What is the phylogenetic signal limit from mitogenomes? the reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Talavera, Gerard ^a,b   Vila, Roger ^a  

^a INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; DATA QUALITY; DATA SET; DIVERGENCE; GENOME; INSECT; MAXIMUM LIKELIHOOD ANALYSIS; MITOCHONDRIAL DNA; MORPHOLOGY; PHYLOGENETICS; PROTEIN; RELATEDNESS;

COLEOPTERA; ENDOPTERYGOTA; HEMIPTERA; HEXAPODA; HYMENOPTERA; INSECTA; PARANEOPTERA; PHTHIRAPTERA; STREPSIPTERA; THYSANOPTERA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CYTOLOGY; GENETICS; INSECT; MITOCHONDRIAL GENOME; PHYLOGENY;

ANIMALS; BAYES THEOREM; GENOME, MITOCHONDRIAL; INSECTS; MODELS, GENETIC; PHYLOGENY;

EID: 80054941921     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-315     Document Type: Article

References (122)

1. Hennig W, Die Stammesgeschichte der Insekten Kramer, Frankfurt 1969
2. Kristensen NP, Phylogeny of extant hexapods. The insects of Australia: A textbook for students and research workers Melbourne University Press 1991
3. Phylogeny of Endopterygote insects, the most successful lineage of living organisms. Kristensen NP, European Journal of Entomology 1999 96 3 237 253 (Pubitemid 30044345)
4. The Stresiptera problem: Phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Whiting MF, Carpenter JC, Wheeler QD, Wheeler WC, Systematic Biology 1997 46 1 1 68 11975347 (Pubitemid 127365607)
5. The phylogeny of the extant hexapod orders. Wheeler WC, Whiting M, Wheeler QD, Carpenter JM, Cladistics 2001 17 4 403 404
6. Aligned 18S and insect phylogeny. Kjer KM, Systematic Biology 2004 53 3 506 514 10.1080/10635150490445922 15503677 (Pubitemid 38946911)
7. Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: a reply to Kjer. Ogden TH, Whiting MF, Wheeler WC, Cladistics 2005 21 3 295 302 10.1111/j.1096-0031.2005.00061.x (Pubitemid 41537318)
8. Quantification of insect genome divergence. Zdobnov EM, Bork P, Trends in Genetics 2007 23 16 20 10.1016/j.tig.2006.10.004 17097187 (Pubitemid 44960528)
9. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Savard J, Tautz D, Richards S, Weinstock G, Gibbs R, Werren J, Tettelin H, M Lercher M, Genome Research 2006 16 11 1334 1338 10.1101/gr.5204306 17065606 (Pubitemid 44664675)
10. Towards an 18S phylogeny of hexapods: Accounting for group-specific character covariance in optimized mixed nucleotide/doublet models. Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A, Zoology 2007 110 5 409 429 10.1016/j.zool.2007.08.003 17964130 (Pubitemid 350026760)
11. Single-copy nuclear genes resolve the phylogeny of the holometabolous insects. Wiegmann BM, Trautwein MD, Kim JW, Cassel BK, Bertone MA, Winterton SL, Yeates DK, BMC Biology 2009 7 36 10.1186/1741-7007-7-36 19558647
12. Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Krauss V, Thümmler C, Georgi F, Lehmann J, Stadler PF, Eisenhardt C, Mol Biol Evol 2008 25 821 830 10.1093/molbev/msn013 18296416
13. Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera. Longhorn SJ, Pohl HW, Vogler AP, Mol Phylogenet Evol 2010 55 3 846 859 10.1016/j.ympev.2010. 03.024 20348001
14. 9-genes reinforce the phylogeny of holometabola and yield alternate views on the phylogenetic placement of Strepsiptera. McKenna DD, Farrell BD, PloS One 2010 5 7 11887 10.1371/journal.pone.0011887 20686704
15. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Talavera G, Castresana J, Systematic Biology 2007 56 4 564 577 10.1080/10635150701472164 17654362 (Pubitemid 47171631)
16. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Hassanin A, Leger N, Deutsch J, Systematic Biology 2005 54 2 277 298 10.1080/10635150590947843 16021696 (Pubitemid 40707808)
17. An improved method for determining codon variability in a gene and its application to rate of fixation of mutations in evolution. Fitch WM, Markowit E, Biochemical Genetics 1970 4 5 579 93 10.1007/BF00486096 5489762
18. Heterotachy and long-branch attraction in phylogenetics. Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F, BMC Evol Biol 2005 5 50 10.1186/1471-2148-5-50 16209710 (Pubitemid 41583758)
19. Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Pagel M, Meade A, Philosophical Transactions of the Royal Society B-Biological Sciences 2008 363 1512 3955 3964 10.1098/rstb.2008.0178
20. A review of arthropod phylogeny: New data based on ribosomal DNA sequences and direct character optimization. Giribet G, Ribera C, Cladistics 2000 16 2 204 231 10.1111/j.1096-0031.2000.tb00353.x (Pubitemid 30427522)
21. Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda). Cameron SL, Miller KB, D'Haese CA, Whiting MF, Barker SC, Cladistics 2004 20 6 534 557 10.1111/j.1096-0031.2004.00040.x (Pubitemid 40218313)
22. Hexapod origins: Monophyletic or paraphyletic? Nardi F, Spinsanti G, Boore JL, Carapelli A, Dallai R, Frati F, Science 2003 299 5614 1887 1889 10.1126/science.1078607 12649480 (Pubitemid 36356656)
23. Comment on "Hexapod origins: Monophyletic or paraphyletic?". Delsuc F, Phillips MJ, Penny D, Science 2003 301 5639 1482 12970549
24. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Cook CE, Yue Q, Akam M, Proc Biol Sci 2005 272 1569 1295 1304 10.1098/rspb.2004.3042 16024395 (Pubitemid 41411352)
25. Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. Carapelli A, Lio P, Nardi F, van der Wath E, Frati F, BMC Evol Biol 2007 7 Suppl 2 8 10.1186/1471-2148-7-S2-S8 17767736 (Pubitemid 351830583)
26. Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers. Timmermans M, Roelofs D, Marin J, van Straalen NM, BMC Evolutionary Biology 2008 8 83 10.1186/1471-2148-8-83 18366624 (Pubitemid 351550359)
27. Deducing the pattern of arthropod phylogeny from mitochondrial-DNA rearrangements. Boore JL, Collins TM, Stanton D, Daehler LL, Brown WM, Nature 1995 13 163 165
28. A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Cameron SL, Lambkin CL, Barker SC, Whiting MF, Systematic Entomology 2007 32 1 40 59 10.1111/j.1365-3113.2006.00355.x (Pubitemid 46016028)
29. Mitochondrial genome organization and phylogeny of two vespid wasps. Cameron SL, Dowton M, Castro LR, Ruberu K, Whiting MF, Austin AD, Diement K, Stevens J, Genome 2008 51 10 800 808 10.1139/G08-066 18923531
30. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Fenn J, Song H, Cameron SL, Whiting MF, Molecular Phylogenetics and Evolution 2008 49 1 59 68 10.1016/j.ympev.2008.07.004 18672078
31. Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes. Hua JM, Li M, Dong P, Cui Y, Xie Q, Bu W, BMC Evolutionary Biology 2009 9 134 10.1186/1471-2148-9-134 19523246
32. Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses. Masta SE, Longhorn SJ, Boore JL, Molecular Phylogenetics and Evolution 2009 50 1 117 128 10.1016/j.ympev.2008.10.010 18992830
33. Mitochondrial genomes: anything goes. Burger G, Gray MW, Lang BF, Trends in Genetics 2003 19 12 709 716 10.1016/j.tig.2003.10.012 14642752 (Pubitemid 37464849)
34. How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Lin C, Danforth B, Mol Phylogenet Evol 2004 30 3 686 702 10.1016/S1055-7903(03)00241-0 15012948 (Pubitemid 38265489)
35. Site specific rates of mitochondrial genomes and the phylogeny of eutheria. Kjer KM, Honeycutt RL, BMC Evolutionary Biology 2007 7 8 10.1186/1471-2148-7-8 17254354 (Pubitemid 46237529)
36. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Shao R, Dowton M, Murrell A, Barker SC, Mol Biol Evol 2003 20 10 1612 1619 10.1093/molbev/msg176 12832626 (Pubitemid 41070822)
37. Contrasting rates of mitochondrial molecular evolution in parasitic diptera and hymenoptera. Castro LR, Austin AD, Dowton M, Mol Biol Evol 2002 19 7 1100 1113 12082129 (Pubitemid 34743234)
38. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Lartillot N, Philippe H, Molecular Biology and Evolution 2004 21 6 1095 1109 10.1093/molbev/msh112 15014145 (Pubitemid 38658218)
39. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Kolaczkowski B, Thornton J, Nature 2004 431 980 984 10.1038/nature02917 15496922 (Pubitemid 39434418)
40. Detecting and overcoming systematic errors in genome-scale phylogenies. Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H, Systematic Biology 2007 56 3 389 399 10.1080/10635150701397643 17520503 (Pubitemid 46826902)
41. Cases in which parsimony or compatibility methods will be positively misleading. Felsenstein J, Systematic Zoology 1978 27 4 401 410 10.2307/2412923
42. Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the drosophilidae. Tarrío R, Rodriguez-Trelles F, Ayala F, Mol Biol Evol 2001 18 8 1464 1473 11470837 (Pubitemid 32735094)
43. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Rosenberg M, Kumar S, Mol Biol Evol 2003 20 4 610 621 10.1093/molbev/msg067 12679548 (Pubitemid 36437911)
44. Taxon sampling, bioinformatics, and phylogenomics. Rosenberg M, Kumar S, Systematic Biology 2003 52 1 119 124 10.1080/10635150390132894 12554445 (Pubitemid 36300064)
45. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Brinkmann H, Van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H, Systematic Biology 2005 54 5 743 757 10.1080/10635150500234609 16243762 (Pubitemid 43142294)
46. Phylogenomics. Philippe H, Delsuc F, Brinkmann H, Lartillot N, Annual Review of Ecology, Evolution and Systematics 2005 36 541 562 10.1146/annurev.ecolsys.35.112202.130205 (Pubitemid 43068870)
47. Phylogenetic position of Salinibacter ruber based on concatenated protein alignments. Soria-Carrasco V, Valens-Vadell M, Pena A, Anton J, Amann R, Castresana J, Rossello-Mora R, Syst Appl Microbiol 2007 30 3 171 179 10.1016/j.syapm.2006.07.001 16971080 (Pubitemid 46428506)
48. Parallel evolution of the genetic code in arthropod mitochondrial genomes. Abascal F, Posada D, Knight RD, Zardoya R, PLoS Biology 2006 4 711 718
49. MtArt: a new model on amino acid replacement for Arthropoda. Abascal F, Posada D, Zardoya R, Mol Biol Evol 2007 24 1 5 17043087 (Pubitemid 46026273)
50. Acoel flatworms: Earliest extant bilaterian metazoans, not members of Platyhelminthes. Ruiz-Trillo I, Riutort M, Littlewood DT, Herniou EA, Bagũ J, Science 1999 283 5409 1919 1923 10.1126/science.283.5409.1919 10082465 (Pubitemid 29144210)
51. Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Brinkmann H, Philippe H, Mol Biol Evol 1999 16 6 817 825 10368959 (Pubitemid 29260835)
52. Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life. Burleigh J, Mathews S, American Journal of Botany 2004 91 1599 1613 10.3732/ajb.91.10.1599 21652311 (Pubitemid 43193720)
53. Four new avian mitochondrial genomes help get to basic evolutionary questions in the late Cretaceous. Harrison GL, McLenachan PA, Phillips MJ, Slack KE, Cooper A, Penny D, Mol Biol Evol 2004 21 6 974 983 10.1093/molbev/msh065 14739240 (Pubitemid 38658205)
54. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. Lartillot N, Brinkmann H, Philippe H, BMC Evolutionary Biology 2007 7 Suppl 1 4 10.1186/1471-2148-7-S1-S4 17767732 (Pubitemid 351826841)
55. Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference. Roure B, Philippe H, BMC Evolutionary Biology 2011 11 17 10.1186/1471-2148-11-17 21235782
56. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Lartillot N, Lepage T, Blanquart S, Bioinformatics 2009 25 17 2286 2288 10.1093/bioinformatics/btp368 19535536
57. Phylogenomics Revives Traditional Views on Deep Animal Relationships. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Wörheide G, Manuel M, Current Biology 2009 19 8 706 712 10.1016/j.cub.2009.02.052 19345102
58. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Lartillot N, Philippe H, Philos Trans R Soc Lond B Biol Sci 2008 363 1463 1472 10.1098/rstb.2007.2236 18192187 (Pubitemid 351363988)
59. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly or Eumetazoa. Sperling EA, Peterson KJ, Pisani D, Mol Biol Evol 2009 26 10 2261 2274 10.1093/molbev/msp148 19597161
60. Ecdysozoan mitogenomics: evidence for a common origin of the legged invertebrates, the Panarthropoda. Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, Blaxter M, Lavrov DV, Genome Biology and Evolution 2010 2 425 440 10.1093/gbe/evq030 20624745
61. Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors? Baurain D, Brinkmann H, Philippe H, Mol Biol Evol 2007 24 6 9 17012374 (Pubitemid 46026274)
62. Acoel flatworms are not platyhelmintes: evidence from phylogenomics. Philippe H, Brinkmann H, Martinez P, Riutort M, Bagũa J, PLoS ONE 2007 2 717 10.1371/journal.pone.0000717 17684563 (Pubitemid 351330799)
63. Additional molecular support for the new chordate phylogeny. Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H, Genesis 2008 46 11 592 604 10.1002/dvg.20450 19003928
64. The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Carapelli A, Vannini L, Nardi F, Boore JL, Beani L, Dallai R, Frati F, Gene 2006 376 2 248 259 10.1016/j.gene.2006.04.005 16766140
65. Long-Branch Distraction and the Strepsiptera. Whiting MF, Systematic Biology 1998 47 1 134 138 10.1080/106351598261076 12064233 (Pubitemid 128449790)
66. Crowson RA, The biology of the Coleoptera London: Academic Press 1981
67. Review of the order Strepsiptera. Kathirithamby J, Systematic Entomology 1989 14 1 41 92 10.1111/j.1365-3113.1989.tb00265.x
68. Evolution of the hind wing in coleoptera. Kukalova-Peck J, Lawrence J, Canadian Entomologist 1993 125 181 258 10.4039/Ent125181-2
69. Phylogeny of the holometabolous insect orders: molecular evidence. Whiting MF, Zoologica Scripta 2002 31 3 17 10.1046/j.0300-3256.2001.00093.x (Pubitemid 34145807)
70. Strongly expanded 18S rRNA genes correlated with a peculiar morphology in the insect order of Strepsiptera. Chalwatzis N, Baur A, Stetzer E, Kinzelbach R, Zimmermann F, Zoologica 1995 98 115 126
71. 18S ribosomal RNA genes of insects: Primary structure of the genes and molecular phylogeny of the Holometabola. Chalwatzis N, Hauf J, Van de Peer Y, Kinzelbach R, Zimmermann F, Annals of the Entomological Society of America 1996 89 788 803 (Pubitemid 126545616)
72. Molecular phylogenetics at the Felsenstein zone: Approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences. Hwang UW, Kim W, Tautz D, Friedrich M, Molecular Phylogenetics and Evolution 1998 9 3 470 480 10.1006/mpev.1998.0518 9667995 (Pubitemid 128351481)
73. Do long branches attract flies? Carmean D, Crespi B, Nature 1995 373 666 666 7854445
74. Systematic Bias in Phylogenetic Analysis: Is the Strepsiptera Problem Solved? Huelsenbeck JP, Systematic Biology 1998 47 3 519 537 12066692 (Pubitemid 128451090)
75. Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Rokas A, Kathirithamby J, Holland PW, Insect Molecular Biology 1999 8 4 527 530 10.1046/j.1365-2583.1999. 00149.x 10620047
76. The structure of the USP/RXR of Xenos pecki indicates that Strepsiptera are not closely related to Diptera. Hayward DC, Trueman JW, Bastiani MJ, Ball EE, Development Genes and Evolution 2005 215 4 213 219 10.1007/s00427-004-0461-x 15660250 (Pubitemid 40552955)
77. The rapid divergence of the ecdysone receptor is a synapomorphy for Mecopterida that clarifies the Strepsiptera problem. Bonneton F, Brunet FG, Kathirithamby J, Laudet V, Insect Molecular Biology 2006 15 3 351 362 10.1111/j.1365-2583.2006.00654.x 16756554 (Pubitemid 43821208)
78. Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR. Bonneton F, Zelus D, Iwema T, Robinson-Rechavi M, Laudet V, Mol Biol Evol 2003 20 4 541 553 10.1093/molbev/msg054 12654933 (Pubitemid 36437904)
79. Goodbye Halteria? The thoracic morphology of Endopterygota (Insecta) and its phylogenetic implications. Friedrich F, Beutel RG, Cladistics 2010 26 1 34 10.1111/j.1096-0031.2009.00297.x
80. Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola. Beutel RG, Friedrich F, Hörnschemeyer T, Phol H, Hünefeld F, Beckmann F, Meier R, Misof B, Whiting MF, Vilhelmsen L, Cladistics 2010 26 1 15 10.1111/j.1096-0031.2009.00297.x
81. The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae). Castro LR, Dowton M, Molecular Phylogenetics and Evolution 2005 34 3 469 479 10.1016/j.ympev.2004.11.005 15683922 (Pubitemid 40427960)
82. Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers. Castro LR, Dowton M, Systematic Entomology 2007 32 1 60 69 10.1111/j.1365-3113.2006.00356.x (Pubitemid 46011028)
83. Boudreaux HB, Arthropod phylogeny with special reference to insects New York: John Wiley & Sons 1979
84. Ultrastructure of attachment specializations of hexapods, (Arthropoda): evolutionary patterns inferred from a revised ordinal phylogeny. Beutel R, Gorb S, Journal Of Zoological Systematics And Evolutionary Research 2001 39 177 207 10.1046/j.1439-0469.2001.00155.x (Pubitemid 34029808)
85. Evidence from mouthpart structure on interordinal relationships in Endopterygota? Krenn HW, Arthropod Systematics & Phylogeny 2007 65 1 7 14 21940893
86. Phylogeny of the Holometabolous Insects. Whiting M, Assembling the Tree of Life Oxford University Press 2004 345 359
87. Gullan PJ, Cranston PS, The Insects: An Outline Of Entomology (3rd Edition) Wiley-Blackwell 2004
88. Phylogenetic significance of the wing-base of the Holometabola (Insecta). Hornschemeyer T, Zoologica Scripta 2002 31 17 29 10.1046/j.0300-3256.2001. 00086.x (Pubitemid 34145808)
89. Grimaldi D, Engel M, Evolution of the insects Cambrigde University Press 2005
90. Endopterygote systematics-where do we stand and what is the goal (Hexapoda, Arthropoda)? Beutel RG, Pohl H, Systematic Entomology 2006 31 2 202 219 10.1111/j.1365-3113.2006.00341.x
91. Paraphyly of Homoptera and Auchenorrhyncha inferred from 18S rDNA nucelotide sequences. Campbell BC, Steffen-Campbell JD, Sorensen JT, Gill RJ, Systematic Entomology 1995 20 3 175 194 10.1111/j.1365-3113.1995.tb00090.x
92. Non-Monophyly of Auchenorrhyncha (Homoptera), Based Upon 18s rDNA Phylogeny-Eco-Evolutionary and Cladistic Implications within Pre-Heteropterodea Hemiptera (s.l) and a Proposal for New Monophyletic Suborders. Sorensen JT, Campbell BC, Gill RJ, Steffen-Campbell JD, Pan-Pacific Entomologist 1995 71 1 31 60
93. Molecular Phylogeny of the Homoptera: A Paraphyletic Taxon. Von Dohlen CD, Moran NA, Journal of Molecular Evolution 1995 41 211 223 7666451
94. Zur Systematik der Hexapoden. Borner C, Zool Anz 1904 27 511 533
95. Phylogenetic analysis of paraneopteran orders (Insecta: Neoptera) based on forewing base structure, with comments on monophyly of Auchenorrhyncha (Hemiptera). Yoshizawa K, Saigusa T, Systematic Entomology 2001 26 1 1 13 10.1046/j.1365-3113.2001.00133.x (Pubitemid 32100640)
96. Multiple origins of parasitism in lice. Johnson KP, Yoshizawa K, Smith VS, Proc Biol Sci 2004 271 1550 1771 1776 10.1098/rspb.2004.2798 15315891
97. The phylogeny of hexapod orders a critical review of recent accounts. Kristensen NP, Journal of Zoological Sytematics and Evolutionary Research 1975 13 1 1 44
98. Phylogeny of insect orders. Kristensen NP, Annual Review Of Entomology 1981 26 135 157 10.1146/annurev.en.26.010181.001031
99. The phylogeny of hexapod orders a critical review of recent accounts. Kristensen NP, Journal of Zoological Sytematics and Evolutionary Research 1975 13 1 1 44
100. Phylogeny of insect orders. Kristensen NP, Annual Review Of Entomology 1981 26 135 157 10.1146/annurev.en.26.010181.001031
101. Morphology and evolution of the rhynchotan head (insecta, hemiptera, homoptera). Hamilton K, Canadian Entomologist 1981 113 11 953 974 10.4039/Ent113953-11
102. Hennig W, Pont A, Schlee D, Insect phylogeny John Wiley & Sons 1981
103. Sharov AG, Basic arthropodan stock with special reference to insects Pergamon Press, New York 1966
104. The phylogenetic relations of the order Thysanoptera. Sharov AG, Entomol Obozr 1972 51 4 854 858
105. Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic. Murrell A, Barker SC, Parasitol Res 2005 97 4 274 80 10.1007/s00436-005-1413-8 16007465 (Pubitemid 41483282)
106. The Highly Rearranged Mitochondrial Genome of the Plague Thrips, Thrips imaginis (Insecta: Thysanoptera): Convergence of Two Novel Gene Boundaries and an Extraordinary Arrangement of rRNA Genes. Shao R, Barker SC, Mol Biol Evol 2003 20 3 362 370 10.1093/molbev/msg045 12644556 (Pubitemid 36427170)
107. Mammalian mitogenomic relationships and the root of the eutherian tree. Arnason U, Adegoke JA, Bodin K, Born EW, Esa YB, Gullberg A, Nilsson M, Short RV, Xu X, Janke A, Proc Natl Acad Sci USA 2002 99 12 8151 8156 10.1073/pnas.102164299 12034869 (Pubitemid 34651021)
108. The root of the mammalian tree inferred from whole mitochondrial genomes. Phillips MJ, Penny D, Molecular Phylogenetics and Evolution 2003 28 2 171 185 10.1016/S1055-7903(03)00057-5 12878457 (Pubitemid 37446823)
109. Mitogenomics: digging deeper with complete mitochondrial genomes. Curole J, Kocher T, Trends Ecol Evol 1999 14 10 394 398 10.1016/S0169-5347(99)01660-2 10481201 (Pubitemid 29428461)
110. Which mammalian supertree to bark up? Springer M, de Jong W, Science 2001 291 1709 1711 10.1126/science.1059434 11253193 (Pubitemid 32198958)
111. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Katoh K, Kuma K, Toh H, Miyata T, Nucleic Acids Research 2005 33 2 511 518 10.1093/nar/gki198 15661851 (Pubitemid 40360980)
112. PutGaps: DNA gapped file from Amino Acid alignment. Fitzpatrick D, Pentony M, http://bioinf.nuim.ie/software/putgaps
113. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Castresana J, Mol Biol Evol 2000 17 540 552 10742046 (Pubitemid 30210700)
114. ProbCons: Probabilistic consistency-based multiple sequence alignment. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S, Genome Research 2005 15 2 330 340 10.1101/gr.2821705 15687296 (Pubitemid 40309398)
115. Empirical profile mixture models for phylogenetic reconstruction. Quant LS, Gascuel O, Lartillot N, Bioinformatics 2008 24 2317 2323 10.1093/bioinformatics/btn445 18718941
116. A simple, fasta and accurate algorithm to estimate phylogenies by maximum likelihood. Guindon S, Gascuel O, Systematic Biology 2003 52 5 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
117. MRBAYES: Bayesian inference of phylogenetic trees. Huelsenbeck JP, Ronquist F, Bioinformatics 2001 17 8 754 755 10.1093/bioinformatics/17.8.754 11524383 (Pubitemid 32851390)
118. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Schmidt HA, Strimmer K, Vingron M, Von Haeseler A, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758 (Pubitemid 34284960)
119. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneious sequence evolution. Blanquart S, Lartillot N, Mol Biol Evol 2006 23 11 2058 2071 10.1093/molbev/msl091 16931538 (Pubitemid 44540180)
120. A site- and time-heterogeneous model of amino acid replacement. Blanquart S, Lartillot N, Mol Biol Evol 2008 25 5 842 858 10.1093/molbev/msn018 18234708
121. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ, Nature 2011 470 255 258 10.1038/nature09676 21307940
122. The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Soria-Carrasco V, Talavera G, Igea J, Castresana J, Bioinformatics 2007 23 2954 2956 10.1093/bioinformatics/btm466 17890735 (Pubitemid 350162906)