quicke, D.L.J., Fitton, M.G., Broad, G.R., Crocker, B., Laurenne, N.M., Miah, I.M., 2005. The parasitic wasp genera Skiapus, Hellwigia, Nonnus, Chriodes and Klutiana (Hymenoptera, Ichneumonidae): recognition of the Nesomesochorinae stat. rev. & Nonninae stat. nov. & transfer of Skiapus and Hellwigia to the Ophioninae. J. Nat. Hist. 39, 2559-2578.
63. Rasnitsyn, A.P., Siitan, U.V., 1981. Ichneumoninae [in Russian]. In: Kasparyan, D.R. (Ed.), [a Guide to the Identification of Insects of the European Part of the USSR, Vol. 3. Hymenoptera]. Opredeliteli Faune SSSR. Nauka Press, Moscow.
64. Sääksjärvi, I.E., Haataja, S., Neuvonen, S., Gauld, I.D., Jussila, R., Salo, J., Burgos, A.M., 2004. High local species richness of parasitic wasps (Hymenoptera: Ichneumonidae; Pimplinae and Rhyssinae) from the lowland rainforests of Peruvian Amazonia. Ecol. Entomol. 29, 735-743.
65. Sawoniewicz, J., 1980. Revision of European species of the genus Bathythrix Foerster (Hymenoptera, Ichneumonidae). Ann. Zool. 35, 1-47.
66. Schulmeister, S., Wheeler, W.C., Carpenter, J.M., 2002. Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis. Cladistics, 18, 455-484.
67. Schwarz, M., Shaw, M.R., 1998. Western Palaearctic Cryptinae (Hymenoptera: Ichneumonidae) in the National Museums of Scotland, with nomenclatural changes, taxonomic notes, rearing records and special reference to the British check-list. Part 1. Tribe Cryptini. Entomologist's Gaz. 49, 101-127.
68. Schwarz, M., Shaw, M.R., 2000. Western Palaearctic Cryptinae (Hymenoptera: Ichneumonidae) in the National Museums of Scotland, with nomenclatural changes, taxonomic notes, rearing records and special reference to the British check list. Part 3. Tribe Phygadeuontini, subtribes Chiroticina, Acrolytina, Hemitelina and Gelina (excluding Gelis), with descriptions of new species. Entomologist's Gaz. 51, 147-186.
69. Selfa, J., Diller, E., 1994. Illustrated key to the Western Palearctic genera of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae). Entomofauna, 15, 237-251.
70. Sharkey, M.J., Wahl, D.B., 1992. Cladistics of the Ichneumonoidea. J. Hym. Res. 1, 15-24.
71. Shaw, M.R., Bennett, F.D., 2001. Host prepupal mummification by Colpognathus Wesmael (Hymenoptera: Ichneumonidae, Ichneumoninae). Entomologist's Gaz. 52, 201-203.
72. Short, J.R.T., 1978. The final larval instars of the Ichneumonidae. Mem. Am. Entomol. Inst. 25, 1-508.
73. Sikes, D.L., Lewis, O.P., 2001. Beta software, Version 1. PAUPrat: PAUP* Implementation of the Parsimony Ratchet. Distributed by the Authors. Department of Ecology and Evolutionary Biology. University of Connecticut, Storrs, CT.
74. Soltis, P.S., Soltis, D.E., Wolf, P.G., Nickrent, D.L., Chaw, S.M., Chapman, R.L., 1999. The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol. Biol. Evol. 16, 1774-1784.
75. Swofford, D.L., 1999. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Version 4.0b10. Sinauer, Sunderland, MA.
76. Townes, H.K., 1969. The genera of Ichneumonidae, part 1. Mem. Am. Entomol. Inst. 11, 1-300.
77. Townes, H.K., 1970. The genera of Ichneumonidae, part 2. Mem. Am. Entomol. Inst. 12, 1-537.
78. Townes, H.K., Townes, M., 1951. Family Ichneumonidae. In: Muesebeck, C.F.W., Krombein, K.V., Townes, H.K. et al. (Eds.), Hymenoptera of America North of Mexico - Synoptic Catalog. US Department of Agriculture, no. 2, 184-409.
79. Townes, H.K., Townes, M., 1966. A catalogue and reclassification of the Neotropic Ichneumonidae. Mem. Am. Entomol. Inst. 8, 1-367.
80. Townes, H.K., Townes, M., Gupta, V.K., 1961. A catalogue and reclassification of the Indo-Australian Ichneumonidae. Mem. Am. Entomol. Inst. 1, 1-522.
81. Townes, H.K., Momoi, S., Townes, M., 1965. A catalogue and reclassification of the Eastern Palearctic Ichneumonidae. Mem. Am. Entomol. Inst. 5, 1-661.
82. Vilhelmsen, L., Isidoro, N., Romani, R., Basibuyuk, H.H., Quicke, D.L.J., 2001. Host location and oviposition in a basal group of parasitic wasps: the subgenual organ, ovipositor apparatus, and associated structures in the Orussidae (Hymenoptera, Insecta). Zoomorphology, 121, 63-84.
83. Wahl, D.B., 1991. The status of Rhimphoctona, with special reference to the higher categories within Campopleginae and the relationships of the subfamily (Hymenoptera: Ichneumonidae). Trans. Am. Entomol. Soc. 117, 193-213.
84. Wahl, D.B., 1993. Cladistics of the genera of Labeninae (Hymenoptera: Ichneumonidae). Entomol Gen. 18, 91-105.
85. Wahl, D.B., Gauld, I.D., 1998. Cladistics of the Pimpliformes. Syst. Entomol. 23, 265-298.
86. Wahl, D.B., Mason, W.R.M., 1995. The family-group names of the Ichneumoninae (Hymenoptera: Ichneumonidae). J. Hym. Res. 4, 285-293.
87. Wheeler, W., 2001. Homology and the optimization of DNA sequence data. Cladistics, 17, 3-11.
88. Yu, D.S., Horstmann, K., 1997. A catalogue of world Ichneumonidae (Hymenoptera). Mem. Am. Entomol. Inst. 58, 1-1558.
89. Zwickl, D.J., Hillis, D.M., 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51, 588-598.