Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation

Michael F Hammer, Tatiana Karafet, A. Rasanayagam, E. T. Wood, T. K. Altheide, T. Jenkins, R. C. Griffiths, A. R. Templeton, S. L. Zegura

Research output: Contribution to journalArticle

265 Citations (Scopus)

Abstract

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of ~150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested claristic analyses of human mtDNA and β-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.

Original languageEnglish (US)
Pages (from-to)427-441
Number of pages15
JournalMolecular Biology and Evolution
Volume15
Issue number4
StatePublished - 1998

Fingerprint

Chromosomes, Human, Y
Y chromosome
cladistics
Chromosomes
chromosome
range expansion
Genes
Y Chromosome
phylogeny
Haplotypes
haplotypes
Gene Flow
Population
gene flow
Globins
replacement
Coalescence
Oceania
Mitochondrial DNA
Gene Pool

Keywords

  • Coalescence times
  • Human evolution
  • Nested cladistic test
  • Population structure
  • Y chromosome haplotypes

ASJC Scopus subject areas

  • Molecular Biology
  • Agricultural and Biological Sciences (miscellaneous)
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Biochemistry
  • Genetics

Cite this

Hammer, M. F., Karafet, T., Rasanayagam, A., Wood, E. T., Altheide, T. K., Jenkins, T., ... Zegura, S. L. (1998). Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation. Molecular Biology and Evolution, 15(4), 427-441.

Out of Africa and back again : Nested cladistic analysis of human Y chromosome variation. / Hammer, Michael F; Karafet, Tatiana; Rasanayagam, A.; Wood, E. T.; Altheide, T. K.; Jenkins, T.; Griffiths, R. C.; Templeton, A. R.; Zegura, S. L.

In: Molecular Biology and Evolution, Vol. 15, No. 4, 1998, p. 427-441.

Research output: Contribution to journalArticle

Hammer, MF, Karafet, T, Rasanayagam, A, Wood, ET, Altheide, TK, Jenkins, T, Griffiths, RC, Templeton, AR & Zegura, SL 1998, 'Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation', Molecular Biology and Evolution, vol. 15, no. 4, pp. 427-441.
Hammer, Michael F ; Karafet, Tatiana ; Rasanayagam, A. ; Wood, E. T. ; Altheide, T. K. ; Jenkins, T. ; Griffiths, R. C. ; Templeton, A. R. ; Zegura, S. L. / Out of Africa and back again : Nested cladistic analysis of human Y chromosome variation. In: Molecular Biology and Evolution. 1998 ; Vol. 15, No. 4. pp. 427-441.
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