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Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population

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Abstract

The inference of the demographic history of populations from genetic variability data is not only of academic interest. It also provides background information for the identification of genes which may have played a role in human evolution or in the aetiology of human disease. To obtain a clear picture of this background, it is necessary to compare data obtained from a number of genomic loci. Due to its very low recombination rate, the NF1 gene region can be regarded as a further suitable locus. A combined resequencing and SNP typing project in a European population disclosed the presence of only two well separated subgroups of NF1 sequences. Statistical analysis revealed a bimodal distribution of the pairwise differences, a positive value of Tajima’s D and a TMRCA of 700,000 years for the whole sample, and pairwise differences indicative for a growing population and TMRCAs of 130,000 to 150,000 years for the subgroups. Together, the data lead to a model that the recent European population went through a bottleneck during the last 150,000 years of its history. Regarding the given timeframe, this bottleneck could either reflect a speciation event which led to the anatomically modern human (AMH), or a severe reduction of the population size during the emigration of AMHs out of Africa or the immigration into Europe.

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Abbreviations

AMH:

Anatomically modern human

FLD:

Fu and Li’s D

FLF:

Fu and Li’s F

LD:

Linkage disequilibrium

MRCA:

Most recent common ancestor

TD:

Tajima’s D

TMRCA:

Time to most recent common ancestor

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Acknowledgments

We thank Britta Pietsch, Birgit Schmoll and Sigrid Wieland-Lange for excellent technical assistance. This work was supported by the Deutsche Forschungsgemeinschaft.

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Correspondence to Günter Assum.

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Schmegner, C., Hoegel, J., Vogel, W. et al. Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population. Hum Genet 118, 276–286 (2005). https://doi.org/10.1007/s00439-005-0056-2

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Keywords

  • Population genetics
  • Genetic variability
  • Long-range LD
  • Ancient European subpopulations