Decisive data sets in phylogenomics: Lessons from studies on the phylogenetic relationships of primarily wingless insects

Molecular Biology and Evolution

Volumn 31, Issue 1, 2014, Pages 239-249

  Dell'Ampio, Emiliano ^a   Meusemann, Karen ^b,c   Szucsich, Nikolaus U ^a   Peters, Ralph S ^b   Meyer, Benjamin ^d   Borner, Janus ^e   Petersen, Malte ^b   Aberer, Andre J ^f   Stamatakis, Alexandros ^f,g   Walzl, Manfred G ^a   Minh, Bui Quang ^a   Von Haeseler, Arndt ^a   Ebersberger, Ingo ^h   Pass, Günther ^a   Misof, Bernhard ^b  

^a UNIVERSITY OF VIENNA   (Austria)

^b ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

^c CSIRO   (Australia)

^d UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^e UNIVERSITY OF HAMBURG   (Germany)

^f HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^g KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^h GOETHE UNIVERSITY   (Germany)

Author keywords

Collembola; conflicting hypotheses; Diplura; Ellipura; Entognatha; ESTs; likelihood quartet mapping; missing data; Nonoculata; phylogenomics; Protura

Indexed keywords

ACERENTOMON; ANURIDA MARITIMA; ARCHAEOGNATHA; ARTICLE; CAMPODEA FRAGILIS; COLLEMBOLA; CRYPTOPYGUS ANTARCTICUS; DIPLURA; FOLSOMIA CANDIDA; GENE MAPPING; INSECT; LEPISMACHILIS Y SIGNATA; MEGAJAPYX; NONHUMAN; NUCLEOTIDE SEQUENCE; ONYCHIURUS ARCTICUS; ORCHESELLA CINCTA; ORTHOLOGY; PHYLOGENETIC TREE; PHYLOGENOMICS; PHYLOGENY; THERMOBIA DOMESTICA; THYSANURA; TRICHOLEPISMA AUREA;

COLLEMBOLA; CONFLICTING HYPOTHESES; DIPLURA; ELLIPURA; ENTOGNATHA; ESTS; LIKELIHOOD QUARTET MAPPING; MISSING DATA; NONOCULATA; PHYLOGENOMICS; PROTURA;

ANIMALS; CHROMOSOME MAPPING; DATABASES, FACTUAL; EVOLUTION, MOLECULAR; GENOMICS; GENOTYPING TECHNIQUES; INSECTS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; TRANSCRIPTOME;

EID: 84891755492     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst196     Document Type: Article

References (70)

1. Aberer AJ, Komprass D, Stamatakis A. 2013. Pruning Rogue Taxa improves phylogenetic accuracy: An efficient algorithm and web service. Syst Biol. 62(1):162-166.
2. Aberer AJ, Stamatakis A. 2011. A simple and accurate method for rogue taxon identification. IEEE BIBM 2011:118-122.
3. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Aut Control. 19:716-723.
4. Bitsch C, Bitsch J. 2000. The phylogenetic interrelationships of the higher taxa of apterygote hexapods. Zool Scr. 29:131-156.
5. Bitsch C, Bitsch J. 2004. Phylogenetic relationships of basal hexapods among the mandibulate arthropods: A cladistic analysis based on comparative morphological characters. Zool Scr. 33:511-550.
6. Beutel RG, Gorb SN. 2006. A revised interpretation of attachment structures in Hexapoda with special emphasis on Mantophasmatodea. Arthropod Syst Phylogeny. 64:3-25.
7. Börner C. 1910. Die phylogenetische Bedeutung der Protura. Sdr Biolog Centralbl. 30:633-641.
8. Carapelli A, Frati F, Nardi F, Dallai R, Simon C. 2000.Molecular phylogeny of the apterygote insects based on nuclear andmitochondrial genes. Pedobiologia 44:361-373.
9. Colgan DJ, McLauchlan A, Wilson GDF, Livingston S, Macaranas J, Edgecombe D, Cassis G, Gray MR 1998. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust J Zool. 46:419-437.
10. Dallai R, Mercati D, Carapelli A, Nardi F, Machida R, Sekiya K, Frati F. 2011. Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s. Arthropod Struct Dev. 40: 77-92.
11. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends Ecol Evol. 24: 332-340.
12. Dell'Ampio E, Szucsich NU, Carapelli A, Frati F, Steiner G, Steinacher A, Pass G. 2009. Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: Influence of character dependence and character choice in analyses of 28S rRNA sequences. Zool Scr. 38:155-170.
13. Dell'Ampio E, Szucsich NU, Pass G. 2011. Protura and molecular phylogenetics: Status quo of a young love. Soil Organisms 83:347-358.
14. Ebersberger I, Strauss S, Von Haeseler A. 2009. HaMStR: Profile hidden Markov model based search for orthologs in ESTs. BMC Evol Biol. 9:157.
15. Edgecombe GD, Wilson GDF, Colgan DJ, Gray MR, Cassis G 2000. Arthropod cladistics: Combined analysis of Histone H3 and U2 snRNA sequences and morphology. Cladistics 16:155-203.
16. Gao Y, Bu Y, Luan Y. 2008. Phylogenetic relationships of basal hexapods reconstructed from nearly complete 18S and 28S rRNA gene sequences. Zool Sci. 25:1139-1145.
17. Giribet G, Edgecombe GD, Carpenter JM, D'Haese CA, Wheeler WC. 2004. Is Ellipura monophyletic?. A combined analysis of basal hexapod relationships with emphasis on the origin of insects. Org Div Evol. 4:319-340.
18. Giribet G, Edgecombe GD, Wheeler WC. 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413:157-161.
19. Giribet G, Richter S, Edgecombe GD, Wheeler WC. 2005. The position of crustaceans within Arthropoda-evidence from nine molecular loci and morphology. In: Koenemann S, Jenner RA, editors. Crustacea and arthropod relationships. Crustacean issues 16: Festschrift for F. R. Schram. Boca Raton (FL): Taylor & Francis. p. 307-352.
20. Giribet G, Wheeler WC. 2001. Some unusual small-subunit ribosomal DNA sequences of metazoans. Am Mus Novit. 3337:1-14.
21. Grimaldi DA. 2010. 400 million years on six legs: On the origin and early evolution of Hexapoda. Arthropod Struct Dev. 39:191-203.
22. Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 89:10915-10919.
23. Hennig W. 1953. Kritische Bemerkungen zum phylogenetischen System der Insekten. Beitr Entomol Sonderheft. 3:1-85.
24. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
25. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6:29.
26. Kjer KM, Carle FL, Litman J, Ware J. 2006. A molecular phylogeny of Hexapoda. Arthropod Syst Phylogeny. 64:3-44.
27. Knowles LL. 2009. Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes. Syst Biol. 58: 463-467.
28. Koch M. 1997. Monophyly and phylogenetic position of the Diplura (Hexapoda). Pedobiologia 41:9-12.
29. Kristensen NP. 1981. Phylogeny of insect orders. Annu Rev Entomol. 26: 135-157.
30. Kristensen NP. 1997. The ground plan and basal diversification of the hexapods. In: Fortey RA, Thomas RH, editors. Arthropod relationships, systematic association. Special volume series 55. London: Chapman & Hall. p. 281-293.
31. Kück P. 2009. ALICUT: A Perlscript which cuts ALISCORE identified RSS. Version 2.0 ed. Bonn (Germany): Department of Bioinformatics, Zoologisches Forschungs Museum A. Koenig (ZFMK). [cited 2013 Oct 30]. Available from: Http://www.zfmk.utilities.de.
32. Kück P, Meusemann K. 2010. FASconCAT: Convenient handling of data matrices. Mol Phylogenet Evol. 56:1115-1118.
33. Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, Waegele JW, Misof B. 2010. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Front Zool. 7:10.
34. Kukalová-Peck J. 1987. New Carboniferous Diplura, Monura and Thysanura, the hexapod ground plan, and the role of thoracic side lobes in the origin of wings (Insecta). Can J Zool. 65:2327-2345.
35. Kukalová-Peck J. 1991. Fossil history and the evolution of hexapod structures. In: Naumann ID, editor. Insects of Australia: A textbook for students and research workers. Melbourne (Australia): CSIRO, Melbourne University Press. p. 141-179.
36. Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
37. Lehtonen S. 2011. Can sensitivity analysis help to detect long-branch attractioñ. Mol Phylogenet Evol. 61:899-903.
38. Luan Y, Mallatt JM, Xie R, Yang Y, Yin W. 2005. The phylogenetic positions of three basal-hexapod groups (Protura, Diplura, and Collembola) based on ribosomal RNA gene sequences. Mol Biol Evol. 22:1579-1592.
39. Machida R. 2006. Evidence from embryology for reconstructing the relationships of hexapod basal clades. Arthropod Syst Phylogeny. 64:95-104.
40. Mallatt J, Giribet G. 2006. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol Phylogenet Evol. 40:772-794.
41. Mallatt JM, Craig CW, Yoder MJ. 2010. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol. 55:1-17.
42. Meusemann K, von Reumont BM, Simon S, et al.. (16 co-Authors). 2010. A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol. 27:2451-2464.
43. Meyer B, Misof B. 2010. MARE: Matrix reduction-A tool to select optimized data subsets from supermatrices for phylogenetic inference. Bonn (Germany): Zentrum für Molekulare Biodiversitätsforschung (zmb) am ZFMK. [cited 2013 Oct 30]. Available from: Http://mare.zfmk.de (current version).
44. Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30:1188-1195.
45. Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A 2007. Towards an 18S phylogeny of hexapods: Accounting for groupspecific character covariance in optimized mixed nucleotide/doublet models. Zoology 110:409-429.
46. Misof B, Misof K. 2009. A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: A more objective means of data exclusion. Syst Biol. 58:21-34.
47. Ott M, Zola J, Stamatakis A, Aluru S. 2007. Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. Proceedings of the 2007 ACM/IEEE conference on Supercomputing
48. IEEE/ACM Supercomputing conference 2007 (SC2007); November 2007. Reno (NV): ACM.
49. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. 2010. How many bootstrap replicates are necessary?. J Comput Biol. 17:337-354.
50. Pfeiffer W, Stamatakis A. 2010. Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. Paper presented at HICOMB workshop, held in conjunction with IPDPS 2010; April 2010; Atlanta, G.A.
51. Philippe H, Brinkmann H, Lavrov DV, Littlewood DT, Manuel M, Worheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biol. 9: E1000602.
52. Regier JC, Shultz JW, Ganley AR, et al.. (11 co-Authors). 2008. Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst Biol. 57:920-938.
53. Regier J, Shultz J, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463:1079-1083.
54. Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331.
55. Sanderson MJ, McMahon MM, Steel M. 2010. Phylogenomics with incomplete taxon coverage: The limits to inference. BMC Evol Biol. 10:155.
56. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREEPUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
57. Shao HG, Zhang YP, Xie RD, Yin WY. 1999. Mitochondria cytochrome b sequences variation of Protura and molecular systematics of Apterygota. Chin Sci Bull. 44:2031-2036.
58. Simmons MP, Freudenstein JV. 2011. Spurious 99% bootstrap and jackknife support for unsupported clades. Mol Phylogenet Evol. 61: 177-191.
59. Simon S, Narechania A, DeSalle R, Hadrys H. 2012. Insect phylogenomics: Exploring the source of incongruence using new transcriptomic data. Genome Biol Evol. 4:1295-1309.
60. Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
61. Steel M, Sanderson MJ. 2010. Characterizing phylogenetically decisive taxon coverage. Appl Math Lett. 23:82-86.
62. Strimmer K, von Haeseler A. 1997. Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A. 94:6815-6819.
63. Stöver BC, Müller KF. 2010. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7.
64. Szucsich NU, Pass G. 2008. Incongruent phylogenetic hypotheses and character conflicts in morphology: The root and early branches of the hexapodan tree. Mitt Dtsch Ges Allg Angew Ent. 16:415-430.
65. Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. 2012. Advances in insect phylogeny at the dawn of the postgenomic era. Annu Rev Entomol. 57:449-468.
66. von Reumont BM, Meusemann K, Szucsich N, et al.. (14 coauthors). 2009. Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses?. A case study on major arthropod relationships. BMC Evol Biol. 9:119.
67. von Reumont MB, Jenner RA, Wills MA, et al.. (13 co-Authors). 2012. Pancrustacean phylogeny in the light of new phylogenomic data: Support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol. 29:1031-1045.
68. Wiens JJ. 2006. Missing data and the design of phylogenetic analyses. J Biomed Inform. 39:34-42.
69. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol. 11(9):367-372.
70. Zhang Y, Zhang Y, Luan Y, Chen Y, Yin W. 2001. Phylogeny of higher taxa of Hexapoda according to 12sRNA sequences. Chin Sci Bull. 46: 840-842.