16. Hampl V., Hug L., Leigh J.W. et al. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic «supergroups» // Proc. Natl. Acad. Sci. U.S.A. 2009. Vol. 106, № 10. P. 3859-3864.
17. Minge M.A., Silberman J.D., Orr R.J. et al. Evolutionary position of breviate amoebae and the primary eukaryote divergence // Proc. Biol. Sci. 2009. Vol. 276, № 1657. P. 597-604.
18. Fitzpatrick D.A., Logue M.E., Stajich J.E., Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis // BMC Evol. Biol. 2006. Vol. 6. P. 99.
19. Wang H., Xu Z., Gao L., Hao B. A fungal phylogeny based on 82 complete genomes using the composition vector method // BMC Evol. Biol. 2009. Vol. 9. P. 195.
20. Dopazo H., Dopazo J. Genome-scale evidence of the nematode-arthropod clade // Genome Biol. 2005. Vol. 6, № 5. P. R41.
21. Irimia M., Maeso I., Penny D. et al. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata // Mol. Biol. Evol. 2007. Vol. 24, № 8. P. 1604-1607.
22. Philippe H., Brinkmann H., Martinez P. et al. Acoel flatworms are not platyhelminthes: evidence from phylogenomics // PLoS One. 2007. Vol. 2, № 1. P. e717.
23. Lartillot N., Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria // Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008. Vol. 363, № 1496. P. 1463-1472.
24. Marletaz F., Le Parco Y. Careful with understudied phyla: the case of chaetognath // BMC Evol. Biol. 2008. Vol. 8. P. 251.
25. Helmkampf M., Bruchhaus I., Hausdorf B. Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept // Proc. Biol. Sci. 2008. Vol. 275, № 1645. P. 1927-1933.
26. Roy S.W., Irimia M. Rare genomic characters do not support Coelomata: intron loss/gain // Mol. Biol. Evol. 2008. Vol. 25, № 4. P. 620-623.
27. Podsiadlowski L., Braband A., Struck T.H. et al. Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea // BMC Genomics. 2009. Vol. 10. P. 364.
28. Holland L.Z., Albalat R., Azumi K. et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology // Genome Res. 2008. Vol. 18, № 7. P. 1100-1111.
29. Swalla B.J., Smith A.B. Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives // Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008. Vol. 363, № 1496. P. 1557-1568.
30. Singh T.R., Tsagkogeorga G., Delsuc F. et al. Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny // BMC Genomics. 2009. Vol. 10. P. 534.
31. Hallstrom B.M., Kullberg M., Nilsson M.A., Janke A. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups // Mol. Biol. Evol. 2007. Vol. 24, № 9. P. 2059-2068.
32. Kitazoe Y., Kishino H., Waddell P.J. et al. Robust time estimation reconciles views of the antiquity of placental mammals // PLoS One. 2007. Vol. 2, № 4. P. e384.
33. Kjer K.M., Honeycutt R.L. Site specific rates of mitochondrial genomes and the phylogeny of eutheria // BMC Evol. Biol. 2007. Vol. 7. P. 8.
34. Murphy W.J., Pringle T.H., Crider T.A. et al. Using genomic data to unravel the root of the placental mammal phylogeny // Genome Res. 2007. Vol. 17, № 4. P. 413-421.
35. Hou Z.C., Romero R., Wildman D.E. Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data // Mol. Phylogenet. Evol. 2009. Vol. 52, № 3. P. 660-664.
36. Krauss V., Thummler C., Georgi F. et al. Near intron positions are reliable phylogenetic markers: an application to holometabolous insects // Mol. Biol. Evol. 2008. Vol. 25, № 5. P. 821-830.
37. Kolaczkowski B., Thornton J.W. A mixed branch length model of heterotachy improves phylogenetic accuracy // Mol. Biol. Evol. 2008. Vol. 25, № 6. P. 1054-1066.
38. Archambault V., Buchler N.E., Wilmes G.M. et al. Two-faced cyclins with eyes on the targets // Cell Cycle. 2005. Vol. 4, № 1. P. 125-130.
39. Vogel C., Chothia C. Protein Family Expansions and Biological Complexity // PLoS Comput. Biol. 2006. Vol. 2, № 5. P. e48.
40. Wilson D., Pethica R., Zhou Y. et al. SUPERFAMILY - Comparative Genomics, Datamining and Sophisticated Visualisation // Nucleic Acids Res. 2009. Vol. 37, Database issue. P. D380-D386.
41. Hughes A.L. The evolution of functionally novel proteins after gene duplication // Proc. R. Soc. Lond. Ser. B Biol. Sci. 1994. Vol. 256, № 1346. P. 119-124.
42. Brandeis M., Rosewell I., Carrington M. et al. Cyclin B2-null mice develop normally and are fertile whereas cyclin B1-null mice die in utero // Proc. Natl. Acad. Sci. U.S.A. 1998. Vol. 95, № 8. P. 4344-4349.
43. Оно С. Генетические механизмы прогрессивной эволюции. М. : Мир, 1973. 227 с.
44. Teichmann S.A., Babu M.M. Gene regulatory network growth by duplication // Nat. Genet. 2004. Vol. 36, № 5. P. 492-496.
45. van der Voet M., Lorson M.A., Srinivasan D.G. et al. C. elegans mitotic cyclins have distinct as well as overlapping functions in chromosome segregation // Cell Cycle. 2009. Vol. 8, № 4. P. 4091-4102.
46. Miles D.C., van den Bergen J.A., Sinclair A.H., Western P.S. Regulation of the female mouse germ cell cycle during entry into meiosis // Cell Cycle. 2010. Vol. 9, № 2. P. 408-418.
47. Nguyen T.B., Manova K., Capodieci P. et al. Characterization and expression of mammalian cyclin b3, a prepachytene meiotic cyclin // J. Biol. Chem. 2002. Vol. 277, № 44. P. 41960- 41969.
48. Refik-Rogers J., Manova K., Koff A. Misexpression of cyclin B3 leads to aberrant spermatogenesis // Cell Cycle. 2006. Vol. 5, № 17. P. 1966-1973.
49. Benton M.J., Donoghue P.C. Paleontological evidence to date the tree of life // Mol. Biol. Evol. 2007. Vol. 24, № 1. P. 26-53.
50. Peterson K.J., Cotton J.A., Gehling J.G., Pisani D. The Ediacaran emergence of bilaterians:
51. congruence between the genetic and the geological fossil records // Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008. Vol. 363, № 1496. P. 1435-1443.
52. Budd G.E. The earliest fossil record of the animals and its significance // Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008. Vol. 363, № 1496. P. 1425-1434.
53. Taylor J.W., Berbee M.L. Dating divergences in the Fungal Tree of Life: review and new analyses // Mycologia. 2006. Vol. 98, № 6. P. 838-849.
54. Berbee M.L., Taylor J.W. Dating the molecular clock in fungi - how close are we? // Fungal Biol. Rev. 2010. Vol. 24, № 1-2. P. 1-16.
55. Vihinen M., Torkkila E., Riikonen P. Accuracy of protein flexibility predictions // Proteins. 1994. Vol. 19, № 2. P. 141-149.
56. Chou P.Y., Fasman G.D. Prediction of the secondary structure of proteins from their amino acid sequence // Adv. Enzymol. 1978. Vol. 47. P. 45-148.
57. Fisher D.L., Nurse P. A single fission yeast mitotic cyclin B p34cdc2 kinase promotes both S-phase and mitosis in the absence of G1 cyclins // EMBO J. 1996. Vol. 15, № 4. P. 850-860.
58. Bloom J., Cross F.R. Multiple levels of cyclin specificity in cell-cycle control // Nat. Rev.