Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)

Zoologica Scripta

Volumn 38, Issue 1, 2009, Pages 43-62

  Maddison, David R ^a   Moore, Wendy ^a,b   Baker, Michael D ^a,c   Ellis, Tana M ^a,d   Ober, Karen A ^a,e   Cannone, Jamie J ^f   Gutell, Robin R ^f  

^a UNIVERSITY OF ARIZONA   (United States)

^b CALIFORNIA ACADEMY OF SCIENCES   (United States)

^c IOWA STATE UNIVERSITY   (United States)

^d OREGON STATE UNIVERSITY   (United States)

^e Center for Interdisciplinary Studies   (United States)

^f UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADEPHAGA; ARCHOSTEMATA; CARABIDAE; COLEOPTERA; HYDRADEPHAGA; MYXOPHAGA; POLYPHAGA (COLEOPTERA); SCIRTOIDEA; TRACHYPACHIDAE;

EID: 57649231179     PISSN: 03003256     EISSN: 14636409     Source Type: Journal    
DOI: 10.1111/j.1463-6409.2008.00359.x     Document Type: Article

References (96)

1. Abascal, F., Zardoya, R. Posada, D. (2005). ProtTest: Selection of best-fit models of protein evolution. Bioinformatics, 21, 2104 2105.
2. Alarie, Y. Bilton, D. T. (2005). Larval morphology of Aspidytidae (Coleoptera: Adephaga) and its phylogenetic implications. Annals of the Entomological Society of America, 98, 417 430.
3. Alarie, Y. Michat, M. C. (2007). Primary setae and pores on the maxilla of larvae of the subfamily Hydroporinae (Coleoptera: Adephaga: Dytiscidae): Ground plan pattern reconsidered. Coleopterists Bulletin, 61, 310 317.
4. Alverson, A. J., Cannone, J. J., Gutell, R. R. Theriot, E. C. (2006). The evolution of elongate shape in diatoms. Journal of Phycology, 42, 655 668.
5. Arndt, E. (1989). Carabid larvae (Coleoptera, Carabidae) as subject of phylogenetical research. Entomologische Nachrichten und Berichte, 33, 255 260.
6. Arndt, E. Beutel, R. G. (1995). Larval morphology of Systolosoma Solier and Trachypachus Motschulsky (Coleoptera: Trachypachidae) with phylogenetic considerations. Entomologica Scandinavica, 26, 439 446.
7. Attygalle, A. B., Wu, X. G., Ruzicka, J., Rao, S., Garcia, S., Herath, K. et al 2004). Defensive chemicals of two species of Trachypachus Motschulski. Journal of Chemical Ecology, 30, 577 588.
8. Baehr, M. (1979). Vergleichende Untersuchungen am Skelett und an der Coxalmuskulatur des Prothorax der Coleoptera. Ein Beitrag zur Klarung der phylogenetischen Beziehungen der Adephaga (Coleoptera, Insecta). Zoologica (Stuttgart), 44, 1 76. No. 130.
9. Bell, R. T. (1966). Trachypachus and the origin of the Hydradephaga (Coleoptera). Coleopterists Bulletin, 20, 107 112.
10. Bell, R. T. (1967). Coxal cavities and the classification of the Adephaga (Coleoptera). Annals of the Entomological Society of America, 60, 101 107.
11. Bell, R. T. (1983). What is Trachypachus? (Coleoptera: Trachypachidae). Coleopterists Bulletin, 36, 590 596.
12. Bell, R. T. (1994). Beetles that cannot bite: Functional morphology of the head of adult rhysodines (Coleoptera: Carabidae or Rhysodidae). Canadian Entomologist, 126, 667 672.
13. Beutel, R. G. (1988). Studies of the metathorax of the trout-stream beetle, Amphizoa lecontei Matthews (Coleoptera, Amphizoidae) - contribution towards clarification of the systematic position of Amphizoidae. International Journal of Insect Morphology and Embryology, 17, 63 81.
14. Beutel, R. G. (1989). The head of Spanglerogyrus albiventris Folkerts (Coleoptera: Gyrinidae) contribution towards clarification of the phylogeny of Gyrinidae and Adephaga. Zoologische Jahrbuecher Abteilung Fuer Anatomie und Ontogenie der Tiere, 118, 431 461.
15. Beutel, R. G. (1990). Metathoracic features of Omoglymmius hamatus and their significance for classification of Rhysodini (Coleoptera, Adephaga). Entomologia Generalis, 15, 185 201.
16. Beutel, R. G. (1992a). Larval head structures of Omoglymmius hamatus and their implications for the relationships of Rhysodidae (Coleoptera, Adephaga). Entomologica Scandinavica, 23, 169 184.
17. Beutel, R. G. (1992b). Phylogenetic analysis of thoracic structures of Carabidae (Coleoptera, Adephaga). Zeitschrift Fur Zoologische Systematik und Evolutionsforschung, 30, 53 74.
18. Beutel, R. G. (1992c). Study on the systematic position of Metriini based on characters of the larval head (Coleoptera, Carabidae). Systematic Entomology, 17, 207 218.
19. Beutel, R. G. (1993). Phylogenetic analysis of Adephaga (Coleoptera) based on characters of the larval head. Systematic Entomology, 18, 127 147.
20. Beutel, R. G. (1994). Study on the systematic position of Systolosoma breve Solier (Adephaga, Trachypachidae) based on characters of the thorax. Studies on Neotropical Fauna and Environment, 29, 161 167.
21. Beutel, R. G. (1995). The Adephaga (Coleoptera): phylogeny and evolutionary history. In J. Pakaluk S. A. Slipinski (Eds) Biology, Phylogeny, and Classification of Coleoptera (pp. 173 218). Warzawa : Museum Zoologii PAN.
22. Beutel, R. G. (1997). Über Phylogenese und Evolution der Coleoptera (Insecta), insbesondere der Adephaga. Abhandlungen des Naturwissenshaftlichen Vereins in Hamburg, 31, 1 164.
23. Beutel, R. G. (1998). Trachypachidae and the phylogeny of Adephaga. In : G. E. Ball, A. Casale A. V. Taglianti (Eds) Phylogeny and Classification of Carabidea (Coleoptera: Adephaga). Proceedings of XX International Congress of Entomology Symposium, 28 August 1996, Florence, Italy (pp. 81 106). Torino, Italy : Museo Regional Science Naturali.
24. Beutel, R. G. Haas, A. (1996). Phylogenetic analysis of larval and adult characters of Adephaga (Coleoptera) using cladistic computer programs. Entomologica Scandinavica, 27, 197 205.
25. Beutel, R. G. Haas, F. (2000). Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics - the International Journal of the Willi Hennig Society, 16, 103 141.
26. Beutel, R. G. Roughley, R. E. (1988). On the systematic position of the family Gyrinidae (Coleoptera, Adephaga). Zeitschrift Fur Zoologische Systematik und Evolutionsforschung, 26, 380 400.
27. Beutel, R. G. Roughley, R. E. (1993). Phylogenetic analysis of Gyrinidae based on characters of the larval head (Coleoptera, Adephaga). Entomologica Scandinavica, 24, 459 468.
28. Beutel, R. G., Balke, M. Steiner, W. E. (2006). The systematic position of Meruidae (Coleoptera, Adephaga) and the phylogeny of the smaller aquatic adephagan beetle families. Cladistics, 22, 102 131.
29. Beutel, R. G., Ribera, I. Bininda-Emonds, O. R. P. (2007). A genus-level supertree of Adephaga (Coleoptera). Organisms Diversity and Evolution, 7, 255 269.
30. Beutel, R. G., Ge, S.-Q. Hörnschemeyer, T. (2008). On the head morphology of Tetraphalerus, the phylogeny of Archostemata and the basal branching events in Coleoptera. Cladistics, 24, 270 298.
31. Bils, W. (1976). Das Abdomende weiblicher, terrestrisch lebender Adephaga (Coleoptera) und seine Bedeutung für die Phylogenie. Zoomorphologie, 84, 113 193.
32. Bousquet, Y. (1986). Description of 1st-instar larva of Metrius contractus Eschscholtz (Coleoptera, Carabidae) with remarks about phylogenetic-relationships and ranking of the genus Metrius Eschscholtz. Canadian Entomologist, 118, 373 388.
33. Burmeister, E. G. (1976). Ovipositor of Hydradephaga (Coleoptera) and its phylogenetic significance, with special considerations of Dytiscidae. Zoomorphologie, 85, 165 257.
34. Burmeister, E. G. (1990a). On the systematic position of Amphizoidae, emphasizing features of the female genital organs (Insecta: Coleoptera: Adephaga). Quaestiones Entomologicae, 26, 245 272.
35. Burmeister, E. G. (1990b). The female genital structures of Spanglerogyrus albiventris Folkerts, 1979: a contribution to the systematic position of the Gyrinidae. Spixiana, 13, 253 265.
36. Caterino, M. S., Shull, V. L., Hammond, P. M. Vogler, A. P. (2002). Basal relationships of Coleoptera inferred from 18S rDNA sequences. Zoologica Scripta, 31, 41 49.
37. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. et al 2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31, 3497 3500.
38. Crowson, R. A. (1960). The phylogeny of Coleoptera. Annual Review of Entomology, 5, 111 134.
39. Dettner, K. (1985). Ecological and phylogenetic significance of defensive compounds from pygidial glands of Hydradephaga (Coleoptera). Proceedings of the Academy of Natural Sciences of Philadelphia, 137, 156 171.
40. Deuve, T. (1993). L'abdomen et les genitalia des femelles de Coléoptères Adephaga. Mémoires du Muséum National D'Histoire Naturelle, 155, 1 184.
41. Drummond, A. Strimmer, K. (2001). PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics, 17, 662 663.
42. Erwin, T. L. (1985). The taxon pulse: a general pattern of lineage radiation and extinction among carabid beetles. Series Entomologica (Dordrecht), 437 472.
43. Evans, M. E. G. (1982). Early evolution of the Adephaga - some locomotor speculations. Coleopterists Bulletin, 36, 597 607.
44. Forsyth, D. J. (1972). The structure of the pygidial defence glands of Carabidae (Coleoptera). Transactions of the Zoological Society of London, 32, 249 309.
45. Friedrich, F. Beutel, R. G. (2006). The pterothoracic skeletomuscular system of Scirtoidea (Coleoptera: Polyphaga) and its implications for the high-level phylogeny of beetles. Journal of Zoological Systematics and Evolutionary Research, 44, 290 315.
46. Green, P. (1999). Phrap. Version 0.990329. Available at URL: http://phrap.org.
47. Green, P. Ewing, B. (2002). Phred. Ver. 0.020425c. Available via http://phrap.org.
48. Guindon, S. Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696 704.
49. Gutell, R. R., Lee, J. C. Cannone, J. J. (2002). The accuracy of ribosomal RNA comparative structure models. Current Opinion in Structural Biology, 12, 301 310.
50. Gutell, R. R., Weiser, B., Woese, C. R. Noller, H. F. (1985). Comparative anatomy of 16S-like ribosomal RNA. Progress in Nucleic Acid Research and Molecular Biology, 32, 155 216.
51. Hammond, P. M. (1979). Wing-folding mechanisms of beetles, with special reference to investigations of Adephagan phylogeny (Coleoptera). In T. L. Erwin, G. E. Ball, D. R. Whitehead A. L. Halpern (Eds) Carabid Beetles: Their Evolution, Natural History, and Classification (pp. 113 180). The Hague : Dr W. Junk bv.
52. Heath, R. V. Evans, M. E. G. (1990). The relationship between the ventral nerve cord, body size and phylogeny in ground beetles (Coleoptera: Carabidae). Zoological Journal of Linnean Society, 98, 259 294.
53. Huelsenbeck, J. P., Rannala, B. Masly, J. P. (2000). Accommodating phylogenetic uncertainty in evolutionary studies. Science, 288, 2349 2350.
54. Huelsenbeck, J. Ronquist, F. (2005). MrBayes. Version 3.1.2. Available at URL: http://www.mrbayes.net.
55. Hunt, T., Bergsten, J., Levkanicova, Z., Papadopoulou, A., John, O. S., Wild, R. et al 2007). A Comprehensive Phylogeny of Beetles Reveals the Evolutionary Origins of a Superradiation. Science, 318, 1913 1916.
56. Kanehisa, K. Murase, M. (1977). Comparative study of the pygidial defensive systems of carabid beetles. Applied Entomology and Zoology, 12, 225 235.
57. Kavanaugh, D. H. (1986). A systematic review of Amphizoid beetles (Amphizoidae: Coleoptera) and their phylogenetic relationships to other Adephaga. Proceedings of the California Academy of Sciences, 44, 67 109.
58. Kukalová-Peck, J. Lawrence, J. F. (1993). Evolution of the hind wing in Coleoptera. Canadian Entomologist, 125, 181 258.
59. Lawrence, J. F. (1999). The Australian Ommatidae (Coleoptera: Archostemata): new species, larva and discussion of relationships. Invertebrate Taxonomy, 13, 369 390.
60. Lawrence, J. F. (2001). A new genus of valdivian Scirtidae (Coleoptera) with comments on Scirtoidea and the beetle suborders. Special Publication of the Japanese Coleoptera Society, Osaka, 1, 351 361.
61. Lawrence, J. F. Newton, A. F. Jr (1982). Evolution and classification of beetles. Annual Review of Ecology Evolution and Systematics, 13, 261 290.
62. Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50, 913 925.
63. Lorenz, W. (2005). A Systematic List of Extant Ground Beetles of the World (Coleoptera 'Geadephaga': Trachypachidae and Carabidae incl. Paussinae, Cicindelinae, Rhysodinae). Tutzing : Lorenz, W.
64. Maddison, D. R. (2008). Systematics of the North American beetle subgenus Pseudoperyphus (Coleoptera: Carabidae: Bembidion) based upon morphological, chromosomal, and molecular data. Annals of Carnegie Museum, 77, 147 193.
65. Maddison, D. R. Maddison, W. P. (2005). MacClade 4: Analysis of Phylogeny and Character Evolution, Version 4.08. Sunderland, Massachusetts : Sinauer Associates.
66. Maddison, D. R. Maddison, W. P. (2007). Chromaseq: a Mesquite module for analyzing sequence chromatograms. Version 0.92. Available at URL: http://mesquiteproject.org/packages/chromaseq.
67. Maddison, D. R., Baker, M. D. Ober, K. A. (1999). Phylogeny of carabid beetles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae). Systematic Entomology, 24, 103 138.
68. Maddison, W. P. Maddison, D. R. (2008). Mesquite: a modular system for evolutionary analysis. Version 2.5. Available at URL: http://mesquiteproject. org.
69. Moore, B. P. (1979). Chemical defense in carabids and its bearing on phylogeny. In T. L. Erwin, G. E. Ball, D. R. Whitehead A. L. Halpern (Eds) Carabid Beetles: Their Evolution, Natural History, and Classification (pp. 193 203). The Hague : Dr. W. Junk bv.
70. Moore, W. (2008). Phylogeny of the Western Hemisphere Ozaenini (Coleoptera: Carabidae: Paussinae) based on DNA sequence data. Annals of Carnegie Museum, 77, 79 92.
71. Nichols, S. W. (1985). Omophron and the origin of Hydradephaga (Insecta: Coleoptera: Adephaga). Proceedings of the Academy of Natural Sciences of Philadelphia, 137, 182 201.
72. Nilsson, A. N. (2001). Dytiscidae (Coleoptera). World Catalogue of Insects, 3, 1 395.
73. Noller, H. F., Kop, J., Wheaton, V., Brosius, J., Gutell, R. R., Kopylov, A. M. et al 1981). Secondary structure model for 23S ribosomal RNA. Nucleic Acids Research, 9, 6167 6189.
74. Ober, K. A. (2002). Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data. Molecular Phylogenetics and Evolution, 24, 228 248.
75. Paradis, E., Claude, J. Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 289 290.
76. Ponomarenko, A. G. (1977). Suborder Adephaga. In L. V. Arnoldi, V. V. Zherikin, L. M. Nikritin A. G. Ponomarenko (Eds) (pp. 1 104). Moscow : Trudi Paleontologiceskogo Instituta, Academija Nauk SSSR.
77. Posada, D. (2005). ModelTest: A tool to select the best-fit model of nucleotide substitution. Version 3.7. Available at URL: http://darwin.uvigo.es.
78. Rambaut, A. Drummond, A. (2004). Tracer. Version 1.3. Available at URL: http://evolve.zoo.ox.ac.uk/software.html?id=tracer.
79. Ribera, I., Hogan, J. E. Vogler, A. P. (2002). Phylogeny of hydradephagan water beetles inferred from 18S rRNA sequences. Molecular Phylogenetics and Evolution, 23, 43 62.
80. Roughley, R. E. (1981). Trachypachidae and Hydradephaga (Coleoptera) - a monophyletic unit? Pan-Pacific Entomologist, 57, 273 285.
81. Sanderson, M. J. (2002). Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101 109.
82. Sankoff, D. D. (1975). Minimal mutation trees of sequences. SIAM Journal of Applied Mathematics, 28, 35 42.
83. Seeger, W. (1971). Morphologie, Bionomie und Ethologie von Halipliden, unter besonderer Berücksichtigung funktionsmorphologischer Gesichtspunkte (Haliplidae; Coleoptera). Archiv für Hydrobiologie, 68, 400 435.
84. Shull, V. L., Vogler, A. P., Baker, M. D., Maddison, D. R. Hammond, P. M. (2001). Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: Evidence for monophyly of aquatic families and the placement of Trachypachidae. Systematic Biology, 50, 945 969.
85. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, btl446.
86. Swofford, D. L. (2002). paup*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version. 4.0b10. Sunderland : Sinauer Associates.
87. Thiele, H. (1977). Carabid Beetles in Their Environments: a Study on Habitat Selection by Adaptations in Physiology and Behaviour. Berlin : Springer-Verlag.
88. Van der Auwera, G., Chapelle, S. De Wachter, R. (1994). Structure of the large ribosomal subunit RNA of Phytophthora megasperma, and phylogeny of the oomycetes. FEBS Letters, 338, 133 136.
89. Ward, R. D. (1979). Metathoracic wing structures as phylogenetic indicators in the Adephaga (Coleoptera). In T. L. Erwin, G. E. Ball, D. R. Whitehead A. L. Halpern (Eds) Carabid Beetles: Their Evolution, Natural History, and Classification (pp. 181 191). The Hague : Dr W. Junk bv.
90. Ward, P. S. Downie, D. A. (2005). The ant subfamily Pseudomyrmecinae (Hymenoptera: Formicidae): phylogeny and evolution of big-eyed arboreal ants. Systematic Entomology, 30, 310 335.
91. Wheeler, T. J. Kececioglu, J. D. (2007). Multiple alignments by aligning alignments. Bioinformatics, 23, i559 i568.
92. Wild, A. L. Maddison, D. R. (2008). Evaluating nuclear protein-coding genes for phylogenetic utility in beetles. Molecular Phylogenetics and Evolution, 48, 877 891.
93. Woese, C. R., Magrum, L. J., Gupta, R., Siegel, R. B., Stahl, D. A., Kop, J. et al 1980). Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Research, 8, 2275 2293.
94. Wray, C. G., Lee, J. J. Desalle, R. (1993). Extraction and Enzymatic Characterization of Foraminiferal DNA. Micropaleontology, 39, 69 73.
95. Yahiro, K. (1990). A comparative morphology of the alimentary canal in the adults of ground-beetles (Coleoptera). I. Classification into the types. Esakia, 60, 35 44.
96. Zwickl, D. J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Thesis. The University of Texas at Austin.