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Phylogeny

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Introduction to Evolutionary Genomics

Part of the book series: Computational Biology ((COBO,volume 17))

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Abstract

DNA replications generate phylogenies. Therefore, the phylogenetic relationship of DNA sequences is fundamental for describing individuals, genes, chromosomes, populations, and species. Their relationships and differences are discussed as well as the biologically important concepts such as gene genealogy, paralogy, orthology, and horizontal gene transfer. Basic concepts of trees and networks are then explained including mathematical definition, number of possible tree topologies, and description of trees and networks. Biological implications of trees and the relationship with taxonomy are also discussed.

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References

  1. Darwin, C. (1859). On the origin of species. London: John Murray.

    Google Scholar 

  2. Deppe, U., et al. (1978). Cell lineages of the embryo of the nematode Caenorhabditis elegans. Proceedings of the National Academy of Sciences USA, 75, 376–380.

    Article  Google Scholar 

  3. Wood, L. D., et al. (2007). The genomic landscapes of human breast and colorectal cancers. Science, 318, 1108–1113.

    Article  Google Scholar 

  4. Uchi, R., et al. (2016). Integrated multiregional analysis proposing a new model of colorectal cancer evolution. PLoS Genetics, 12, e1005778.

    Article  Google Scholar 

  5. Saitou, N. (1996). Contrasting gene trees and population trees on the evolution of modern humans. In A. J. Boyce & C. G. N. Mascie-Taylor (Eds.), Molecular biology and human diversity (pp. 265–282). Cambridge: Cambridge University Press.

    Chapter  Google Scholar 

  6. Ahn, S. M., et al. (2011). Genome Research, 16, 1622–1629.

    Google Scholar 

  7. International HapMap Project Home Page. http://hapmap.ncbi.nlm.nih.gov/.

  8. Hansen, A. K., et al. (2007). American Journal of Botany, 94, 42–46.

    Article  Google Scholar 

  9. Saitou, N. (2004). Genome and evolution (in Japanese,). Tokyo: Shin-yosha.

    Google Scholar 

  10. Jinam, T. A., Hong, L.-C., Phipps, M. E., Stoneking, M., Ameen, M., Edo, J., HUGO Pan-Asian SNP Consortium, & Saitou, N. (2012). Evolutionary history of Continental Southeast Asians: “Early train” hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Molecular Biology and Evolution, 29, 3513–3527.

    Article  Google Scholar 

  11. Kitano, T., Noda, R., Takenaka, O., & Saitou, N. (2009). Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis. Molecular Phylogenetics and Evolution, 51, 465–471.

    Article  Google Scholar 

  12. Nei, M. (1987). Molecular evolutionary genetics. New York: Columbia University Press.

    Google Scholar 

  13. Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford/New York: Oxford University Press.

    Google Scholar 

  14. Hedges, S. B., Dodley, J., & Kumar, S. (2006). TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics, 22, 2971–2972.

    Article  Google Scholar 

  15. Kitano, T., Satou, M., & Saitou, N. (2010). Evolution of two Rh blood group-related genes of the amphioxus species Branchiostoma floridae. Genes & Genetic Systems, 85, 121–127.

    Article  Google Scholar 

  16. Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular and Biological Evolution, 4, 406–425.

    Google Scholar 

  17. Takezaki, N., Rzhetsky, A., & Nei, M. (1995). Phylogenetic test of the molecular clock and linearized trees. Molecular and Biological Evolution, 12, 823–833.

    Google Scholar 

  18. Ezawa, K., Ikeo, K., Gojobori, T., & Saitou, N. (2011). Evolutionary patterns of recently emerged animal duplogs. Genome Biology and Evolution, 3, 1119–1135.

    Article  Google Scholar 

  19. Fitch, W. M. (1970). Distinguishing homologous from analogous proteins. Systematic Zoology, 19, 99–113.

    Article  Google Scholar 

  20. Wolfe, K. (2000). Robustness—It’s not where you think it is. Nature Genetics, 25, 3–4.

    Article  Google Scholar 

  21. Sonnhammer, E. L. L., & Koonin, E. V. (2002). Orthology, paralogy, and proposed classification for paralog subtypes. Trends in Genetics, 18, 619–620.

    Article  Google Scholar 

  22. Kawamura, S., Saitou, N., & Ueda, S. (1992). Concerted evolution of the primate immunoglobulin alpha gene through gene conversion. Journal of Biological Chemistry, 267(11), 7359–7367.

    Google Scholar 

  23. Kitano, T., Sumiyama, K., Shiroishi, T., & Saitou, N. (1998). Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene. Biochemical and Biophysical Research Communications, 249, 78–85.

    Article  Google Scholar 

  24. Kitano, T., & Saitou, N. (1999). Evolution of Rh blood group genes have experienced gene conversions and positive selection. Journal of Molecular Evolution, 49, 615–626.

    Article  Google Scholar 

  25. Kitano, T., Kim, C.-G., Blancher, A., & Saitou, N. (2016). No distinction of orthology/paralogy between human and chimpanzee Rh blood group genes. Genome Biology and Evolution, 8, 519–527.

    Article  Google Scholar 

  26. Koonin, E. V., Makarova, K. S., & Aravind, L. (2001). Horizontal gene transfer in prokaryotes: Quantification and classification. Annual Review of Microbiology, 55, 709–742.

    Article  Google Scholar 

  27. Heinrichs, D. E., Yethon, J. A., & Whitfield, C. (1998). Molecular basis for structural diversity in the core regions of the lipopolysaccharides of Escherichia coli and Salmonella enterica. Molecular Microbiology, 30, 221–232.

    Article  Google Scholar 

  28. Saitou, N. (2007). Introduction to genome evolutionary studies (in Japanese). Tokyo: Kyoritsu Shuppan.

    Google Scholar 

  29. Archibald, J. M., & Richards, T. A. (2011). Gene transfer: Anything goes in plant mitochondria. BMC Biology, 8, 147.

    Article  Google Scholar 

  30. Dehal, P., et al. (2002). The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science, 298, 2157–2167.

    Article  Google Scholar 

  31. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.

    Article  Google Scholar 

  32. Kryukov, K., & Saitou, N. (2010). MISHIMA—A new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. BMC Bioinformatics, 11, 142.

    Article  Google Scholar 

  33. Gouy, M., Guindon, S., & Gascuel, O. (2010). SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution, 27, 221–224.

    Article  Google Scholar 

  34. Nei, M. (1986). Stochastic errors in DNA evolution and molecular phylogeny. In Evolutionary perspectives and the new genetics, 1987.

    Google Scholar 

  35. Saitou, N., & Nei, M. (1986). The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence. Journal of Molecular Evolution, 24, 189–204.

    Article  Google Scholar 

  36. Kitano, T., Liu, Y.-H., Ueda, S., & Saitou, N. (2004). Human specific amino acid changes found in 103 protein coding genes. Molecular Biology and Evolution, 21, 936–944.

    Article  Google Scholar 

  37. Dress, A., Huber, K. T., Koolen, J., Moulton, V., & Spillner, A. (2011). Basic phylogenetic combinatorics. Cambridge: Cambridge University Press.

    Book  Google Scholar 

  38. Cavalli-Sforza, L. L., & Edwards, A. (1967). Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics, 19, 233–257.

    Google Scholar 

  39. Felsenstein, J. (1978). The number of evolutionary trees. Systematic Zoology, 27, 27–33.

    Article  Google Scholar 

  40. http://evolution.genetics.washington.edu/phylip/newicktree.html.

  41. Courant, R., Robbins, H., & Stewart, I. (1996). What is mathematics?. Oxford: Oxford University Press.

    MATH  Google Scholar 

  42. Robinson, D. F., & Foulds, L. R. (1981). Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131–147.

    Article  MathSciNet  Google Scholar 

  43. Yule, G. U. (1924). A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S. Philosophical Transaction of Royal Society of London Series B, 213, 21–87.

    Article  Google Scholar 

  44. Sarich, V. M., & Wilson, A. C. (1967). Immunological time scale for hominoid evolution. Science, 158, 1200–1204.

    Article  Google Scholar 

  45. Hara, Y., Imanishi, T., & Satta, Y. (2012). Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes. Genome Biology and Evolution, 4, 1133–1145.

    Article  Google Scholar 

  46. Sokal, R., & Michener, C. D. (1958). A statistical method for evaluating systematic relationship. University of Kansas Science Bulletin, 38, 1409–1438.

    Google Scholar 

  47. Sneath, P. H. A., & Sokal, R. R. (1973). Numerical taxonomy. San Francisco: W. H. Freeman & Company.

    MATH  Google Scholar 

  48. Huxley, J. (1958). Evolutionary process and taxonomy with special reference to grades (pp. 21–38). Uppsala: Uppsala University Arsskr.

    Google Scholar 

  49. Simpson, G. G. (1961). Principles of animal taxonomy. New York: Columbia University Press.

    Google Scholar 

  50. Eck, R. V., & Dayhoff, M. (1966). Atlas of protein sequence and structure. Silver Spring: National Biomedical Research Foundation.

    Google Scholar 

  51. Lemey, P., Salemi, M., & Vandamme, A.-M. (2009). The phylogenetic handbook (2nd ed.). Cambridge: Cambridge University Press.

    Book  Google Scholar 

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Correspondence to Naruya Saitou .

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Saitou, N. (2018). Phylogeny. In: Introduction to Evolutionary Genomics. Computational Biology, vol 17. Springer, Cham. https://doi.org/10.1007/978-3-319-92642-1_4

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  • DOI: https://doi.org/10.1007/978-3-319-92642-1_4

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