Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data

Daniel Garrigan, Sarah B. Kingan, Maya M. Pilkington, Jason A Wilder, Murray P. Cox, Himla Soodyall, Beverly Strassmann, Giovanni Destro-Bisol, Peter De Knijff, Andrea Novelletto, Jonathan Friedlaender, Michael F. Hammer

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population ∼40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history of population bottlenecks and suggest that they began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian populations.

Original languageEnglish (US)
Pages (from-to)2195-2207
Number of pages13
JournalGenetics
Volume177
Issue number4
DOIs
StatePublished - Dec 2007
Externally publishedYes

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Gene Flow
Y Chromosome
X Chromosome
Population Density
Population
Y-Linked Genes
Mitochondrial Genes
Mitochondrial DNA
Markov Chains

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data. / Garrigan, Daniel; Kingan, Sarah B.; Pilkington, Maya M.; Wilder, Jason A; Cox, Murray P.; Soodyall, Himla; Strassmann, Beverly; Destro-Bisol, Giovanni; De Knijff, Peter; Novelletto, Andrea; Friedlaender, Jonathan; Hammer, Michael F.

In: Genetics, Vol. 177, No. 4, 12.2007, p. 2195-2207.

Research output: Contribution to journalArticle

Garrigan, D, Kingan, SB, Pilkington, MM, Wilder, JA, Cox, MP, Soodyall, H, Strassmann, B, Destro-Bisol, G, De Knijff, P, Novelletto, A, Friedlaender, J & Hammer, MF 2007, 'Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data', Genetics, vol. 177, no. 4, pp. 2195-2207. https://doi.org/10.1534/genetics.107.077495
Garrigan, Daniel ; Kingan, Sarah B. ; Pilkington, Maya M. ; Wilder, Jason A ; Cox, Murray P. ; Soodyall, Himla ; Strassmann, Beverly ; Destro-Bisol, Giovanni ; De Knijff, Peter ; Novelletto, Andrea ; Friedlaender, Jonathan ; Hammer, Michael F. / Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data. In: Genetics. 2007 ; Vol. 177, No. 4. pp. 2195-2207.
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