Genome Structure and Primate Evolution

Part of the Primatology Monographs book series (PrimMono)


Sequences of the entire human genome reveal a relative richness in structure with repetitive elements, tandem repeats, inverted repeats, and palindrome structures. Focusing on structure, the evolution of X and Y chromosomes in primates is reviewed here, and the relationship between gene expression and gene structure on autosomes is explored. In a four-stratum scenario of mammalian sex chromosome evolution, a region of exceptionally low sequence divergence has been identified, and the reasons for this low sequence divergence are presented here. In addition, the construction of palindromes on the human Y chromosome is discussed in relationship to the emergence of genes in the male-specific region on the Y chromosome. Based on these observations, six of eight palindromes on the human Y chromosome are considered to have formed before the divergence of Old World monkeys and hominoids. The relationship between gene expression patterns and copy number variation illustrates the role of negative selection in the retention of high copy number to maintain the coordination of gene expression in a network of gene expression.


Copy Number Variation Repetitive Element Segmental Duplication Duplication Rate International Human Genome Sequencing Consortium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.





Amylase 1




CMP-N-acetylneuraminic acid hydroxylase


Copy number variation


Chimpanzee-specific palindrome 1


Deleted in azoospermia




Human (Homo sapiens) Y chromosome


Heat-shock transcription factor


Kallman syndrome


Long interspersed elements


Major histocompatibility complex


Million years


New World monkeys


Old World monkeys


Pseudo-autosomal region 1


Chimpanzee (Pan troglodytes) Y chromosome


RNA-binding motif


Short interspersed elements


Variable charge


X Kell blood-related



The author thanks Drs. Mineyo Iwase and Hielim Kim for their help in the analysis and discussion. The findings presented here are from research supported in part by a grant (16107001) from the Japan Science Promotion Society (JSPS) and in part by a grant (17018032) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).


  1. Bailey JA, Yavor AM, Viggiano L et al (2002) Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. Am J Hum Genet 70:83–100PubMedCrossRefGoogle Scholar
  2. Bhowmick BK, Satta Y, Takahata N (2007) The origin and evolution of human ampliconic gene families and ampliconic structure. Genome Res 17:441–450PubMedCrossRefGoogle Scholar
  3. Blekhman R, Oshlack A, Gilad Y (2009) Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics 182:627–630PubMedCrossRefGoogle Scholar
  4. Cheng Z, Ventura M, She X et al (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature (Lond) 437:88–93CrossRefGoogle Scholar
  5. Drummond-Borg M, Deeb SS, Motulsky AG (1989) Molecular patterns of X chromosome-linked color vision genes among 134 men of European ancestry. Proc Natl Acad Sci USA 86:983–987PubMedCrossRefGoogle Scholar
  6. Ebersberger I, Metzler D, Schwarz C et al (2002) Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70:1490–1497PubMedCrossRefGoogle Scholar
  7. Fu N, Drinnenberg I, Kelso J et al (2007) Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS One 2(2):e216PubMedCrossRefGoogle Scholar
  8. Groot PC, Mager WH, Frants RR (1991) Interpretation of polymorphic DNA patterns in the human alpha-amylase multigene family. Genomics 10:779–785PubMedCrossRefGoogle Scholar
  9. Hayakawa T, Satta Y, Gagneux P et al (2001) Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene. Proc Natl Acad Sci USA 98:11399–11140PubMedCrossRefGoogle Scholar
  10. Hughes JF, Skaletsky H, Pyntikova T et al (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536–539PubMedCrossRefGoogle Scholar
  11. Iafrate AJ, Feuk L, Rivera MN et al (2004) Detection of large-scale variation in the human genome. Nat Genet 36:949–951PubMedCrossRefGoogle Scholar
  12. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature (Lond) 409:860–921CrossRefGoogle Scholar
  13. Iwase M, Satta Y, Hirai Y et al (2003) The amelogenin loci span an ancient pseudoautosomal boundary in diverse mammalian species. Proc Natl Acad Sci USA 100:5258–5263PubMedCrossRefGoogle Scholar
  14. Iwase M, Satta Y, Hirai H et al (2010) Frequent gene conversion events between the X and Y homologous chromosomal regions in primates. BMC Evol Biol 10:225PubMedCrossRefGoogle Scholar
  15. Khaitovich P, Muetzel B, She X et al (2004) Regional patterns of gene expression in human and chimpanzee brains. Genome Res 14:1462–1473PubMedCrossRefGoogle Scholar
  16. Kuroda-Kawaguchi T, Skaletsky H, Brown LG et al (2001) The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat Genet 29(3):279–286PubMedCrossRefGoogle Scholar
  17. Kuroki Y, Toyoda A, Noguchi H et al (2006) Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 38:158–167PubMedCrossRefGoogle Scholar
  18. Lahn BT, Page DC (1999) Four evolutionary strata on the human X chromosome. Science 286:964–967PubMedCrossRefGoogle Scholar
  19. Lahn BT, Page DC (2000) A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. Hum Mol Genet 9:311–319PubMedCrossRefGoogle Scholar
  20. Li WH, Gu Z, Wang H et al (2001) Evolutionary analyses of the human genome. Nature (Lond) 409:847–849CrossRefGoogle Scholar
  21. Marques-Bonet T, Kidd JM, Ventura M et al (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature (Lond) 457:877–881CrossRefGoogle Scholar
  22. Perry GH, Dominy NJ, Claw KG et al (2007) Diet and the evolution of human amylase gene copy number variation. Nat Genet 39:1256–1260PubMedCrossRefGoogle Scholar
  23. Ross MT, Grafham DV, Coffey AJ et al (2005) The DNA sequence of the human X chromosome. Nature (Lond) 434:325–337CrossRefGoogle Scholar
  24. Samonte RV, Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3:65–72PubMedCrossRefGoogle Scholar
  25. Sawai H, Kawamoto Y, Takahata N et al (2004) Evolutionary relationships of major histocompatibility complex class I genes in simian primates. Genetics 166:1897–1907PubMedCrossRefGoogle Scholar
  26. Sinzelle L, Izsvák Z, Ivics Z (2009) Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci 66:1073–1093PubMedCrossRefGoogle Scholar
  27. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ et al (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature (Lond) 423:825–837CrossRefGoogle Scholar
  28. Szabó Z, Levi-Minzi SA, Christiano AM et al (1999) Sequential loss of two neighboring exons of the tropoelastin gene during primate evolution. J Mol Evol 49:664–671PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2012

Authors and Affiliations

  1. 1.Department of Evolutionary Studies of BiosystemsThe Graduate University for Advanced StudiesHayamaJapan

Personalised recommendations