Insect phylogenomics

Insect Molecular Biology

Volumn 24, Issue 4, 2015, Pages 403-411

  Behura, S K ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

insects; next generation sequencing; phylogenetics; phylogenomics; phylogeny

Indexed keywords

HEXAPODA;

ANIMAL; CLASSIFICATION; EVOLUTION; GENETICS; GENOMICS; INSECT; INSECT GENOME; PHYLOGENY;

ANIMALS; BIOLOGICAL EVOLUTION; GENOME, INSECT; GENOMICS; INSECTS; PHYLOGENY;

EID: 84937022695     PISSN: 09621075     EISSN: 13652583     Source Type: Journal    
DOI: 10.1111/imb.12174     Document Type: Review

References (86)

1. Andrew, D.R., (2011) A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics. Arthropod Struct Dev 40: 289-302.
2. Bapteste, E., and, Burian, R.M., (2010) On the need for integrative phylogenomics, and some steps towards its creation. Biol Philos 25: 711-736.
3. Behura, S.K., (2006) Molecular marker systems in insects: current trends and future avenues. Mol Ecol 15: 3087-3113.
4. Behura, S.K., (2007) Insect microRNAs: structure, function and evolution. Insect Biochem Mol Biol 37: 3-9.
5. Bininda-Emonds, O.R., and, Sanderson, M.J., (2001) Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst Biol 50: 565-579.
6. Blair, C., and, Murphy, R.W., (2011) Recent trends in molecular phylogenetic analysis: where to next? J Hered 102: 130-138.
7. Boussau, B., Walton, Z., Delgado, J.A., Collantes, F., Beani, L., Stewart, I.J., et al,. (2014) Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One 9: e107709.
8. Brown, D., and, Sjölander, K., (2006) Functional classification using phylogenomic inference. PLoS Comput Biol 2: e77.
9. Buljan, M., and, Bateman, A., (2009) The evolution of protein domain families. Biochem Soc Trans 37: 751-755.
10. Campbell, L.I., Rota-Stabelli, O., Edgecombe, G.D., Marchioro, T., Longhorn, S.J., Telford, M.J., et al,. (2011) MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci USA 108: 15920-15924.
11. Chan, C.X., and, Ragan, M.A., (2013) Next-generation phylogenomics. Biol Direct 8: 3.
12. Comas, I., Moya, A., and, González-Candelas, F., (2007) From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst Biol 56: 1-16.
13. Dalquen, D.A., Altenhoff, A.M., Gonnet, G.H., and, Dessimoz, C., (2013) The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. PLoS ONE 8: e56925.
14. Degnan, J.H., and, Rosenberg, N.A., (2009) Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends Ecol Evol 24: 332-340.
15. Dell'Ampio, E., Meusemann, K., Szucsich, N.U., Peters, R.S., Meyer, B., Borner, J., et al,. (2014) Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol 31: 239 -2 49.
16. Delsuc, F., Brinkmann, H., and, Philippe, H., (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
17. Doolittle, W.F., (1999) Lateral genomics. Trends Cell Biol 9: M5-M8.
18. Driskell, A.C., Ane, C., Burleigh, J.G., McMahon, M.M., O'Meara, B.C., and, Sanderson, M.J., (2004) Prospects for building the tree of life from large sequence databases. Science 306: 1172-1174.
19. Edwards, S.V., Fertil, B., Giron, A., and, Deschavanne, P.J., (2002) A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst Biol 51: 599-613.
20. Eisen, J.A., (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167.
21. Felsenstein, J., (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401-410.
22. Fontaine, M.C., Pease, J.B., Steele, A., Waterhouse, R.M., Neafsey, D.E., Sharakhov, I.V., et al,. (2015) Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347: 1258524.
23. Foottit, R.G., and, Adler, P.H., (2009) Insect Biodiversity: Science and Society. Wiley, Oxford.
24. Giribet, G., and, Edgecombe, G.D., (2012) Reevaluating the arthropod tree of life. Annu Rev Entomol 57: 167-186.
25. Hu, F., Lin, Y., and, Tang, J., (2014) MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinformat 15: 354.
26. Hughes, J., Longhorn, S.J., Papadopoulou, A., Theodorides, K., de Riva, A., Mejia-Chang, M., et al,. (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol Biol Evol 23: 268-278.
27. Huelsenbeck, J.P., and, Lander, K.M., (2003) Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst Biol 52: 641-648.
28. i5K Consortium. (2013) The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. J Hered 104: 595-600.
29. Jensen, R.A., (2001) Orthologs and paralogs-we need to get it right. Genome Biol 2: INTERACTIONS1002.
30. Johnson, B.R., Borowiec, M.L., Chiu, J.C., Lee, E.K., Atallah, J., and, Ward, P.S., (2013) Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol 23: 2058-2062.
31. Jones, B., (2015) Building the insect tree-of-life. Nat Rev Genet 16: 2-3.
32. Kamali, M., Xia, A., Tu, Z., and, Sharakhov, I.V., (2012) A new chromosomal phylogeny supports the repeated origin of vectorial capacity in malaria mosquitoes of the Anopheles gambiae complex. PLoS Pathog 8: e1002960.
33. Kamali, M., Marek, P.E., Peery, A., Antonio-Nkondjio, C., Ndo, C., Tu, Z., et al,. (2014) Multigene phylogenetics reveals temporal diversification of major African malaria vectors. PLoS ONE 9: e93580.
34. Kawahara, A.Y., and, Breinholt, J.W., (2014) Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc Biol Sci 281: 20140970.
35. Kembel, S.W., Eisen, J.A., Pollard, K.S., and, Green, J.L., (2011) The phylogenetic diversity of metagenomes. PLoS ONE 6: e23214.
36. Kolaczkowski, B., and, Thornton, J.W., (2008) A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol 25: 1054-1066.
37. Kristensen, N.P., (1991) Phylogeny of extant hexapods. In The Insects of Australia. A textbook for students and research workers, Vol. I, 2nd edn. (, Naumann, I.D., Carne, P.B., Lawrence, J.F., Nielsen, E.S., Spradbery, J.P., Taylor, R.W., et al., eds), pp. 125-140. Oxford University Press, Oxford.
38. Kumar, S., Filipski, A.J., Battistuzzi, F.U., Kosakovsky Pond, S.L., and, Tamura, K., (2012) Statistics and truth in phylogenomics. Mol Biol Evol 29: 457-472.
39. Legg, D.A., Sutton, M.D., and, Edgecombe, G.D., (2013) Arthropod fossil data increase congruence of morphological and molecular phylogenies. Nat Commun 4: 2485.
40. Letsch, H., and, Simon, S., (2013) Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera). Sys Entomol 38: 783-793.
41. Letsch, H.O., Meusemann, K., Wipfler, B., Schütte, K., Beutel, R., and, Misof, B., (2012) Insect phylogenomics: results, problems and the impact of matrix composition. Proc Biol Sci 279: 3282-3290.
42. Liang, J., Cai, W., and, Sun, Z., (2014) Single-cell sequencing technologies: current and future. J Genet Genomics 41: 513-528.
43. Maddison, W.P., (1997) Gene trees in species trees. Syst Biol 46: 523-536.
44. May, R.M., (1988) How many species are there on earth? Science 241: 1441-1449.
45. Meusemann, K., von Reumont, B.M., Simon, S., Roeding, F., Strauss, S., Kück, P., et al,. (2010) A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol. 27: 2451-2464.
46. Misof, B., Liu, S., Meusemann, K., Peters, R.S., Donath, A., Mayer, C., Frandsen, P.B., et al,. (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science. 346: 763-767.
47. Munstermann, L.E., and, Conn, J.E., (1997) Systematics of mosquito disease vectors (Diptera, Culicidae): impact of molecular biology and cladistic analysis. Annu Rev Entomol 42: 351-369.
48. Murphy, W.J., Pevzner, P.A., and, O'Brien, S.J., (2004) Mammalian phylogenomics comes of age. Trends Genet 20: 631-639.
49. Neafsey, D.E., Christophides, G.K., Collins, F.H., Emrich, S.J., Fontaine, M.C., Gelbart, W., et al., (2013) The evolution of the Anopheles 16 genomes project. G3 3: 1191-1194.
50. Neafsey, D.E., Waterhouse, R.M., Abai, M.R., Aganezov, S.S., Alekseyev, M.A., Allen, J.E., et al,. (2015) Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 347: 1258522.
51. Olsen, G.J., and, Woese, C.R., (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7: 113-123.
52. O'Loughlin, S.M., Magesa, S., Mbogo, C., Mosha, F., Midega, J., Lomas, S., et al,. (2014) Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories. Mol Biol Evol 31: 889-902.
53. Page, R.D.M., and, Charleston, M.A., (1997) From gene to organismal phylogeny: reconciled trees and the gene tree species tree problem. Mol Phylogenet Evol 7: 231-240.
54. Pagel, M., (1999) Inferring the historical patterns of biological evolution. Nature 401: 877-884.
55. Pamilo, P., and, Nei, M., (1988) Relationships between gene trees and species trees. Mol Biol Evol 5: 568-583.
56. Parkinson, J., and, Blaxter, M., (2009) Expressed sequence tags: an overview. Methods Mol Biol 533: 1-12.
57. Peters, R.S., Meusemann, K., Petersen, M., Mayer, C., Wilbrandt, J., Ziesmann, T., et al,. (2014) The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evol Biol 14: 52.
58. Philippe, H., Snell, E.A., Bapteste, E., Lopez, P., Holland, P.W., and, Casane, D., (2004) Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol 21: 1740-1752.
59. Qi, J., Wang, B., and, Hao, B.I., (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58: 1-11.
60. Rannala, B., and, Yang, Z., (2008) Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet 9: 217-231.
61. Reidenbach, K.R., Cook, S., Bertone, M.A., Harbach, R.E., Wiegmann, B.M., and, Besansky, N.J., (2009) Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology. BMC Evol Biol 9: 298.
62. Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., and, Beeman, R.W., et al,. (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452: 949-955.
63. Robinson, G.E., Hackett, K.J., Purcell-Miramontes, M., Brown, S.J., Evans, J.D., Goldsmith, M.R., et al,. (2011) Creating a buzz about insect genomes. Science 331: 1386.
64. Rota-Stabelli, O., Campbell, L., Brinkmann, H., Edgecombe, G.D., Longhorn, S.J., Peterson, K.J., et al,. (2011) A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc Biol Sci 278: 298-306.
65. Salichos, L., and, Rokas, A., (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331.
66. Salichos, L., Stamatakis, A., and, Rokas, A., (2014) Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol 31: 1261-1271.
67. Salipante, S.J., and, Horwitz, M.S., (2007) A phylogenetic approach to mapping cell fate. Curr Top Dev Biol 79: 157-184.
68. Savard, J., Tautz, D., Richards, S., Weinstock, G.M., Gibbs, R.A., Werren, J.H., et al,. (2006) Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of holometabolous insects. Genome Res 16: 1334-1338.
69. Severson, D.W., and, Behura, S.K., (2012) Mosquito genomics: progress and challenges. Annu Rev Entomol 57: 143-166.
70. Siepel, A., (2009) Phylogenomics of primates and their ancestral populations. Genome Res 19: 1929-1941.
71. Simon, S., Narechania, A., Desalle, R., and, Hadrys, H., (2012) Insect phylogenomics: exploring the source of incongruence using new transcriptomic data. Genome Biol Evol 4: 1295-1309.
72. Shapiro, E., Biezuner, T., and, Linnarsson, S., (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14: 618-630.
73. Sharakhov, I.V., (2013) Chromosome phylogenies of malaria mosquitoes. Tsitologiia 55: 238-240.
74. Sjölander, K., (2004) Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 20: 170-179.
75. Sonnhammer, E.L., Gabaldõn, T., Sousa da Silva, A.W., Martin, M., Robinson-Rechavi, M., Boeckmann, B., et al,. (2014) Quest for Orthologs consortium. Big data and other challenges in the quest for orthologs. Bioinformatics 30: 2993-2998.
76. Sperling, E.A., and, Peterson, K.J., (2009) microRNAs and metazoan phylogeny: big trees from little genes. In Animal evolution- Genomes, Trees and Fossils (eds Telford MJ, Littlewood DTJ), pp. 157-170, Oxford University Press, Oxford.
77. Storm, C.E., and, Sonnhammer, E.L., (2003) Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res 13: 2353 -2362.
78. Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., and, Rogers, J.S., (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst Biol 50: 525-539.
79. Tesler, G., and, Bourque, G., (2008) Computational tools for the analysis of rearrangements in mammalian genomes. Methods Mol Biol 422: 145-170.
80. Theodorides, K., De Riva, A., Gõmez-Zurita, J., Foster, P.G., and, Vogler, A.P., (2002) Comparison of EST libraries from seven beetle species: towards a framework for phylogenomics of the Coleoptera. Insect Mol Biol 11: 467-475.
81. Trautwein, M.D., Wiegmann, B.M., Beutel, R., Kjer, K.M., and, Yeates, D.K., (2012) Advances in insect phylogeny at the dawn of the postgenomic era. Annu Rev Entomol 57: 449-468.
82. Vishnoi, A., Roy, R., Prasad, H.K., and, Bhattacharya, A., (2010) Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms. PLoS ONE 5: e14159.
83. Waterhouse, R.M., Tegenfeldt, F., Li, J., Zdobnov, E.M., and, Kriventseva, E.V., (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res 41: D358-D365.
84. Wipfler, B., Bai, M., Schoville, S., Dallai, R., Uchifune, T., Machida, R., et al,. (2014) Ice crawlers (Grylloblattodea)-the history of the investigation of a highly unusual group of insects. J Insect Biodiversity 2: 1-25.
85. Wolf, Y.I., Rogozin, I.B., Grishin, N.V., Tatusov, R.L., and, Koonin, E.V., (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1: 8.
86. Zhang, H., Zhong, Y., Hao, B., and, Gu, X., (2009) A simple method for phylogenomic inference using the information of gene content of genomes. Gene 441: 163-168.