Towards the phylogeny of chafers (Sericini): Analysis of alignment-variable sequences and the evolution of segment numbers in the antennal club

Molecular Phylogenetics and Evolution

Volumn 47, Issue 2, 2008, Pages 783-798

  Ahrens, Dirk ^a,b   Vogler, Alfried P ^b,c  

^a ZOOLOGISCHE STAATSSAMMLUNG MÜNCHEN   (Germany)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Antennal lamellae; Chemical communication; Classification; Melolonthinae; Progressive sequence alignment; Scarabaeidae; Sexual selection; Species diversification

Indexed keywords

ANIMAL; ANIMAL ANATOMY; ARTICLE; BEETLE; CONSENSUS SEQUENCE; DNA SEQUENCE; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ANIMAL STRUCTURES; ANIMALS; BEETLES; CONSENSUS SEQUENCE; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CETONIINAE; COLEOPTERA; GLAPHYRIDAE; MALADERA; MELOLONTHINAE; SCARABAEIDAE; SCARABAEOIDEA;

EID: 42749083109     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.02.010     Document Type: Article

References (92)

1. Aagesen L., Petersen G., and Seberg O. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics 21 (2005) 15-30 10.1016/j.ympev.2007.11.029
2. Ahrens D. Taxonomische Studien an Sericinae. Die Gattungen Deroserica Moser,1915, Microsericaria Nikolaev, 1979, Pachyderoserica Moser, 1920 und Microserica Brenske, 1894 (Ins., Col., Melolonth.). Entomol. Abh. (Dresd.) 57 2 (1995) 37-56
3. Ahrens D. Zwei neue Arten der Gattung Chrysoserica aus dem Himalaya (Coleoptera Melolonthidae). Boll. Soc. Entomol. Ital. 133 (2001) 131-145
4. Ahrens D. Neue Arten der Microserica splendidula (Fabricius, 1801)-Gruppe von West-Malayasia, Nias und Sumatra (Coleoptera: Melolonthidae). Koleopterol. Rundsch. 71 (2001) 111-120
5. Ahrens D. Revision der Arten der Microserica viridicollis Arrow, 1913-Gruppe (Coleoptera, Melolonthinae, Sericini). Linz. Biol. Beitr. 34 (2002) 383-412
6. Ahrens D. Zur Identität der Gattung Neoserica Brenske, 1894, nebst Beschreibung neuer Arten (Coleoptera, Melolonthidae, Sericini). Koleopterol. Rundsch. 73 (2003) 169-226
7. Ahrens, D., 2004. Monographie der Sericini des Himalaya (Coleoptera, Scarabaeidae). Dissertation. de-Verlag im Internet GmbH, Berlin, 534pp.
8. Ahrens D. The phylogeny of Sericini and their position within the Scarabaeidae based on morphological characters (Coleoptera: Scarabaeidae). Syst. Entomol. 31 (2006) 113-144
9. Ahrens D. The phylogeny of the genus Lasioserica inferred from adult morphology-implications on the evolution of montane fauna of the South Asian orogenic belt (Coleoptera: Scarabaeidae: Sericini). J. Zool. Syst. Evol. Res. 44 (2006) 34-53
10. Ahrens D. Revision der Gattung Nepaloserica Frey (Coleoptera, Melolonthidae). Frag. Entomol. 28 (1996) 209-243
11. Ahrens D., Monaghan M.T., and Vogler A.P. DNA-based taxonomy for associating adults and larvae in multi-species assemblages of chafers (Coleoptera: Scarabaeidae). Mol. Phylogenet. Evol. 44 (2007) 436-449
12. Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Control 19 (1974) 716-723
13. Allsopp P. Sexual dimorphism in the adult antennae of Antitrogus parvulus Britton and Lepidiota negatoria Blackburn (Coleoptera: Scarabaeidae: Melolonthinae). J. Aust. Entomol. Soc. 29 (1990) 261-266
14. Altekar G., Dwarkadas S., Huelsenbeck J.P., and Ronquist F. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20 (2004) 407-415
15. Balthasar, V., 1963. Monographie der Scarabaeidae und Aphodiidae der palaearktischen und orientalischen Region. Coleoptera: Lamellicornia. Band 1. Prag, Verlag der Tschechoslowakischen Akademie der Wissenschaften, pp. 391.
16. Belshaw R., and Katzourakis A. BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinform. Appl. Note 21 1 (2005) 122-123
17. Brandley M.C., Schmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54 3 (2005) 373-390
18. Brenske E. Die Serica-Arten der Erde. I. Berl. Ent. Ztschr. 42 (1897) 345-438
19. Brower A.V.Z., and Schawaroch V. Three steps of homology assessment. Cladistics 12 (1996) 265-272
20. Browne J., and Scholtz C.H. Evolution of the scarab hind wing articulation and wing base: a contribution toward the phylogeny of the Scarabaeidae (Scarabaeoidea: Coleoptera). Syst. Entomol. 23 (1998) 307-326
21. Browne J., and Scholtz C.H. A phylogeny of the families of Scarabaeoidea. Syst. Entomol. 24 (1999) 51-84
22. Burmeister, H., 1855. Handbuch der Entomologie. Vierter Band. Besondere Entomologie. Fortsetzung. 2. Abteilung, Coleoptera Lamellicornia Phyllophaga chaenochela. TCF Enslin, Berlin, x + 569pp.
23. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
24. De Pinna M.C.C. Concepts and tests of homology in the cladistic paradigm. Cladistics 7 (1991) 367-394
25. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 5 (2004) 1792-1797
26. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5 113 (2004) 1-19
27. Erichson, W.F., 1847. Naturgeschichte der Insecten Deutschlands. Erste Abtheilung. Coleoptera, vol. 3, Lieferung 4. Nicolaische Buchhandlung, Berlin, pp. 481-640.
28. Estabrook G.F., McMorris F.R., and Meacham C.A. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34 (1985) 193-200
29. Evans, A.V., Smith, A.B.T., 2007. An electronic checklist of the New World chafers (Coleoptera: Scarabaeidae: Melolonthinae), Version 2, 349pp.
30. Felsenstein J. Maximum likelihood and minimum-step methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22 (1973) 240-249
31. Gardner P.P., Wilm A., and Washietl S. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33 8 (2005) 2433-2439
32. Gatesy J., DeSalle R., and Wheeler W.C. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2 (1993) 152-157
33. Giribet G., and Wheeler W.C. On gaps. Mol. Phylogenet. Evol. 13 (1999) 132-143
34. Goddard W., Kubicka E., Kubicki G., and McMorris F.R. The agreement metric for labeled binary trees. Math. Biosci. 123 (1994) 215-226
35. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49 4 (2000) 652-670
36. Goloboff P., Farris S., and Nixon K. TNT (Tree analysis using New Technology). Cladistics 20 (2004) 84
37. Gotoh O. An improved algorithm for matching biological sequences. J. Mol. Biol. 162 (1982) 705-708
38. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 5 (2003) 696-704
39. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
40. Hunt T., and Vogler A.P. A protocol for large-scale rRNA sequence analysis: towards a detailed phylogeny of Coleoptera. Mol. Phylogenet. Evol. 47 (2008) 289-301
41. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
42. Katoh K., Misawa K., Kuma K., and Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 14 (2002) 3059-3066
43. Katoh K., Kuma K., Toh H., and Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33 2 (2005) 511-518
44. Koehl M.A.R. The fluid mechanics of arthropod sniffing in turbulent odor plumes. Chem. Senses 31 (2006) 93-105
45. Leal W.S. Chemical ecology of phytophagous scarab beetles. Annu. Rev. Entomol. 43 (1998) 39-61
46. Leal W.S. Mechanisms of chemical communication in scarab beetles. In: Hidaka T., Matsumoto Y., Honda K., Honda H., and Tatsuki K. (Eds). Environmental entomlology: behaviour, physiology, and chemical ecology (1999), University of Tokyo Press, Tokyo 464-478
47. Leal W.S., Wojtasek H., and Miyazawa M. Pheromone-binding proteins of scarab beetles. Ann. NY Acad. Sci. 855 (1998) 301-305
48. Loudon C., and Koehl M.A.R. Sniffing by a silkworm moth: wing fanning enhances air penetration through and pheromone interception by antennae. J. Exp. Biol. 203 (2000) 2977-2990
49. Loudon C., and Davis E.C. Divergence of streamlines approaching a pectinate insect antenna: consequences for chemoreception. J. Chem. Ecol. 31 (2005) 1-13
50. Löytynoja A., and Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. USA 102 30 (2005) 10557-10562
51. Machatschke J.W. Phylogenetische Untersuchungen über die Sericini (sensu Dalla Torre 1912) (Coleoptera: Lamellicornia: Melolonthidae). Beitr. Entomol. 9 (1959) 730-746
52. Maddison, W.P., Maddison, D.R., 1998. MacClade, analysis of phylogeny and character evolution. Ver. 3.08: Sinauer, Sunderland, MA.
53. Meinecke C.C. Riechsensillen und Systematik der Lamellicornia. (Insecta: Coleoptera). Zoomorphologie 82 (1975) 1-42
54. Mickevich M.F., and Farris J.S. The implications of congruence in Menidia. Syst. Zool. 30 (1981) 351-370
55. Monaghan M.T., Inward D.G., Hunt T., and Vogler A.P. A molecular phylogenetic analysis of the Scarabaeinae (dung beetles). Mol. Phylogenet. Evol. 45 (2007) 674-692
56. Morrison D.A., and Ellis J.T. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 14 (1997) 428-441
57. Nikonov A.A., Peng G., Tsurupa G., and Leal W.S. Unisex pheromon detectors and pheromon binding proteins in Scarab beetles. Chem. Senses 27 (2002) 495-504
58. Nomura S. On the Sericini of Japan. I. Tôhô-Gakuhô 23 (1973) 119-152
59. Nomura S. On the Sericini of Taiwan. Tôhô-Gakuhô 24 (1974) 81-115
60. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
61. Ogden T.H., and Rosenberg M.S. How should gaps be treated in parsimony? A comparison of approaches using simulation. Mol. Phylogenet. Evol. 42 (2007) 817-826
62. Pons J., and Vogler A.P. Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. Cladistics 22 (2006) 144-156
63. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinform. Appl. Note 14 (1998) 817-818
64. Rambaut, A., Drummond, A., 2003. Tracer. MCMC Trace Analysis Tool.
65. Reinecke A., Ruther J., and Hilker M. Pre-copulatory isolation in sympatric Melolontha species (Coleoptera: Scarabaeidae). Agri. Forest Entomol. 8 (2006) 289-293
66. Reitter E. Uebersicht der mir bekannten palaearktischen, mit der Coleopteren-Gattung Serica verwandten Gattungen und Arten. Wiener Entomol. Ztg. 15 (1896) 180-188
67. Ritcher P.O. Spiracles of adult Scarabaeoidea (Coleoptera) and their phylogenetic significance. I. The abdominal spiracles. Ann. Entomol. Soc. Am. 62 (1969) 8-63
68. Romero-López A.A., Arzuffi R., Valdez J., Morón M.A., Castrejón-Gómez V., and Villalobos F.J. Sensory organs in the antennae of Phyllophaga obsoleta (Coleoptera: Melolonthidae). Ann. Entomol. Soc. Am. 97 (2004) 1306-1312
69. Ronquist F., and Huelsenbeck J.P. MrBayes 3, Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
70. Ruther J., Reinecke K., Thiemann K., Tolasch T., Francke W., and Hilker M. Mate finding in the forest cockchafer, Melolontha hippocastani, mediated by volatiles from plants and females. Physiol. Entomol. 25 (2000) 172-179
71. Sankoff D. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28 (1975) 35-42
72. Sanmartin I., and Martin-Piera F. First phylogenetic analysis of the subfamily Pachydeminae (Coleoptera. Scarabaeoidea, Melolonthidae): the Palearctic Pachydeminae. J. Zool. Syst. Evol. Res. 41 (2003) 2-46
73. Scholtz C.H., and Chown S.L. The evolution of habitat use and diet in the Scarabaeoidea: a phylogenetic approach. In: Pakaluk J., and Slipinski S.A. (Eds). Biology, Phylogeny, and Classification of Coleoptera: Papers Celebrating the 80th Birthday of Roy A. Crowson (1995), Muzeum i Instytut Zoologii PAN, Warszawa 355-374
74. Scholtz C.H., and Grebennikov V.V. 13. Scarabaeoidea Latreille, 1802. In: Beutel R.G., and Leschen R.A.B. (Eds). Coleoptera, Beetles. vol. 1: Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga partim). Handbook of Zoology. vol. IV Arthropoda: Insecta part 38 (2005), W. de Gruyter-Berlin, New York 367-426
75. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with application s to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
76. Simmons M.P., and Freudenstein J.V. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Mol. Phylogenet. Evol. 26 (2003) 444-451
77. Simmons M.P., Müller K., and Norton A.P. The relative performance of indel-coding methods in simulations. Mol. Phylogenet. Evol. 44 (2007) 724-740
78. Simon C., Frati F., Beckenbach A., et al. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87 (1994) 651-701
79. Smith A.B.T. A review of the family-group names for the Superfamily Scarabaeoidea (Coleoptera) with corrections to nomenclature and a current classification. Coleopterists Soc. Monogr. 5 (2006) 144-204
80. Smith A.B.T., Hawks D.C., and Heraty J.M. An overview of the classification and the evolution of the major scarb beetle clades (Coleoptera: Scarabaeoidea) based on preliminary molecular analyses. Coleopts. Soc. Monogr. 5 (2006) 35-46
81. *, Phylogenetic Analysis using Parsimony. Version 4.0b. Sinauer Associates, Sunderland, MA.
82. Tanaka S., Yukuhiro F., and Wakamura S. Sexual dimorphism in body dimensions and antennal sensilla in the white grub beetle, Dasylepida ishigakiensis (Coleoptera: Scarabaeidae). Appl. Entomol. Zool. 41 (2006) 455-461
83. Terry D.M., and Whiting M.F. Comparison of two alignment techniques within a single complex data set: POY versus Clustal. Cladistics 21 (2005) 272-281
84. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
85. Vogler A.P., and Pearson D.L. A molecular phylogeny of the Tiger beetles (Cicindelidae): congruence of mitochondrial and nuclear rDNA data sets. Mol. Phylogenet. Evol. 6 (1996) 321-338
86. Wheeler W.C. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44 (1995) 321-331
87. Wheeler W.C. Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics 12 (1996) 1-9
88. Wheeler W.C., and Hayashi C.Y. The phylogeny of the extant Chelicerate orders. Cladistics 14 (1998) 173-192
89. Wheeler W.C., Ramírez M.J., Aagesen L., and Schulmeister S. Partition-free congruence analysis: implications for sensitivity analysis. Cladistics 22 (2006) 256-263
90. Wilm A., Mainz I., and Steger G. An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol. 1 19 (2006) 1-11
91. Wong K.M., Suchard M.A., and Huelsenbeck J.P. Alignment uncertainty and genomic analysis. Science 319 (2008) 473-476
92. Yang Z., and Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte carlo method. Mol. Biol. Evol. 14 (1997) 717-724