Biology Bulletin Reviews

, Volume 8, Issue 2, pp 72–88 | Cite as

Variability of Indicators and Processes in Long Structured Phylogenetic Branch of Angiosperms. Part 1. A General Scheme

Article

Abstract

A general pattern of indicators and possible processes in the long structured phylogenetic branch of angiosperms is considered. The notions of the neontological history of evolution, the anisotomy of the phylogenetic process, cryptaffinic taxa and cryptaffinic transition in the angiosperm phylogeny, and the complex structure of phylogenetic branches are discussed. The mechanisms of the macroevolutionary processes in angiosperms are found to be limited by random mutations and selection. The intracellular processes and mechanisms should be the basis of major macroevolutionary transformations. It is emphasized that the manifestation of the studied indices is different in different links of the long structured phylogenetic branch, which requires a differential approach for their study.

Keywords

neontological history of evolution long structured phylogenetic branch cryptaffinic taxa cryptaffinic transition evolution nomogenesis quantum evolution punctuated equilibrium 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abel, O., Paläobiologie und Stammesgeschichte, Jena: Gustav Fischer Verlag, 1925.Google Scholar
  2. Ahrendt, L.W.A., Berberis and Mahonia. A taxonomic revision, Bot. J. Linn. Soc., 1961, vol. 57, pp. 1–369.CrossRefGoogle Scholar
  3. Aleshin, V.V., Phylogeny of invertebrates in terms of molecular data: probable the completion of phylogenetics as a science, Tr. Zool. Inst., Ross. Akad. Nauk, 2013, no. 2, pp. 9–39.Google Scholar
  4. APG III: an update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants, Bot. J. Linn. Soc., 2009, vol. 161, pp. 105–121.Google Scholar
  5. Avdulov, N.P., Karyo-systematic study of family Gramineae, Tr. Prikl. Bot., Genet. Sel., Prilozh., 1934, vol. 44, pp. 1–352.Google Scholar
  6. Berg, L.S., Nomogenez, ili evolyutsiya na osnove zakonomernostei (Nomogenesis or Evolution Determined by Law), St. Petersburg: GIS, 1922.Google Scholar
  7. Berg, L.S., Nomogenesis or Evolution Determined by Law, Cambridge, Ma: MIT Press, 1969.Google Scholar
  8. Berkhout, B., Grigoriev, A., Bakker, M., and Lukashov, V.V., Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide genomes, AIDS Res. Hum. Retroviruses, 2002, vol. 218, pp. 133–141.CrossRefGoogle Scholar
  9. Bird, A., DNA methylation and frequency of CpG in animal DNA, Nucleic Acids Res., 1980, vol. 8, pp. 1499–1504.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Bird, A., DNA methylation patterns and epigenetic memory, Genes Dev., 2002, vol. 16, pp. 6–21.CrossRefPubMedGoogle Scholar
  11. Bouchenak-Khelladi, Y., Salamin, N., Savolainen, V., et al., Large multigene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling, Mol. Phylogen. Evol., 2008, vol. 48, pp. 488–505.CrossRefGoogle Scholar
  12. Brundin, L.Z., Croizat’s panbiogeography versus phylogenetic biogeography, in Vicariance Biogeography: A Critique, Nelson, G. and Rosen, D., Eds., New York: Columbia Univ. Press, 1981, pp. 94–148.Google Scholar
  13. Cardon, L., Burge, C., Claiton, D., and Karlin, S., Pervasive CpG suppression in animal mitochondrial genomes, Proc. Natl. Acad. Sci. U.S.A., 1994, vol. 91, pp. 3799–3803.CrossRefPubMedPubMedCentralGoogle Scholar
  14. Chase, M.W., Fay, M.F., Davey, D.S., et al., Multigene analyses of monocot relationships: a summary, Aliso, 2006, vol. 22, pp. 63–75.CrossRefGoogle Scholar
  15. Chupov, V.S., Phylogeny and system of orders Liliales and Asparagales, Bot. Zh., 1994, vol. 79, no. 3, pp. 1–12.Google Scholar
  16. Chupov, V.S., On possible functional genome differentiation in the course of evolution and some approaches to its study. I. Neontological annals of evolution and its analysis, Tsitologiya, 2001, vol. 43, no. 10, pp. 975–986.Google Scholar
  17. Chupov, V.S., The shape of the lateral phylogenetic branch in plants according to the neontological taxonomic history of evolution, Usp. Sovrem. Biol., 2002, vol. 121, pp. 227–238.Google Scholar
  18. Chupov, V.S., Specific evolutionary features of biological species Homo sapiens L., Materialy Vserossiiskoi nauchnoi konferentsii “Futurologicheskii kongress: Budushchee Rossii i mira,” Moskva, 4 iyunya 2010 g. (Proc. All-Russ. Sci. Conf. “Futurological Congress: Future of Russia and the World,” Moscow, June 4, 2010), Moscow: Tsentr Probl. Anal. Gos.-Uprav. Proekt., 2010, pp. 247–257.Google Scholar
  19. Chupov, V.S., Dynamics of chromosome number in long structured phylogenetic branch of monocotyledons: A general scheme of karyotype evolution, Biol. Bull. Rev., 2013, vol. 3, no. 6, pp. 456–480.CrossRefGoogle Scholar
  20. Chupov, V.S., The emergence of subclasses of Alismatidae and Liliidae from the point of view of the concept of the cryptaffine transition, Materialy mezhdunarodnoi konferentsii “Sovremennye problemy evolyutsii i ekologii,” Ul’yanovsk, 7–9 aprelya 2014 g. (Proc. Int. Conf. “Modern Problems of Evolution and Ecology,” Ulyanovsk, April 7–9, 2014), Ulyanovsk: Ul’yanovsk. Gos. Pedagog. Univ., 2014, pp. 162–170.Google Scholar
  21. Chupov, V.S., Relationship and reciprocal influence of the theory of biological evolution and global evolutionism, Materialy II mezhdunarodnoi konferentsii “Sovremennye problemy biologicheskoi evolyutsii,” Moskva, 11–14 marta 2014 g. (Proc. II Int. Conf. “Modern Problems of Biological Evolution,” Moscow, March 11–14, 2014), Moscow: Gos. Darvin. Muz., 2015a, pp. 443–447.Google Scholar
  22. Chupov, V.S., Analysis of intergeneric boundaries in the phylogenetic sequences Mahonia–Berberis and Vancouveria–Epimedium, Materialy XIV mezhdunarodnoi nauchno-prakticheskoi konferentsii “Problemy botaniki Yuzhnoi Sibiri i Mongolii,” Barnaul, 25–29 maya 2015 g. (Proc. XIV Int. Sci.-Pract. Conf. “Problems of Botany of Southern Siberia and Mongolia,” Barnaul, May 25–29, 2015), Barnaul: Altaisk. Gos. Univ., 2015b, pp. 380–393.Google Scholar
  23. Chupov, V.S., The hypothesis of intellectogenesis as an alternative to the random evolutionary process—the tychogenesis (using the analogy method), Biosfera, 2016a, vol. 8, no. 2, pp. 155–163.CrossRefGoogle Scholar
  24. Chupov, V.S., Analysis of cryptaffine transition between the genera Berberis L. and Mahonia Nuttall (Berberidaceae, Angiospermae), Usp. Sovrem. Biol., 2016b, vol. 136, no. 1, pp. 68–80.Google Scholar
  25. Chupov, V.S. and Machs, E.M., Variations in nucleotide composition of the region ITS1–5.8S rDNA–ITS2 in evolutionary advanced and evolutionary static branches of the monocotyledonous plants, Proc. 5th Int. Conf. on Bioinformatics, Genome Regulation, and Structure, Novosibirsk, 2006, vol. 3, pp. 133–137.Google Scholar
  26. Chupov, V.S. and Machs, E.M., Nucleotide substitutions in rDNA of evolutionary static angiosperm groups, Biol. Bull. Rev., 2011a, vol. 1, no. 2, pp. 110–124.CrossRefGoogle Scholar
  27. Chupov, V.S. and Machs, E.M., Saltation in evolution and destiny of species Homo sapiens L., in Problems of Contemporary World Futurology, Yacunin, V.I., Ed., Cambridge: Cambridge Scholar Publ., 2011b, pp. 200–236.Google Scholar
  28. Chupov, V.S. and Machs, E.M., Cryptaffine transition in phylogeny of angiosperms, Bot. Zh., 2013, vol. 98, pp. 665–689.Google Scholar
  29. Chupov, V.S., Punina, E.O., Machs, E.M., and Rodionov, A.V., Nucleotide composition and CpG and CpNpG content of ITS1, ITS2, and the 5.8S rRNA in representatives of the phylogenetic branches Melanthiales–Liliales and Melanthiales–Asparagales (Angiospermae, Monocotyledones) reflect the specifics of their evolution, Mol. Biol. (Moscow), 2007, vol. 41, no. 5, pp. 737–755.Google Scholar
  30. Chupov, V.S., Machs, E.M., and Rodionov, A.V., Dinucleotide patterns of the rDNA elements as the indicator of the evolutionary level and phylogenetic marker in the branches Melanthiales–Liliales and Melanthiales–Asparagales (Monocotyledones, Angiospermae). I. General methods of the changes in dinucleotide composition, Usp. Sovrem. Biol., 2008a, vol. 128, no. 5, pp. 481–496.Google Scholar
  31. Chupov, V.S., Machs, E.M., and Rodionov, A.V., Dinucleotide patterns of the rDNA elements as the indicator of the evolutionary level and phylogenetic marker in the branches Melanthiales–Liliales and Melanthiales–Asparagales (Monocotyledones, Angiospermae). II. Peculiarity of dinucleotide composition of cryptaffine taxons, Usp. Sovrem. Biol., 2008b, vol. 128, no. 6, pp. 542–552.Google Scholar
  32. Clay, O., Schaffner, W., and Matsuo, K., Periodicity of eight nucleotides in purine distribution around human genomic CpG dinucleotides, Somatic Cell Mol. Genet., 1995, vol. 21, pp. 91–98.CrossRefGoogle Scholar
  33. Cronquist, A., An Integrated System of Classification of Flowering Plants, New York: Columbia Univ. Press, 1981.Google Scholar
  34. Darwin, Ch., On the Origin of Species by Means of Natural Selection, London: Watt, 1937.Google Scholar
  35. Davis, J., Petersen, G., Seberg, O., et al., Are mitochondrial genes useful for the analysis of monocot relationships? Taxon, 2006, vol. 55, pp. 857–870.CrossRefGoogle Scholar
  36. Ehrendorfer, F., Polyploidy and distribution, in Polyploidy: Biological Relevance, Levis, W., Ed., New York: Plenum, 1980, pp. 45–66.Google Scholar
  37. Eldredge, N. and Gould, S.J., Punctuated equilibria: an alternative to phyletic gradualism, in Models in Paleobiology, Schopf, T.J.M., Ed., San Francisco: Freeman Cooper, 1972, pp. 82–115.Google Scholar
  38. Elenkin, A.A., Evolution of lower algae and the theory of equivalentogenesis, Mater. Inst. Sporovykh Rast., Glav. Bot. Sada, 1926, vol. 4, pp. 1–26.Google Scholar
  39. Escobar, J.S., Glemin, S., and Galter, N., GC-biased gene conversion impacts ribosomal DNA evolution in vertebrates, angiosperms, and other eucaryotes, Mol. Biol. Evol., 2011, vol. 28, pp. 2561–2575.CrossRefPubMedGoogle Scholar
  40. Gould, S.J., The Structure of Evolutionary Theory, Cambridge, Ma: Harvard Univ. Press, 2002.Google Scholar
  41. Gould, S.J. and Eldredge, N., Punctuated equilibria: the tempo and mode of evolution reconsidered, Paleobiology, 1977, vol. 3, pp. 115–151.CrossRefGoogle Scholar
  42. GPWG Phylogeny and subfamilial classification of the grasses (Poaceae), Ann. Mo. Bot. Gard., 2001, vol. 88, pp. 373–457.Google Scholar
  43. Gromova, E.S. and Khoroshaev, A.V., Prokaryotic DNA methyltransferases: the structure and the mechanism of interaction with DNA, Mol. Biol. (Moscow), 2003, vol. 37, no. 2, pp. 260–272.CrossRefGoogle Scholar
  44. Haeckel, E., Natürliche Schöpfungsgeschichte. Gemeinverständliche Wissenschaftliche Vorträge über die Entwicklungslehre im Allgemeinen und Diejenige von Darwin, Goethe und Lamarck im Besonderen, über die Anwendung Derselben auf den Ursprung des Menschen und Andere Damit Zusammenhängende Grundfragen der Naturwissenschaft, Berlin: G. Reimer, 1868.Google Scholar
  45. Hendrich, B. and Tweedie, S., The methyl-CpG binding domain and the evolving role of DNA methylation in animals, Trends Genet., 2003, vol. 19, pp. 269–277.CrossRefPubMedGoogle Scholar
  46. Hennig, W., Phylogenetic Systematics, Urbana: Univ. Illinois Press, 1966.Google Scholar
  47. Hirabayashi, Y. and Gotoh, Y., Epigenetic control of neural precursor cell fate during development, Nat. Rev. Neurosci., 2010, vol. 11, pp. 377–388.CrossRefPubMedGoogle Scholar
  48. Hubscher, U., Maga, G., and Spadari, S., Eukaryotic DNA polymerases, Ann. Rev. Biochem., 2002, vol. 71, pp. 133–163.CrossRefPubMedGoogle Scholar
  49. Jansson, S., Meyer-Gauen, G., Cerff, R., and Martin, W., Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes, J. Mol. Evol., 1994, vol. 34, pp. 34–46.Google Scholar
  50. King, K., Torres, R., Zentgraf, U., and Hemleben, V., Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of Cucurbitaceae, J. Mol. Evol., 1993, vol. 36, pp. 144–152.CrossRefPubMedGoogle Scholar
  51. Kim, Y.-D., Kim, S.-H., and Landrum, L.R., Taxonomic and phytogeographic implication from ITS phylogeny in Berberis (Berberidaceae), J. Plant Res., 2004a, vol. 117, pp. 175–182.CrossRefPubMedGoogle Scholar
  52. Kim, Y.-D., Kim, S.-H., Kim, C.H., and Jansen, R.K., Phylogeny of Berberidaceae based on sequences of the chloroplast gene ndhF, Biochem. Syst. Ecol., 2004b, vol. 32, pp. 291–301.CrossRefGoogle Scholar
  53. Knock, E., Pereira, J., Lombard, P.D., et al., The methyl binding domain 3 nucleosome remodeling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex, Neural Dev., 2015, vol. 10, pp. 13–20. doi 10.1186/s13064-015-0040-zCrossRefPubMedPubMedCentralGoogle Scholar
  54. Kovarik, A., Matyasek, R., Leitch, A., et al., Variability in CpNpG methylation in higher plant genomes, Gene, 1997, vol. 204, pp. 25–33.CrossRefPubMedGoogle Scholar
  55. Krutyakov, V.M., Eukaryotic error-prone DNA polymerases: the presumed roles in replication, repair, and mutagenesis, Mol. Biol. (Moscow), 2006, vol. 40, no. 1, pp. 1–8.CrossRefGoogle Scholar
  56. Levitinskii, G.A., Karyo- and genotype changes during evolution, in Tsitologiya rastenii. Izbrannye trudy (The Plant Cytology: Selected Works), Moscow: Nauka, 1976, pp. 216–238.Google Scholar
  57. Matsuo, K., Clay, O., Takahashi, T., et al., Evidence for erosion of mouse CpG islands during mammalian evolution, Somatic Cell Mol. Genet., 1993, vol. 19, pp. 543–555.CrossRefGoogle Scholar
  58. Mazin, A.L. and Vanyushin, B.F., The loss of CpG dinucleotides from DNA. 2. Methylated and non-methylated genes of vertebrates, Mol. Biol. (Moscow), 1987, vol. 21, pp. 552–561.Google Scholar
  59. Mazin, A.L. and Vanyushin, B.F., The loss of CpG dinucleotides from DNA. 5. Traces of “fossil” methylation in the Drosophila genome, Mol. Biol. (Moscow), 1988, vol. 22, pp. 1399–1404.Google Scholar
  60. Moor, G., Abbo, S., Cheung, W., et al., Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases, Genomics, 1993, vol. 15, pp. 472–482.CrossRefGoogle Scholar
  61. Patrushev, L.I., Ekspressiya genov (Gene Expression), Moscow: Nauka, 2000.Google Scholar
  62. Pavlow, A.P., Le cretace inferiore de la Russie et sa faune, Nouv. Mém. Soc. Impér. Nat. Moscou, 1901, vol. 16, no. 3, pp. 1–87.Google Scholar
  63. Popov, I.Yu., Ortogenez protiv darvinizma: istoriko-nauchnyi analiz kontseptsii napravlennoi evolyutsii (Ortogenesis against Darwinism: Historical-Scientific Analysis of the Concept of Directed Evolution), St. Petersburg: S.-Peterb. Gos. Univ., 2005.Google Scholar
  64. Sanchez-Ken, J.G., Clark, L.G., Kellog, E.A., and Kay, E.E., Reinstatement and emendation of subfamily Micrarioideae (Poaceae), Syst. Bot., 2007, vol. 32, pp. 71–80.CrossRefGoogle Scholar
  65. Severtsov, A.N., Etyudy po teorii evolyutsii: Individual’noe razvitie i evolyutsiya (Studies on the Theory of Evolution: Individual Development and Evolution), Moscow: Librokom, 2012.Google Scholar
  66. Severtsov, A.S., Vvedenie v teoriyu evolyutsii (Introduction to the Theory of Evolution), Moscow: Mosk. Gos. Univ., 1981.Google Scholar
  67. Severtsov, A.S., Teoriya evolyutsii (The Theory of Evolution), Moscow: Vlados, 2005.Google Scholar
  68. Shatalkin, A.I., Taksonomiya. Osnovaniya, printsipy i pravila (Taxonomy: Principles and Rules), Moscow: KMK, 2012.Google Scholar
  69. Simpson, G.G., Tempo and Mode in Evolution, New York: Columbia Univ. Press, 1944.Google Scholar
  70. Stebbins, G.L., Chromosomal Evolution in Higher Plants, London: Edward Arnold, 1971.Google Scholar
  71. Suslov, V.V. and Kolchanov, N.A., Darwinian evolution and regulatory gene structure, Vavilovskii Zh. Genet. Selekts., 2009, vol. 13, no. 2, pp. 410–431.Google Scholar
  72. Takhtadzhan, A.L., Osnovy evolyutsionnoi morfologii pokrytosemennykh (Fundamentals of the Evolutionary Morphology of Angiosperms), Moscow: Nauka, 1964.Google Scholar
  73. Takhtadzhan, A.L., Sistema magnoliofitov (A System of Magnoliophytes), Leningrad: Nauka, 1987.Google Scholar
  74. Takhtajan, A.L., Evolutionary Trends in Flowering Plants, New York: Columbia Univ. Press, 1991.Google Scholar
  75. Thorne, R.A., Phylogenetic classification of the Angiospermae, Evol. Biol., 1976, vol. 9, pp. 35–106.Google Scholar
  76. Thorne, R.F. and Reveal, J.L., An updated classification of the class Magnoliopsida (“Angiospermae”), Bot. Rev., 2007, vol. 73, pp. 67–182.CrossRefGoogle Scholar
  77. Walsh, J., Interaction of selection and biased gene conversion in a multigene family, Proc. Natl. Acad. Sci. U.S.A., 1985, vol. 82, pp. 153–157.CrossRefPubMedPubMedCentralGoogle Scholar
  78. Zherikhin, V.V., Biocoenotic regulation of evolution, Paleontol. Zh., 1986, no. 1, pp. 3–12.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  1. 1.Komarov Botanical InstituteRussian Academy of SciencesSt. PetersburgRussia

Personalised recommendations