Comparative analysis of chimpanzee and human y chromosomes unveils complex evolutionary pathway

Nature Genetics

Volumn 38, Issue 2, 2006, Pages 158-167

  Kuroki, Yoko ^a   Toyoda, Atsushi ^a   Noguchi, Hideki ^a   Taylor, Todd D ^a   Itoh, Takehiko ^c   Kim, Dae Soo ^d   Kim, Dae Won ^d   Choi, Sang Haeng ^d   Kim, Il Chul ^d   Choi, Han Ho ^d   Kim, Yong Sung ^d   Satta, Yoko ^f   Saitou, Naruya ^g   Yamada, Tomoyuki ^b   Morishita, Shinichi ^b   Hattori, Masahira ^a,h   Sakaki, Yoshiyuki ^a   Park, Hong Seog ^d,e   Fujiyama, Asao ^a,i  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c MITSUBISHI RESEARCH INSTITUTE   (Japan)

^d Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^e University of Science and Technology (UST)   (South Korea)

^f GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^g NATIONAL INSTITUTE OF GENETICS   (Japan)

^h KITASATO UNIVERSITY   (Japan)

ⁱ NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; HUMAN; MALE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PAN TROGLODYTES; SEQUENCE ALIGNMENT; SYNTENY; Y CHROMOSOME;

ANIMALS; CHROMOSOMES, HUMAN, Y; EVOLUTION, MOLECULAR; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PAN TROGLODYTES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYNTENY; Y CHROMOSOME;

EID: 84984761809     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1729     Document Type: Article

References (51)

1. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
3. Gagneux, P. & Varki, A. Genetic differences between humans and great apes. Mol. Phylogenet. Evol. 18, 2-13 (2001).
4. Fujiyama, A. et al. Construction and analysis of a human-chimpanzee comparative clone map. Science 295, 131-134 (2002).
5. Ebersberger, I., Metzler, D., Schwarz, C. & Paabo, S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490-1497 (2002).
6. Chou, H.H. et al. Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc. Natl. Acad. Sci. USA 99, 11736-11741 (2002).
7. Enard, W. et al. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869-872 (2002).
8. Sakaki, Y. et al. Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication. Cold Spring Harb. Symp. Quant. Biol. 68, 455-460 (2003).
9. Olson, M.V. & Varki, A. Sequencing the chimpanzee genome: Insights into human evolution and disease. Nat. Rev. Genet. 4, 20-28 (2003).
10. The International Chimpanzee Chromosome 22 Consortium. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429, 382-388 (2004).
11. Ptak, S.E. et al. Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37, 429-434 (2005).
12. Ohno, S. Sex Chromosomes and Sex-Linked Genes (Springer, Berlin, 1967).
13. Bishop, C. et al. Extensive sequence homologies between Y and other human chromosomes. J. Mol. Biol. 173, 403-417 (1984).
14. Graves, J.A. The origin and function of the mammalian Y chromosome and Y-borne genes-an evolving understanding. Bioessays 17, 311-320 (1995).
15. Lahn, B.T. & Page, D.C. Four evolutionary strata on the human X chromosome. Science 286, 964-967 (1999).
16. Waters, P.D. et al. The human Y chromosome derives largely from a single autosomal region added to the sex chromosomes 80-130 million years ago. Cytogenet. Cell Genet. 92, 74-76 (2001).
17. Lahn, B.T., Pearson, N.M. & Jegalian, K. The human Y chromosome, in the light of evolution. Nat. Rev. Genet. 2, 207-216 (2001).
18. Page, D.C., Harper, M.E., Love, J. & Botstein, D. Occurrence of a transposition from the X-chromosome long arm to the Y-chromosome short arm during human evolution. Nature 311, 119-123 (1984).
19. Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825-837 (2003).
20. Ross, M.T. et al. The DNA sequence of the human X chromosome. Nature 434, 325337 (2005).
21. Archidiacono, N. et al. Evolution of chromosome Y in primates. Chromosoma 107, 241-246 (1998).
22. Gerrard, D.T. & Filatov, D.A. Positive and negative selection on mammalian Y chromosomes. Mol. Biol. Evol. 22, 1423-1432 (2005).
23. Miyata, T. et al. Male-driven molecular evolution: A model and nucleotide sequence analysis. Cold Spring Harb. Symp. Quant. Biol. 52, 863-867 (1987).
24. Erlandsson, R., Wilson, J.F. & Paabo, S. Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans. Mol. Biol. Evol. 17, 804-812 (2000).
25. Makova, K.D. & Li, W.H. Strong male-driven evolution of DNA sequences in humans and apes. Nature 416, 624-626 (2002).
26. Saitou, N. & Ueda, S. Evolutionary rate of insertions and deletions in non-coding nucleotide sequences of primates. Mol. Biol. Evol. 11, 504-512 (1994).
27. Stone, A.C. et al. High levels of Y-chromosome nucleotide diversity in the genus Pan. Proc. Natl. Acad. Sci. USA 99, 43-48 (2002).
28. Filatov, D.A. A gradient of silent substitution rate in the human pseudoautosomal region. Mol. Biol. Evol. 21, 410 417 (2004).
29. Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
30. Liu, G. et al. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res. 13, 358-368 (2003).
31. Hedges, D.J. et al. Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 14, 1068-1075 (2004).
32. Orti, R. et al. Conservation of pericentromeric duplications of a 200-kb part of the human 21q22.1 region in primates. Cytogenet. Cell Genet. 83, 262-265 (1998).
33. Golfier, G. et al. The 200-kb segmental duplication on human chromosome 21 originates from a pericentromeric dissemination involving human chromosomes 2, 18 and 13. Gene 312, 51-59 (2003).
34. Bonner, T.I. et al. Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA. J. Virol. 43, 914-924 (1982).
35. Kjellman, C., Sjogren, H.O. & Widegren, B. The Y chromosome: A graveyard for endogenous retroviruses. Gene 161, 163-170 (1995).
36. Yohn, C.T. et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 3, e110 (2005).
37. Gibbons, R. et al. Distinguishing humans from great apes with AluYb8 repeats. J. Mol. Biol. 339, 721-729 (2004).
38. Han, K. et al. Under the genomic radar: The stealth model of Alu amplification. Genome Res. 15, 655-664 (2005).
39. Schwartz, A. et al. Reconstructing hominid Y evolution: X-homologous block, created by X-Y transposition, was disrupted by Yp inversion through LINE-LINE recombination. Hum. Mol. Genet. 7, 1-11 (1998).
40. Rosen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873-876 (2003).
41. Li, W.-H. Molecular Evolution 237-267 (Sinauer, Sunderland, Massachusetts, 1997).
42. Thomson, R., Pitchard, J.K., Shen, P., Oefner, P.J. & Feldman, M.W. Recent common ancestry of human y chromosomes: Evidence from DNA sequence data. Proc. Natl. Acad. Sci. USA 97, 7360-7365 (2000).
43. Underhill, P.A. et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 7, 947-949 (1997).
44. Underhill, P.A. et al. Y chromosome sequence variation and the history of human populations. Nat. Genet. 26, 358-361 (2000).
45. The Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339-348 (2002).
46. Kittler, R. et al. Apparent intrachromosomal exchange on the human Y chromosome explained by population history. Eur. J. Hum. Genet. 11, 304-314 (2003).
47. Kuroki, Y. et al. Spermatogenic ability is different among males in different Y chromosome lineage. J. Hum. Genet. 44, 289-292 (1999).
48. Nakahori, Y. The Y chromosome-a hypothesis on the evolution of sex chromosomes. in Sexual Differentiation and Maturation. Frontier in Endocrinology 17 (Hibi, I. & Tanaka, T., eds.) 1-14 (Ares-Serono Symposia Publications, Rome, 1996).
49. Yamada, T. & Morishita, S. Computing highly specific and noise tolerant oligomers efficiently. J. Bioinform. Comput. Biol. 2, 21-46 (2004).
50. Brudno, M. et al. LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731 (2003).
51. Hughes, J.F. et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing. Nature 437, 100-105 (2005).