Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): Data release and new measure of taxonomic congruence

Molecular Ecology Resources

Volumn 12, Issue 4, 2012, Pages 676-685

  Quicke, Donald L J ^a,b   Alex Smith, M ^c   Janzen, Daniel H ^d   Hallwachs, Winnie ^d   Fernandez Triana, Jose ^c,e   Laurenne, Nina M ^f,g   Zaldívar Riverón, Alejandro ^h   Shaw, Mark R ⁱ   Broad, Gavin R ^b   Klopfstein, Seraina ^j,k   Shaw, Scott R ^l   Hrcek, Jan ^m   Hebert, Paul D N ^c   Miller, Scott E ⁿ   Rodriguez, Josephine J ^o   Whitfield, James B ^p   Sharkey, Michael J ^q   Sharanowski, Barbara J ^r,t   Jussila, Reijo ^s   Gauld, Ian D ^b   Chesters, Douglas ^a,b   Vogler, Alfried P ^a,b   more..

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c UNIVERSITY OF GUELPH   (Canada)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

^e CEF   (Canada)

^f AALTO UNIVERSITY   (Finland)

^g UNIVERSITY OF HELSINKI   (Finland)

^h DEPARTAMENTO DE ZOOLOGÍA   (Mexico)

ⁱ DEPARTMENT OF NATURAL SCIENCES   (United Kingdom)

^j NATURHISTORISCHES MUSEUM DER BURGERGEMEINDE BERN   (Switzerland)

^k UNIVERSITY OF BERN   (Switzerland)

^l UNIVERSITY OF WYOMING   (United States)

^m UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

ⁿ SMITHSONIAN INSTITUTION   (United States)

^o NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^p UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^q UNIVERSITY OF KENTUCKY   (United States)

^r NORTH CAROLINA STATE UNIVERSITY   (United States)

^s NONE   (Finland)

^t UNIVERSITY OF MANITOBA   (Canada)

more..

Author keywords

Braconidae; Cytochrome oxidase 1; Ichneumonidae; Sampling density; Simpson dominance index; Taxonomic retention index

Indexed keywords

BRACONIDAE; HYMENOPTERA; ICHNEUMONIDAE; ICHNEUMONOIDEA; VESPOIDEA;

EID: 84862173465     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2012.03143.x     Document Type: Article

References (52)

1. Aliabadian M, Kaboli M, Nijman V, Vences M (2009) Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species. PLoS One, 4, e4119.
2. Belshaw R, Fitton MG, Herniou E, Gimeno C, Quicke DLJ (1998) A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28S ribosomal DNA. Systematic Entomology, 23, 109-123.
3. Belshaw R, Dowton M, Quicke DLJ, Austin AD (2000) Estimating ancestral geographic distributions: a Gondwanan origin for the aphid parasitoids. Proceedings of the Royal Society, London B, 267, 491-496.
4. Dowton M, Austin AD, Antolin MF (1998) Evolutionary relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA gene sequences. Insect Molecular Biology, 7, 129-150.
5. Dowton M, Belshaw R, Austin AD, Quicke DLJ (2002) Simultaneous molecular and morphological analysis of braconid relationships (Insecta: Hymenoptera: Braconidae) indicates independent mt-tRNA gene inversions within a single wasp family. Journal of Molecular Evolution, 54, 210-226.
6. Farris JS (1989) The retention index and the rescaled consistency index. Cladistics, 5, 417-419.
7. Fitch WM (1970) Distinguishing homologous from analogous proteins. Systematic Zoology, 19, 99-113.
8. Gauld ID, Mound LA (1982) Homoplasy and the delineation of holophyletic genera in some insect groups. Systematic Entomology, 7, 73-86.
9. Giavelli G, Rossi O, Sartore F (1986) Comparative evaluation of four species diversity indices related to two specific ecological situations. Field Studies, 6, 429-438.
10. Gillespie JJ, Yoder MJ, Wharton RA (2005) Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation. Journal of Molecular Evolution, 61, 114-137.
11. Goloboff P, Farris JS, Nixon K (2003) TNT: Tree Analysis Using New Technology version 1.1. [Program and documentation]. The authors, Tucumán, Argentina. Available from .
12. Graybeal A (1994) Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Systematic Biology, 43, 174-193.
13. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society, London B, 270, 313-321.
14. Hrcek J, Miller SE, Quicke DLJ, Smith MA (2011) Molecular detection of trophic links in a complex insect host-parasitoid food web. Molecular Ecology Resources, 11, 786-794.
15. Hunt T, Vogler AP (2008) A protocol for large-scale rRNA sequence analysis: towards a detailed phylogeny of Coleoptera. Molecular Phylogenetics and Evolution, 47, 289-301.
16. Janzen DH, Hallwachs W, Blandin P et al. (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources, 9(Suppl. 1), 1-26.
17. Kallersjö M, Albert VA, Farris JS (1999) Homoplasy increases phylogenetic structure. Cladistics, 15, 91-93.
18. Klopfstein S, Kropf C, Quicke DLJ (2010) An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). Systematic Biology, 59, 226-241.
19. Laurenne NM, Broad GR, Quicke DLJ (2006) Direct optimization and multiple alignment of 28S D2-3 rDNA sequences: problems with indels on the way to a molecular phylogeny of the cryptine ichneumon wasps (Insecta: Hymenoptera). Cladistics, 22, 442-473.
20. Lukhtanov VA, Sourakov A, Zakharovs EV, Hebert PDN (2009) DNA barcoding Central Asian butterflies: increasing geographical dimension does not significantly reduce the success of species identification. Molecular Ecology Resources, 9, 1302-1310.
21. Mardulyn P, Whitfield JB (1999) Phylogenetic signal in the COI, 16S, and 28S genes for inferring relationships among genera of Micrograstrinae (Hymenoptera; Braconidae): evidence of a high diversiWcation rate in this group of parasitoids. Molecular Phylogenetics and Evolution, 12, 282-294.
22. Murphy N, Banks JC, Whitfield JB, Austin AD (2008) Phylogeny of the microgastroid complex of subfamilies of braconid parasitoid wasps (Hymenoptera) based on sequence data from seven genes, with an improved estimate of the time of origin of the lineage. Molecular Phylogenetics and Evolution, 47, 378-395.
23. Pitz KM, Dowling AP, Sharanowski BJ, Boring CA, Seltmann KC, Sharkey MJ (2007) Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea): a reassessment of Shi et al. (2005). Molecular Phylogenetics and Evolution, 43, 338-343.
24. Poe S (1998) Sensitivity of phylogeny estimation to taxonomic sampling. Systematic Biology, 47, 18-31.
25. Purvis A, Quicke DLJ (1997) Phylogeny reconstruction: are the big easy? Trends in Ecology & Evolution, 12, 49-50.
26. Quicke DLJ, Achterberg Cvan (1990) Phylogeny of the subfamilies of the family Braconidae (Hymenoptera, Ichneumonoidea). Zoologische Verhandelingen, 258, 1-95.
27. Quicke DLJ, Belshaw R (1999) Incongruence between morphological data sets: an example from the evolution of endoparasitism among parasitic wasps (Hymenoptera: Braconidae). Systematic Biology, 48, 436-454.
28. Quicke DLJ, Basibuyuk HH, Fitton MG, Rasnitsyn AP (1999) Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta). Zoologica Scripta, 28, 175-202.
29. Quicke DLJ, Fitton MG, Broad GR, Crocker B, Laurenne NM, Miah IM (2005) The parasitic wasp genera Skiapus, Hellwigia, Nonnus, Chriodes and Klutiana (Hymenoptera, Ichneumonidae): recognition of the Nesomesochorinae stat. rev. and Nonninae stat. nov. and transfer of Skiapus and Hellwigia to the Ophioninae. Journal of Natural History, 39, 2559-2578.
30. Quicke DLJ, Laurenne NM, Fitton MG, Broad GR (2009) A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision. Journal of Natural History, 43, 1305-1421.
31. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, Available from .
32. Rannala B, Huelsenbeck JP, Yang Z, Nielsen R (1998) Taxon sampling and the accuracy of large phylogenies. Systematic Biology, 47, 702-710.
33. Ratnasingham S, Hebert PDN (2007) BOLD : the Barcode of Life Data System Molecular Ecology Notes, 7, 355-364.
34. Russell RD, Beckenbach AT (2008) Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code. Journal of Molecular Evolution, 67, 682-695.
35. Sharanowski BJ, Dowling APG, Sharkey MJ (2011) Molecular phylogenetics of Braconidae (Hymenoptera: Ichneumonoidea), based on multiple nuclear genes, and implications for classification. Systematic Entomology, 36, 549-572.
36. Sharkey MJ, Laurenne NM, Quicke DLJ, Sharanowshi BJ, Murray D (2006) Revision of the Agathidinae (Hymenoptera: Braconidae) with comparisons of static and dynamic alignments. Cladistics, 22, 546-567.
37. Shi M, Chen XX, Achterberg Cvan (2005) Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA, 28S rDNA D2, 18S rDNA gene sequences and morphological characters. Molecular Phylogenetics and Evolution, 37, 104-116.
38. Simpson EH (1949) Measurement of biodiversity. Nature, 163, 688.
39. Smith MA, Wood DM, Janzen DH, Hallwachs W, Hebert PDN (2007) DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists. Proceedings of the National Academy of Sciences, 104, 4967-4972.
40. Smith MA, Rodríguez JJ, Whitfield JB et al. (2008) Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology. and collections. Proceedings of the National Academy of Sciences, 105, 12359-12364.
41. Smith MA, Fernandez-Triana J, Roughley R, Hebert PDN (2009) DNA barcode accumulation curves for understudied taxa and areas. Molecular Ecology Resources, 9(Suppl.1), 208-216.
42. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456-463.
43. Swofford DL (2001) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, Massachusetts.
44. Wahl DB, Gauld ID (1998) The cladistics and higher classification of the Pimpliformes (Hymenoptera: Ichneumonidae). Systematic Entomology, 23, 265-298.
45. Wharton RA, Shaw SR, Sharkey MJ et al. (1992) Phylogeny of the subfamilies of the family Braconidae (Hymenoptera: Ichneumonoidea): a reassessment. Cladistics, 8, 199-235.
46. Whitfield JB (1992) The polyphyletic origin of endoparasitism in the cyclostome lineages of Braconidae (Hymenoptera). Systematic Entomology, 17, 273-286.
47. Whitfield JB (2002) Estimating the age of the polydnavirus/braconid wasp symbiosis. Proceedings of the National Academy of Science, 99, 7508-7513.
48. Whitfield JB, Mardulyn P, Austin AD, Dowton M (2002) Phylogeny of the Microgastrinae (Hymenoptera: Braconidae) based on 16S, COI and 28S genes and morphology. Systematic Entomology, 27, 337-359.
49. Yu D, van Achterberg C, Horstmann K (2005) World Ichneumonoidea 2004. Taxonomy, Biology, Morphology and Distribution. Taxapad, Vancouver, Canada.
50. Zaldívar-Riverón A, Mori M, Quicke DLJ (2006) Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): a simultaneous molecular and morphological Bayesian approach. Molecular Phylogenetics and Evolution, 38, 130-145.
51. Zaldívar-Riverón A, Belokobylskij SA, Leon-Regagnon V, Briceno-G R, Quicke DLJ (2008) Molecular phylogeny and historical biogeography of the cosmopolitan parasitic wasp subfamily Doryctinae (Hymenoptera: Braconidae). Invertebrate Systematics, 22, 345-363.
52. Zwickl DJ, Hillis DM (2002) Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology, 51, 588-598.