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  • Review Article
  • Published:

The human Y chromosome: an evolutionary marker comes of age

Nature Reviews Genetics volume 4, pages 598–612 (2003)Cite this article

Key Points

  • The human Y chromosome is male-sex-determining and haploid, and so escapes recombination for most of its length. Haplotypes, which can be defined by the many binary markers and microsatellites that are available, pass down paternal lineages and change only by mutation.

  • A small effective population size and the practice of patrilocality accentuate drift, which leads to the marked geographical differentiation of Y haplotypes. This makes the Y chromosome a powerful tool for investigating events in human genetic history.

  • The study of mutation on the Y chromosome clarifies intra-allelic processes in general, and provides specific information about mutation rates that is useful in estimating the coalescent times of lineages. Intrachromosomal paralogous sequences are plentiful and cause pathogenic and non-pathogenic structural rearrangements.

  • Selection might be important in shaping Y-chromosome diversity in populations, but it has been difficult to identify. Some studies show associations between deleterious phenotypes and particular haplotypes, but these associations are weak; some coalescence times are younger than expected, which indicates recent selection, but these estimates are uncertain, and population phenomena might be an alternative explanation.

  • The phylogeny of binary Y haplogroups is well established, but the dates of branchpoints are uncertain. Many populations have been poorly sampled, and there is ascertainment bias in the set of available binary markers.

  • The recent coalescence time, rooting of the Y phylogeny in Africa and evidence for an 'Out-of-Africa' range expansion, all show that modern Y-chromosome diversity arose recently in Africa and replaced Y chromosomes elsewhere. The pattern of Y-chromosome variation broadly fits a model of a southern migration that reached Australia, and a northern migration into Eurasia.

  • Many features of the patterns of modern Y-chromosome diversity reflect later range expansions and contractions that were driven by changes in climate and lifestyle. Long-term population size, social structures and social selection have also been important.

  • Future developments in the field are likely to include more markers, and a move towards the unbiased resequencing of samples.

  • Other parts of the genome might show a 'haplotype-block' structure that is made up of regions of strong linkage disequilibrium. If this is so, then methods pioneered in the analysis of the Y chromosome could be widely applicable.

Abstract

Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes — rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up.

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Figure 1: Y-chromosomal genes.
Figure 2: Global distribution of Y haplogroups.
Figure 3: The phylogenetic tree of binary Y-chromosomal haplogroups.

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References

  1. Skaletsky, H. et al. The male-specific region of the human Y chromosome: a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Analysis and evolutionary interpretation of the near-complete sequence of Y euchromatin, including thorough gene identification.

    CAS  PubMed  Google Scholar 

  2. Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003–1007 (2002).

    Article  CAS  PubMed  Google Scholar 

  3. Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12, 339–348 (2002). A collaborative effort by most of the groups in the field to produce a unified phylogeny and nomenclature, with a built-in updating mechanism, which is becoming widely adopted.

  4. Hammer, M. F. A recent common ancestry for human Y chromosomes. Nature 378, 376–378 (1995).

    CAS  PubMed  Google Scholar 

  5. Thomson, R., Pritchard, 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). The largest study of Y-SNP variation free from ascertainment bias, which is based on DHPLC and proposes a common ancestor ∼59 kya.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Murdock, G. P. Ethnographic Atlas (Univ. of Pittsburgh Press, Pittsburgh, 1967).

    Google Scholar 

  7. Burton, M. L., Moore, C. C., Whiting, J. W. M. & Romney, A. K. Regions based on social structure. Curr. Anthropol. 37, 87–123 (1996).

    Google Scholar 

  8. Seielstad, M. T., Minch, E. & Cavalli-Sforza, L. L. Genetic evidence for a higher female migration rate in humans. Nature Genet. 20, 278–280 (1998). This paper proposed that patrilocality, the practice of a wife moving near to the birthplace of her husband after marriage rather than vice versa , could explain most of the excess geographical clustering of Y variants.

    CAS  PubMed  Google Scholar 

  9. Kayser, M. et al. Independent histories of human Y chromosomes from Melanesia and Australia. Am. J. Hum. Genet. 68, 173–190 (2001).

    CAS  PubMed  Google Scholar 

  10. Oota, H., Settheetham-Ishida, W., Tiwawech, D., Ishida, T. & Stoneking, M. Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nature Genet. 29, 20–21 (2001). Empirical support for the hypothesis of Seielstad et al . in reference 8.

    CAS  PubMed  Google Scholar 

  11. Nachman, M. W. & Crowell, S. L. Estimate of the mutation rate per nucleotide in humans. Genetics 156, 297–304 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Crow, J. F. The origins, patterns and implications of human spontaneous mutation. Nature Rev. Genet. 1, 40–47 (2000).

    CAS  PubMed  Google Scholar 

  13. Ebersberger, I., Metzler, D., Schwarz, C. & Pääbo, S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490–1497 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Blanco, P. et al. Divergent outcomes of intra-chromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J. Med. Genet. 37, 752–758 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Kamp, C., Hirschmann, P., Voss, H., Huellen, K. & Vogt, P. H. Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events. Hum. Mol. Genet. 9, 2563–2572 (2000).

    CAS  PubMed  Google Scholar 

  16. Sun, C. et al. Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses. Hum. Mol. Genet. 9, 2291–2296 (2000).

    CAS  PubMed  Google Scholar 

  17. Repping, S. et al. Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure. Am. J. Hum. Genet. 71, 906–922 (2002).

    PubMed  PubMed Central  Google Scholar 

  18. Kuroda-Kawaguchi, T. et al. The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nature Genet. 29, 279–286 (2001).

    CAS  PubMed  Google Scholar 

  19. Bosch, E. & Jobling, M. A. Duplications of the AZFa region of the human Y chromosome are mediated by homologous recombination between HERVs and are compatible with male fertility. Hum. Mol. Genet. 12, 341–347 (2003).

    CAS  PubMed  Google Scholar 

  20. Rozen, S. et al. Abundant gene conversion between arms of massive palindromes in human and ape Y chromosomes. Nature 423, 873–876 (2003).

    CAS  PubMed  Google Scholar 

  21. Heyer, E., Puymirat, J., Dieltjes, P., Bakker, E. & de Knijff, P. Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum. Mol. Genet. 6, 799–803 (1997).

    CAS  PubMed  Google Scholar 

  22. Kayser, M. et al. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am. J. Hum. Genet. 66, 1580–1588 (2000). Still the largest published study to measure the mutation rates at Y-chromosomal microsatellites using father–son pairs. This is more laborious than using deep-rooting pedigrees or sperm pools, but produces more reliable measurements.

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Carvalho-Silva, D. R., Santos, F. R., Hutz, M. H., Salzano, F. M. & Pena, S. D. J. Divergent human Y-chromosome microsatellite evolution rates. J. Mol. Evol. 49, 204–214 (1999).

    CAS  PubMed  Google Scholar 

  24. Holtkemper, U., Rolf, B., Hohoff, C., Forster, P. & Brinkmann, B. Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR techniques. Hum. Mol. Genet. 10, 629–633 (2001).

    CAS  PubMed  Google Scholar 

  25. Jeffreys, A. J., Murray, J. & Neumann, R. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol. Cell 2, 267–273 (1998).

    CAS  PubMed  Google Scholar 

  26. Jobling, M. A., Bouzekri, N. & Taylor, P. G. Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1). Hum. Mol. Genet. 7, 643–653 (1998).

    CAS  PubMed  Google Scholar 

  27. Jobling, M. A., Heyer, E., Dieltjes, P. & de Knijff, P. Y-chromosome-specific microsatellite mutation rates re-examined using a minisatellite, MSY1. Hum. Mol. Genet. 8, 2117–2120 (1999).

    CAS  PubMed  Google Scholar 

  28. Andreassen, R., Lundsted, J. & Olaisen, B. Mutation at minisatellite locus DYF155S1: allele length mutation rate is affected by age of progenitor. Electrophoresis 23, 2377–2383 (2002).

    CAS  PubMed  Google Scholar 

  29. Berta, P. et al. Genetic evidence equating SRY and the testis-determining factor. Nature 348, 448–450 (1990).

    CAS  PubMed  Google Scholar 

  30. Sun, C. et al. An azoospermic man with a de novo point mutation in the Y-chromosomal gene USP9Y. Nature Genet. 23, 429–432 (1999).

    CAS  PubMed  Google Scholar 

  31. Kuroki, Y. et al. Spermatogenic ability is different among males in different Y chromosome lineages. J. Hum. Genet. 44, 289–292 (1999).

    CAS  PubMed  Google Scholar 

  32. Carvalho, C. M. et al. Lack of association between Y chromosome haplogroups and male infertility in Japanese men. Am. J. Med. Genet. 116, 152–158 (2003).

    Google Scholar 

  33. Previderé, C. et al. Y-chromosomal DNA haplotype differences in control and infertile Italian subpopulations. Eur. J. Hum. Genet. 7, 733–736 (1999).

    PubMed  Google Scholar 

  34. Jobling, M. A. et al. A selective difference between human Y-chromosomal DNA haplotypes. Curr. Biol. 8, 1391–1394 (1998). The first example of differential selection acting on Y haplogroups, which is supported by a plausible molecular mechanism.

    CAS  PubMed  Google Scholar 

  35. Krausz, C. et al. Identification of a Y chromosome haplogroup associated with reduced sperm counts. Hum. Mol. Genet. 10, 1873–1877 (2001).

    CAS  PubMed  Google Scholar 

  36. Raitio, M. et al. Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays. Genome Res. 11, 471–482 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Paracchini, S., Arredi, B., Chalk, R. & Tyler-Smith, C. Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry. Nucleic Acids Res. 30, e27 (2002).

    PubMed  PubMed Central  Google Scholar 

  38. Zerjal, T. et al. The genetic legacy of the Mongols. Am. J. Hum. Genet. 72, 717–721 (2003). Selective expansion of a single Y haplotype, which is explained by a social rather than a biological mechanism.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Pritchard, J. K., Seielstad, M. T., Perez-Lezaun, A. & Feldman, M. W. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16, 1791–1798 (1999).

    CAS  PubMed  Google Scholar 

  40. Hammer, M. F. & Zegura, S. L. The human Y chromosome haplogroup tree: nomenclature and phylogeny of its major divisions. Annu. Rev. Anthropol. 31, 303–321 (2002).

    Google Scholar 

  41. Ingman, M., Kaessmann, H., Paabo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 (2000).

    CAS  PubMed  Google Scholar 

  42. Kaessmann, H., Heissig, F., von Haeseler, A. & Paabo, S. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nature Genet. 22, 78–81 (1999).

    CAS  PubMed  Google Scholar 

  43. Harris, E. E. & Hey, J. X chromosome evidence for ancient human histories. Proc. Natl Acad. Sci. USA 96, 3320–3324 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Harding, R. M. et al. Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60, 772–789 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Tremblay, M. & Vezina, H. New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am. J. Hum. Genet. 66, 651–658 (2000). Genealogical research in Quebec, Canada, which shows that the male generation time in this population (∼35 years) is longer than the female generation time (∼29 years) and considerably longer than is commonly assumed (20–25 years).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Helgason, A., Hrafnkelsson, B., Gulcher, J. R., Ward, R. & Stefansson, K. A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes. Am. J. Hum. Genet. 72, 1370–1389 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Brunet, M. et al. A new hominid from the Upper Miocene of Chad, Central Africa. Nature 418, 145–151 (2002).

    CAS  PubMed  Google Scholar 

  48. Jobling, M. A. & Tyler-Smith, C. New uses for new haplotypes: the human Y chromosome, disease, and selection. Trends Genet. 16, 356–362 (2000).

    CAS  PubMed  Google Scholar 

  49. Shen, P. et al. Population genetic implications from sequence variation in four Y chromosome genes. Proc. Natl Acad. Sci. USA 97, 7354–7359 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Hurles, M. E. et al. Native American Y chromosomes in Polynesia: the genetic impact of the Polynesian slave trade. Am. J. Hum. Genet. 72, 1282–1287 (2003). This paper shows the importance of taking historical information into account when interpreting genetic data.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Heyerdahl, T. Kontiki: Across the Pacific by Raft (Rand McNally, Chicago, 1950).

    Google Scholar 

  52. Swisher, C. C. et al. Age of the earliest known hominids in Java, Indonesia. Science 263, 1118–1121 (1994).

    CAS  PubMed  Google Scholar 

  53. Gabunia, L. et al. Earliest Pleistocene hominid cranial remains from Dmanisi, Republic of Georgia: taxonomy, geological setting, and age. Science 288, 1019–1025 (2000).

    CAS  PubMed  Google Scholar 

  54. Bermúdez de Castro, J. M. et al. A hominid from the lower Pleistocene of Atapuerca, Spain: possible ancestor to Neandertals and modern humans. Science 276, 1392–1395 (1997).

    PubMed  Google Scholar 

  55. White, T. D. et al. Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423, 742–747 (2003).

    CAS  PubMed  Google Scholar 

  56. Valladas, H. et al. Thermoluminescence dating of Mousterian 'proto-Cro-Magnon' remains from Israel and the origin of modern man. Nature 331, 614–616 (1988).

    Google Scholar 

  57. Valladas, H. et al. Thermoluminescence dates for the Neanderthal burial site at Kebara in Israel. Nature 330, 159–160 (1987).

    Google Scholar 

  58. Mellars, P. Archaeology and the origins of modern humans: European and African perspectives. Proc. Brit. Acad. 106, 31–47 (2002).

    Google Scholar 

  59. Hammer, M. F. et al. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol. Biol. Evol. 15, 427–441 (1998). A sophisticated model-based approach to testing hypotheses to explain patterns of global Y diversity.

    CAS  PubMed  Google Scholar 

  60. Cruciani, F. et al. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am. J. Hum. Genet. 70, 1197–1214 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Underhill, P. A. et al. Y chromosome sequence variation and the history of human populations. Nature Genet. 26, 358–361 (2000). This study introduced 160 new binary Y markers and revealed much of the shape of the Y phylogeny and the geographical distribution of lineages.

    CAS  PubMed  Google Scholar 

  62. Bowler, J. M. et al. New ages for human occupation and climatic change at Lake Mungo, Australia. Nature 421, 837–840 (2003).

    CAS  PubMed  Google Scholar 

  63. Goebel, T. Pleistocene human colonization of Siberia and peopling of the Americas: an ecological approach. Evol. Anthropol. 8, 208–227 (1999).

    Google Scholar 

  64. Mellars, P. in The Speciation of Modern Homo sapiens (ed. Crow, T. J.) 31–47 (Oxford Univ. Press, Oxford, UK, 2002).

    Google Scholar 

  65. Redd, A. J. et al. Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome. Curr. Biol. 12, 673–677 (2002).

    CAS  PubMed  Google Scholar 

  66. Zerjal, T. et al. Genetic relationships of Asians and northern Europeans, revealed by Y-chromosomal DNA analysis. Am. J. Hum. Genet. 60, 1174–1183 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Phillipson, D. W. African Archaeology 2nd edn (Cambridge Univ. Press, Cambridge, 1993).

    Google Scholar 

  68. Rosser, Z. H. et al. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am. J. Hum. Genet. 67, 1526–1543 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Semino, O. et al. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290, 1155–1159 (2000).

    CAS  PubMed  Google Scholar 

  70. Bhattacharyya, N. P. et al. Negligible male gene flow across ethnic boundaries in India, revealed by analysis of Y-chromosomal DNA polymorphisms. Genome Res. 9, 711–719 (1999).

    CAS  PubMed  Google Scholar 

  71. Ramana, G. V. et al. Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur. J. Hum. Genet. 9, 695–700 (2001).

    CAS  PubMed  Google Scholar 

  72. Kivisild, T. et al. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am. J. Hum. Genet. 72, 313–332 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Karafet, T. M. et al. High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter–gatherer way of life. Hum. Biol. 74, 761–789 (2002). A good example of what can be done with the present set of markers and analytical tools.

    PubMed  Google Scholar 

  74. Zerjal, T., Wells, R. S., Yuldasheva, N., Ruzibakiev, R. & Tyler-Smith, C. A genetic landscape reshaped by recent events: Y-chromosomal insights into Central Asia. Am. J. Hum. Genet. 71, 466–482 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Meltzer, D. A. Monte Verde and the Pleistocene peopling of the Americas. Science 276, 754–755 (1997).

    CAS  Google Scholar 

  76. Pena, S. D. et al. A major founder Y-chromosome haplotype in Amerindians. Nature Genet. 11, 15–16 (1995).

    CAS  PubMed  Google Scholar 

  77. Underhill, P. A., Jin, L., Zemans, R., Oefner, P. J. & Cavalli-Sforza, L. L. A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc. Natl Acad. Sci. USA 93, 196–200 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Karafet, T. M. et al. Ancestral Asian source(s) of New World Y-chromosome founder haplotypes. Am. J. Hum. Genet. 64, 817–831 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Lell, J. T. et al. The dual origin and Siberian affinities of Native American Y chromosomes. Am. J. Hum. Genet. 70, 192–206 (2002).

    CAS  PubMed  Google Scholar 

  80. Tarazona-Santos, E. & Santos, F. R. The peopling of the Americas: a second major migration? Am. J. Hum. Genet. 70, 1377–1380 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Hurles, M. E. et al. European Y-chromosomal lineages in Polynesia: a contrast to the population structure revealed by mitochondrial DNA. Am. J. Hum. Genet. 63, 1793–1806 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Saillard, J., Forster, P., Lynnerup, N., Bandelt, H. -J. & Nørby, S. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am. J. Hum. Genet. 67, 718–726 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Bosch, E. et al. High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis. Hum. Genet. 112, 353–363 (2003).

    PubMed  Google Scholar 

  84. Alves-Silva, J. et al. The ancestry of Brazilian mtDNA lineages. Am. J. Hum. Genet. 67, 444–461 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Carvalho-Silva, D. R., Santos, F. R., Rocha, J. & Pena, S. D. J. The phylogeography of Brazilian Y-chromosome lineages. Am. J. Hum. Genet. 68, 281–286 (2001).

    CAS  PubMed  Google Scholar 

  86. Carvajal-Carmona, L. G. et al. Strong Amerind/white sex bias and a possible Sephardic contribution among the founders of a population in northwest Colombia. Am. J. Hum. Genet. 67, 1287–1295 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Roewer, L. et al. Online reference database of Y-chromosomal short tandem repeat (STR) haplotypes. Forens. Sci. Int. 118, 103–111 (2001).

    Google Scholar 

  88. Butler, J. M. et al. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci. Int. 129, 10–24 (2002).

    CAS  PubMed  Google Scholar 

  89. Di Bernardo, G. et al. Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucl. Acids Res. 30, e16 (2002).

    PubMed  PubMed Central  Google Scholar 

  90. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).

  91. Su, B. et al. Y-chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. Am. J. Hum. Genet. 65, 1718–1724 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Karafet, T. et al. Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am. J. Hum. Genet. 69, 615–628 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Eyre-Walker, A. & Awadalla, P. Does human mtDNA recombine? J. Mol. Evol. 53, 430–435 (2001).

    CAS  PubMed  Google Scholar 

  94. Walzer, S. & Gerald, P. S. A chromosome survey of 13,751 male newborns. in Population Cytogenetics (eds Hook, E. B. & Porter, I. H.) 45–61 (Academic Press, New York, 1977).

    Google Scholar 

  95. Chevret, E. et al. Meiotic behaviour of sex chromosomes investigated by three-colour FISH on 35 142 sperm nuclei from two 47, XYY males. Hum. Genet. 99, 407–412 (1997).

    CAS  PubMed  Google Scholar 

  96. Solari, A. J. & Rey-Valzacchi, G. The prevalence of a YY synaptonemal complex over XY synapsis in an XYY man with exclusive XYY spermatocytes. Chrom. Res. 5, 467–474 (1997).

    CAS  PubMed  Google Scholar 

  97. Pecon-Slattery, J., Sanner-Wachter, L. & O'Brien, S. J. Novel gene conversion between X-Y homologues located in the nonrecombining region of the Y chromosome in Felidae (Mammalia). Proc. Natl Acad. Sci. USA 97, 5307–5712 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Cooke, H. J. & Noel, B. Confirmation of Y/autosome translocations using recombinant DNA. Hum. Genet. 50, 39–44 (1979).

    CAS  PubMed  Google Scholar 

  99. Andersson, M. et al. Y;autosome translocations and mosaicism in the aetiology of 45,X maleness: assignment of fertility factor to distal Yq11. Hum. Genet. 79, 2–7 (1988).

    CAS  PubMed  Google Scholar 

  100. Juvaini, A. -M. The History of the World-Conqueror (UNESCO publishing, 1260) (translated in 1997).

    Google Scholar 

  101. Gill, P., Jeffreys, A. J. & Werrett, D. J. Forensic application of DNA 'fingerprints'. Nature 318, 577–579 (1985).

    CAS  PubMed  Google Scholar 

  102. Sibille, I. et al. Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa. Forens. Sci. Int. 125, 212–216 (2002).

    CAS  Google Scholar 

  103. Rolf, B., Keil, W., Brinkmann, B., Roewer, L. & Fimmers, R. Paternity testing using Y-STR haplotypes: assigning a probability for paternity in cases of mutations. Int. J. Legal Med. 115, 12–15 (2001).

    CAS  PubMed  Google Scholar 

  104. Kayser, M. et al. Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for US populations. J. Forens. Sci. 47, 513–519 (2002).

    Google Scholar 

  105. Jobling, M. A. In the name of the father: surnames and genetics. Trends Genet. 17, 353–357 (2001).

    CAS  PubMed  Google Scholar 

  106. Sykes, B. & Irven, C. Surnames and the Y chromosome. Am. J. Hum. Genet. 66, 1417–1419 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. & Lander, E. S. High-resolution haplotype structure in the human genome. Nature Genet. 29, 229–232 (2001).

    CAS  PubMed  Google Scholar 

  108. Jeffreys, A. J., Kauppi, L. & Neumann, R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genet. 29, 217–222 (2001).

    CAS  PubMed  Google Scholar 

  109. Phillips, M. S. et al. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nature Genet. 33, 382–387 (2003).

    CAS  PubMed  Google Scholar 

  110. Kauppi, L., Sajantila, A. & Jeffreys, A. J. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum. Mol. Genet. 12, 33–40 (2003).

    CAS  PubMed  Google Scholar 

  111. Santos, F. R., Pandya, A. & Tyler-Smith, C. Reliability of DNA-based sex tests. Nature Genet. 18, 103 (1998).

    CAS  PubMed  Google Scholar 

  112. Semino, O., Santachiara-Benerecetti, A. S., Falaschi, F., Cavalli-Sforza, L. L. & Underhill, P. A. Ethiopians and Khoisan share the deepest clades of the human Y-chromosome phylogeny. Am. J. Hum. Genet. 70, 265–268 (2002).

    CAS  PubMed  Google Scholar 

  113. Wells, R. S. et al. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc. Natl Acad. Sci. USA 98, 10244–10249 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Qian, Y. et al. Multiple origins of Tibetan Y chromosomes. Hum. Genet. 106, 453–454 (2000).

    CAS  PubMed  Google Scholar 

  115. Kayser, M. et al. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am. J. Hum. Genet. 72, 281–302 (2003).

    CAS  PubMed  Google Scholar 

  116. Capelli, C. et al. A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania. Am. J. Hum. Genet. 68, 432–443 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Underhill, P. A. et al. Maori origins, Y-chromosome haplotypes and implications for human history in the Pacific. Hum. Mutat. 17, 271–280 (2001).

    CAS  PubMed  Google Scholar 

  118. Tarazona-Santos, E. et al. Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome. Am. J. Hum. Genet. 68, 1485–1496 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Thangaraj, K. et al. Genetic affinities of the Andaman islanders, a vanishing human population. Curr. Biol. 13, 86–93 (2003).

    CAS  PubMed  Google Scholar 

  120. Paracchini, S. et al. Y-chromosomal DNA haplotypes in infertile European males carrying Y-microdeletions. J. Endocrinol. Invest. 23, 671–676 (2000).

    CAS  PubMed  Google Scholar 

  121. Quintana-Murci, L. et al. The relationship between Y chromosome DNA haplotypes and Y chromosome deletions leading to male infertility. Hum. Genet. 108, 55–58 (2001).

    CAS  PubMed  Google Scholar 

  122. Paracchini, S. et al. Relationship between Y-chromosomal DNA haplotype and sperm count in Italy. J. Endocrinol. Invest. 25, 993–995 (2002).

    CAS  PubMed  Google Scholar 

  123. Kittles, R. A. et al. Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits. Proc. Natl Acad. Sci. USA 96, 4204–4209 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Ellis, J. A., Stebbing, M. & Harrap, S. B. Significant population variation in adult male height associated with the Y chromosome and the aromatase gene. J. Clin. Endocrinol. Metab. 86, 4147–4150 (2001).

    CAS  PubMed  Google Scholar 

  125. Charchar, F. J. et al. The Y chromosome effect on blood pressure in two European populations. Hypertension 39, 353–356 (2002).

    CAS  PubMed  Google Scholar 

  126. Ellis, J. A., Stebbing, M. & Harrap, S. B. Association of the human Y chromosome with high blood pressure in the general population. Hypertension 36, 731–733 (2000).

    CAS  PubMed  Google Scholar 

  127. Shoji, M. et al. Lack of association between Y chromosome Alu insertion polymorphism and hypertension. Hypertens. Res. 25, 1–3 (2002).

    CAS  PubMed  Google Scholar 

  128. Ewis, A. A. et al. Linkage between prostate cancer incidence and different alleles of the human Y-linked tetranucleotide polymorphism DYS19. J. Med. Invest. 49, 56–60 (2002).

    PubMed  Google Scholar 

  129. Quintana-Murci, L. et al. Y chromosome haplotypes and testicular cancer in the English population. J. Med. Genet. 40, e20 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Passarino, G. et al. Y chromosome binary markers to study the high prevalence of males in Sardinian centenarians and the genetic structure of the Sardinian population. Hum. Hered. 52, 136–139 (2001).

    CAS  PubMed  Google Scholar 

  131. Jamain, S. et al. Y chromosome haplogroups in autistic subjects. Mol. Psychiatry 7, 217–219 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank T. Karafet for unpublished information on American populations, the Y Chromosome Consortium for consultation and for allowing us to include figure 3, and M. Hurles, F. Santos and three anonymous reviewers for helpful comments on the manuscript. M.A.J. is supported by a Wellcome Trust Senior Fellowship in Basic Biomedical Science. We apologize to those collegues whose work we could not cite because of limited space.

Author information

Authors and Affiliations

  1. Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK

    Mark A. Jobling

  2. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK

    Chris Tyler-Smith

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Related links

Related links

Databases

LocusLink

PRKX

PRKY

USP9Y

Further information

BATWING program

Ensembl

Phylogenetic Network Analysis Shareware Software

Y Chromosome Consortium

Y-STR Haplotype Reference Database Asia

Y-STR Haplotype Reference Database Europe

Y-STR Haplotype Reference Database for US Populations

Glossary

SATELLITE DNA

A large tandemly-repeated DNA array that spans hundreds of kilobases to megabases.

RECOMBINATION

The formation of a new combination of alleles through meiotic crossing over. Some authors include intrachromosomal gene conversion under this heading. As this has been shown on the Y chromosome, they prefer not to refer to it as 'non-recombining'.

EUCHROMATIN

The part of the genome that is decondensed during interphase, which is transcriptionally active.

PHYLOGENETIC TREE

A diagram that represents the evolutionary relationships between a set of taxa (lineages).

PARALOGUES

Sequences, or genes, that have originated from a common ancestral sequence, or gene, by a duplication event.

MICROSATELLITE

A class of repetitive DNA sequences that are made up of tandemly organized repeats that are 2-8 nucleotides in length. They can be highly polymorphic and are frequently used as molecular markers in population genetics studies.

HAPLOGROUP

A haplotype that is defined by binary markers, which is more stable but less detailed than one defined by microsatellites.

NRY, NRPY AND MSY

Several neologisms have been introduced to refer to the portion of the Y chromosome that excludes the pseudoautosomal regions, for example, non-recombining Y (NRY), non-recombining portion Y (NRPY) and male-specific Y (MSY), but none has achieved wide acceptance.

EFFECTIVE POPULATION SIZE

The size of an idealized population that shows the same amount of genetic drift as the population studied. This is approximately 10,000 individuals for humans, in contrast to the census population size of >6 × 109.

PARAGROUP

A group of haplotypes that contain some, but not all, of the descendants of an ancestral lineage.

HOMOLOGUES

Genes or sequences that share a common ancestor.

HOMOPLASY

The generation of the same sequence state at a locus by independent routes (convergent evolution).

GENE CONVERSION

The non-reciprocal exchange of sequence.

BALANCING SELECTION

Selection that favours more than one allele, for example, through heterozygote advantage, and so maintains polymorphism.

FREQUENCY-DEPENDENT SELECTION

Selection that favours the lower-frequency alleles and so maintains polymorphism.

XX MALE

An individual with a 46,XX karyotype but a male phenotype rather than the expected female phenotype

PHYLOGEOGRAPHY

The analysis of the geographical distributions of the different branches of a phylogeny.

MULTIFURCATION/BIFURCATION

The splitting of an ancestral lineage into two or more daughter lineages.

HOLOCENE

The 'wholly recent' geological period that spans the past ∼11,000 years and is characterized by an unusually warm and stable climate.

AZOOSPERMIA

The absence of sperm in the ejaculate.

ENDOGAMY

The practice of marrying within a social group.

ΦST

A measure of the subdivision between populations that takes into account the molecular distance between haplogroups/haplotypes, as well as their frequency.

LINKAGE DISEQUILIBRIUM

The non-random association between alleles in a population owing to their tendency to be co-inherited.

HAPLOTYPE BLOCK

The apparent haplotypic structure of the recombining portions of the genome, in which sets of consecutive co-inherited alleles are separated by short boundaries; there is debate about the origins of haplotype blocks and whether the boundaries correspond to recombination hotspots.

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Jobling, M., Tyler-Smith, C. The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4, 598–612 (2003). https://doi.org/10.1038/nrg1124

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