Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa

Maya Metni Pilkington, Jason A. Wilder, Fernando L. Mendez, Murray P. Cox, August Woerner, Thiep Angui, Sarah Kingan, Zahra Mobasher, Chiara Batini, Giovanni Destro-Bisol, Himla Soodyall, Beverly I. Strassmann, Michael F Hammer

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R2 statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.

Original languageEnglish (US)
Pages (from-to)517-525
Number of pages9
JournalMolecular Biology and Evolution
Volume25
Issue number3
DOIs
StatePublished - Mar 2008

Fingerprint

Chromosomes, Human, Y
Population Growth
Y chromosome
Chromosomes
Mitochondrial DNA
human population
mitochondrial DNA
chromosome
population growth
effective population size
Polymorphism
polymorphism
food
Population
Population Density
Statistics
DNA
population size
population bottleneck
Electron Transport Complex IV

Keywords

  • Homo sapiens
  • Hunter-gatherer
  • mtDNA
  • NRY
  • Population growth
  • Sub-Saharan Africa

ASJC Scopus subject areas

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

Cite this

Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa. / Pilkington, Maya Metni; Wilder, Jason A.; Mendez, Fernando L.; Cox, Murray P.; Woerner, August; Angui, Thiep; Kingan, Sarah; Mobasher, Zahra; Batini, Chiara; Destro-Bisol, Giovanni; Soodyall, Himla; Strassmann, Beverly I.; Hammer, Michael F.

In: Molecular Biology and Evolution, Vol. 25, No. 3, 03.2008, p. 517-525.

Research output: Contribution to journalArticle

Pilkington, MM, Wilder, JA, Mendez, FL, Cox, MP, Woerner, A, Angui, T, Kingan, S, Mobasher, Z, Batini, C, Destro-Bisol, G, Soodyall, H, Strassmann, BI & Hammer, MF 2008, 'Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa', Molecular Biology and Evolution, vol. 25, no. 3, pp. 517-525. https://doi.org/10.1093/molbev/msm279
Pilkington, Maya Metni ; Wilder, Jason A. ; Mendez, Fernando L. ; Cox, Murray P. ; Woerner, August ; Angui, Thiep ; Kingan, Sarah ; Mobasher, Zahra ; Batini, Chiara ; Destro-Bisol, Giovanni ; Soodyall, Himla ; Strassmann, Beverly I. ; Hammer, Michael F. / Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa. In: Molecular Biology and Evolution. 2008 ; Vol. 25, No. 3. pp. 517-525.
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AU - Woerner, August

AU - Angui, Thiep

AU - Kingan, Sarah

AU - Mobasher, Zahra

AU - Batini, Chiara

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N2 - A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R2 statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.

AB - A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R2 statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.

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