Journal of Molecular Evolution

, Volume 34, Issue 1, pp 17–30 | Cite as

Evolution of the primate β-Globin gene region: Nucleotide sequence of the δ-β-globin Intergenic region of gorilla and phylogenetic relationships between African Apes and Man

  • Pascale Perrin-Pecontal
  • Manolo Gouy
  • Victor-Marc Nigon
  • Guy Trabuchet


A 6.0-kb DNA fragment from Gorilla gorilla including the 5′ part of the β-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque δ-β intergenic region. This analysis reveals four tandemly repeated sequences (RS), at the same location in the four species, showing a variable number of repeats generating both intraspecific (polymorphism) and interspecific variability. These tandem arrays delimit five regions of unique sequence called IG for intergenic. The divergence for these IG sequences is 1.85 ± 0.22% between human and gorilla, which is not significantly different from the value estimated in the same region between chimpanzee and human (1.62 ± 0.21%). The CpG and TpA dinucleotides are avoided. CpGs evolve faster than other sequence sites but do not confuse phylogenetic inferences by producing parallel mutations in different lineages. About 75% of CpG doublets have become TpG or CpA since the common ancestor, in agreement with the methylation/deamination pattern. Comparison of this intergenic region gives information on branching order within Hominoidea. Parsimony and distance-based methods when applied to the δ-β intergenic region provide evidence (although not statistically significant) that human and chimpanzee are more closely related to each other than to gorilla. CpG sites are indeed rich in information by carrying substitutions along the short internal branch. Combining these results with those on the ψη—δ intergenic region, shows in a statistically significant way that chimpanzee is the closest relative of human.

Key words

DNA sequencing DNA evolution Gorilla β-globin region Intergenic DNA DNA divergence Homininae phylogeny Repeated sequence 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Berg PE, Williams DM, Qian RL, Cohen RB, Cao SK, Mittelman M, Schechter AN (1989) A common protein binds to two silencers 5′ to the human β globin gene. Nucleic Acids Res 17:8833–8852Google Scholar
  2. Biggin MD, Gibson TJ, Hong GF (1983) Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci USA 80:3963–3965Google Scholar
  3. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504Google Scholar
  4. Bird AP, Taggart MH, Nicholls RD, Higgs DR (1987) Nonmethylated CpG rich islands at the human α-globin locus: implications for evolution of a α-globin pseudogene. EMBO J 6:999–1004Google Scholar
  5. Boudraa M, Perrin P (1987) CpG and TpA frequencies in the plant system. Nucleic Acids Res 15:5729–5737Google Scholar
  6. Brewer AC, Enver T, Greaves DR, Allan J, Patient RK (1988) 5′ structural motifs and Xenopus β-globin gene activation. J Mol Biol 199:575–585Google Scholar
  7. Broderick TP, Schaff DA, Bertino AM, Dush MK, Tischfield JA, Stambrook PJ (1987) Comparative anatomy of the human APRT gene and enzyme: nucleotide sequence divergence and conservation of a nonrandom CpG dinucleotide arrangement. Proc Natl Acad Sci USA 84:3349–3353Google Scholar
  8. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239Google Scholar
  9. Caccone A, Powell JR (1989) DNA divergence among hominoids. Evolution 43:925–942Google Scholar
  10. Chebloune Y, Pagnier J, Trabuchet G, Faure C, Verdier G, Labie D, Nigon V (1988) Structural analysis of the 5'-flanking region of the β-globin gene in African sickle cell anemia patients: further evidence for three origins of the sickle cell mutation in Africa. Proc Natl Acad Sci USA 85:4431–4435Google Scholar
  11. Collins FS, Weissman SM (1984) The molecular genetics of human hemoglobin. Prog Nucleic Acids Res Mol Biol 31: 315–462Google Scholar
  12. Cooper DN, Gerber-Huber S (1985) DNA methylation of CpG suppression. Cell Diff 17:199–205Google Scholar
  13. Cooper DN, Gerber-Huber S, Nardelli D, Schubiger JL, Wahli W (1987) The distribution of the dinucleotide CpG and cytosine methylation in the vitellogenin gene family. J Mol Evol 25:107–115Google Scholar
  14. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780Google Scholar
  15. Doerfler W (1983) DNA methylation and gene activity. Annu Rev Biochem 52:93–124Google Scholar
  16. Economou EP, Bergen AW, Warren AC, Antonarakis SE (1990) The polydeoxyadenylate tract of Alu repetitive element is polymorphic in the human genome. Proc Natl Acad Sci USA 87:2951–2954Google Scholar
  17. Ellis N, Yen P, Neiswanger K, Shapiro LJ, Goodfellow PN (1990) Evolution of the pseudoautosomal boundary in Old World monkeys and great apes. Cell 63:977–986Google Scholar
  18. Felsenstein J (1988a) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521–565Google Scholar
  19. Felsenstein J (1988b) PHYLIP version 3–3 manual. University of Washington, SeattleGoogle Scholar
  20. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416Google Scholar
  21. Fitch WM, Mainone C, Slightom JL, Goodman M (1988) The spider monkey ψη-globin gene and surrounding sequences: recent or ancient insertions of LINE'S and SINEs? Genomics 3:237–255Google Scholar
  22. Gautier C, Gouy M, Louail S (1985) Non-parametric statistics for nucleic acid sequence study. Biochimie 67:449–453Google Scholar
  23. Gonzalez IL, Sylvester JE, Smith TF, Stambolian D, Schmickel RD (1990) Ribosomal RNA gene sequences and hominoid phylogeny. Mol Biol Evol 7:203–219Google Scholar
  24. Goodman M, Koop BF, Czelusniak J, Fitch DHA, Tagle DA, Slightom JL (1989) Molecular phylogeny of the family of apes and humans. Genome 31:316–335Google Scholar
  25. Goodman M, Tagle DA, Fitch DHA, Bailey W, Czelusniak J, Koop BF, Benson P, Slightom JL (1990) Primate evolution at the DNA level and a classification of hominoids. J Mol Evol 30:260–266Google Scholar
  26. Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (1984) ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res 12:121–127Google Scholar
  27. Gouy M, Gautier C, Milleret F (1985) System analysis and nucleic acid sequence banks. Biochimie 67:433–436Google Scholar
  28. Grantham R, Greenland T, Louail S, Mouchiroud D, Prato JL, Gouy M, Gautier C (1985) Molecular evolution of viruses as seen by nucleic acid sequence study. Bull Inst Pasteur 83: 95–148Google Scholar
  29. Grantham R, Perrin P, Mouchiroud D (1986) Patterns in codon usage of different kinds of species. Oxford Surv Evol Biol 3: 48–81Google Scholar
  30. Green PM, Montandon AJ, Bentley DR, Ljung R, Nilsson IM, Giannelli F (1990) The incidence and distribution of CpG-TpG transitions in the coagulation factor IX gene. A fresh look at CpG mutation hotspots. Nucleic Acids Res 18:3227–3231Google Scholar
  31. Hasegawa M, Kishino H, Hayasaka K, Horai S (1990) Mitochondrial DNA evolution in primates: transition rate has been extremely low in the lemur. J Mol Evol 31:113–121Google Scholar
  32. Hasson JF, Mougneau E, Cuzin F, Yaniv M (1984) Simian virus 40 illegitimate recombination occurs near short direct repeats. J Mol Biol 177:53–69Google Scholar
  33. Hayasaka K, Gojobori T, Horai S (1988) Molecular phylogeny and evolution of primate mitochondria DNA. Mol Biol Evol 5:626–644Google Scholar
  34. Holmquist R, Miyamoto MM, Goodman M (1988a) Higherprimate phylogeny-why can't we decide? Mol Biol Evol 5: 201–216Google Scholar
  35. Holmquist R, Miyamoto MM, Goodman M (1988b) Analysis of higher-primate phylogeny from transversion differences in nuclear and mitochondrial DNA by Lake's methods of evolutionary parsimony and operator metrics. Mol Biol Evol 5: 217–236Google Scholar
  36. Jukes TH (1987) Transitions, transversions and the molecular evolutionary clock. J. Mol Evol 26:87–98Google Scholar
  37. Kimura M (1981) Estimation of evolutionary distance between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458Google Scholar
  38. Kolata G (1985) Fitting methylation into development. Science 228:1183–1184Google Scholar
  39. Kolsto AB, Kollias G, Giguere V, Isobe KI, Prydz H, Grosveld F (1986) The maintenance of methylation-free islands in transgenic mice. Nucleic Acids Res 14:9667–9678Google Scholar
  40. Koop BF, Tagle DA, Goodman M, Slightom JL (1989) A molecular view of primate phylogeny and important systematic and evolutionary questions. Mol Biol Evol 6:580–612Google Scholar
  41. Li WH, Wolfe KH, Sourdis J, Sharp PM (1987) Reconstruction of phylogenetic trees and estimation of divergence times under unconstant rates of evolution. Cold Spring Harbor Symp Quant Biol LII:847–856Google Scholar
  42. Li WH (1989) A statistical test of phylogenies estimated from sequence data. Mol Biol Evol 6:424–435Google Scholar
  43. Lindahl T (1981) DNA methylation and control of gene expression. Nature 290:363–364Google Scholar
  44. Maeda N, Bliska JB, Smithies O (1983) Recombination and balanced chromosome polymorphism suggested by DNA sequences 5′ to the human β-globin gene. Proc Natl. Acad Sci USA 80:5012–5016Google Scholar
  45. Maeda N, Wu CI, Bliska J, Reneke J (1988) Molecular evolution of intergenic DNA in higher primates: pattern of DNA changes, molecular clock, and evolution of repetitive sequences. Mol Biol Evol 5:1–20Google Scholar
  46. Margot JB, Demers JW, Hardison RC (1989) Complete nucleotide sequence of the rabbit β-like globin gene cluster. Analysis of intergenic sequences and comparison with the human β-like globin gene cluster. J Mol Biol 205:15–110Google Scholar
  47. McKeon C, Ohkubo H, Pastan I, de Crombrugghe B (1982) Unusual methylation pattern of the α2(I) collagen gene. Cell 29:203–210Google Scholar
  48. Messing J, Vieira J(1982) A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene 19:269–276Google Scholar
  49. Misfield R, Krystal M, Arnheim N (1981) A member of a new repeated segment sequence family which is conserved throughout eucaryotic evolution is found between the human delta and beta-globin genes. Nucleic Acids Res 9:5931–5947Google Scholar
  50. Miyamoto MM, Slightom JL, Goodman M (1987) Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region. Science 238:369–373Google Scholar
  51. Nei M (1987) Parsimony methods. In: Molecular evolutionary genetics. Columbia University Press, New York, p 313–320Google Scholar
  52. Perrin P, Bernardi G (1987) Directional fixation of mutations in vertebrate evolution. J Mol Evol 26:301–310Google Scholar
  53. Perutz MF (1990) Frequency of abnormal human hemoglobins caused by C → T transitions in CpG dinucleotides. J Mol Biol 213:203–206Google Scholar
  54. Poncz M, Schwartz E, Ballantine M, Surrey S (1983) Nucleotide sequence analysis of the delta-beta globin gene region in humans. J Biol Chem 258:11599–11609Google Scholar
  55. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  56. Sanger F, Coulson AR, Barrell BG, Smith AJH, Roe BA (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467Google Scholar
  57. Savatier P, Trabuchet G, Faure C, Chebloune Y, Gouy M, Verdier G, Nigon VM (1985) Evolution of the primate betaglobin gene region: high rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee. J Mol Biol 182:21–29Google Scholar
  58. Savatier P, Trabuchet G, Chebloune Y, Faure C, Verdier G, Nigon V (1987a) Nucleotide sequence of the delta-beta globin intergenic segment in the macaque: structure and evolutionary rates in higher primates. J Mol Evol 24:297–308Google Scholar
  59. Savatier P, Trabuchet G, Chebloune Y, Faure C, Verdier G, Nigon VM (1987b) Nucleotide sequence of the beta-globin genes in gorilla and macaque: the origin of nucleotide polymorphisms in man. J Mol Evol 24:309–318Google Scholar
  60. Semenza GL, Malladi P, Surrey S, Delgrosso K, Poncz M, Schwartz E (1984) Detection of a novel DNA polymorphism in the β globin gene cluster. J Biol Chem 259:6045–6048Google Scholar
  61. Shehee WR, Loeb DD, Adey NB, Burton FH, Casavant NC, Cole P, Davies CJ, McGraw RA, Schichman SA, Severynse DM, Voliva CF, Weyter FW, Wisely GB, Edgell MH, Hutchinson CA III (1989) Nucleotide sequence of the BALB/c mouse β-globin complex. J Mol Biol 205:41–62Google Scholar
  62. Sibley CG, Ahlquist JE (1984) The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J Mol Evol 20:2–15Google Scholar
  63. Sibley CG, Ahlquist JE (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J Mol Evol 26:99–121Google Scholar
  64. Sibley CG, Comstock JA, Ahlquist JE (1990) DNA hybridization evidence of hominoid phylogeny: a reanalysis of the data. J Mol Evol 30:202–236Google Scholar
  65. Smith TF, Waterman MS (1981) Comparison of biosequences. Adv Appl Math 2:482–489Google Scholar
  66. Smith TF, Ralph WW, Goodman, M, Czelusniak J (1985) Codon usage in the vertebrate hemoglobins and its implications. Mol Biol Evol 2:390–398Google Scholar
  67. Spritz RA (1981) Duplication/deletion polymorphism 5′ to the human β-globin gene. Nucleic Acids Res 9:5037–5047Google Scholar
  68. Tabor S, Richardson C (1987) DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci USA 84:4767–4771Google Scholar
  69. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471Google Scholar
  70. Tazi J, Bird A (1990) Alternative chromatin structure at CpG islands. Cell 60:909–920Google Scholar
  71. Trabuchet G, Chebloune Y, Savatier P, Lachuer J, Faure C, Verdier G, Nigon VM (1987) Recent insertion of an Alu sequence in the beta-globin cluster of the gorilla. J Mol Evol 25:288–291Google Scholar
  72. Trabuchet G, Elion J, Baudot G, Pagnier J, Bouhass R, Nigon VM, Labie D, Krishnamoorthy R (1991) On the origin and spread of beta-globin gene mutations in India, Africa and Mediterranea: analysis of the 5'-flanking and intragenic sequences of beta S and beta C genes. Hum Biol 63:241–252Google Scholar
  73. Tykocinski ML, Max EE (1984) CG dinucleotide clusters in MHC genes and in 5′ demethylated genes. Nucleic Acids Res 12:4385–4396Google Scholar
  74. Ueda S, Matsuda F, Honjo T (1988) Multiple recombinational events in primate immunoglobulin-epsilon and alpha genes suggest closer relationship of humans to chimpanzees than to gorillas. J Mol Evol 27:77–83Google Scholar
  75. Ueda S, Watanabe Y, Saitou N, Omoto K, Hayashida H, Miyata T, Hisajima H, Honjo T (1989) Nucleotide sequences of immunoglobulin-epsilon pseudogenes in man and apes and their phylogenetic relationships. J Mol Biol 205:85–90Google Scholar
  76. Williams SA, Goodman G (1989) A statistical test that supports a human/chimpanzee clade based on noncoding DNA sequence data. Mol Biol Evol 6:325–330Google Scholar
  77. Wolf SF, Migeon BR (1985) Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control for housekeeping genes. Nature 314:467–469Google Scholar
  78. Youssoufian H, Kazazian HH Jr, Phillips DG, Aronis S, Tsiftis G, Brown VA, Antonarakis SE (1986) Recurrent mutations in haemophilia A give evidence for CpG mutation hotspots. Nature 324:380–382Google Scholar

Copyright information

© Springer-Verlag New York Inc 1992

Authors and Affiliations

  • Pascale Perrin-Pecontal
    • 1
  • Manolo Gouy
    • 2
  • Victor-Marc Nigon
    • 1
  • Guy Trabuchet
    • 1
  1. 1.Centre de Génétique Moléculaire et Cellulaire, UMR 106Université Claude BernardVilleurbanneFrance
  2. 2.Laboratoire de Biométrie, URA 243Université Claude BernardVilleurbanneFrance

Personalised recommendations