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Originally published as Genetics Published Articles Ahead of Print on December 6, 2006.

Genetics, Vol. 175, 795-804, February 2007, Copyright © 2007
doi:10.1534/genetics.106.064964

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Combining Sperm Typing and Linkage Disequilibrium Analyses Reveals Differences in Selective Pressures or Recombination Rates Across Human Populations

Vanessa J. Clark*, Susan E. Ptak{dagger}, Irene Tiemann{ddagger}, Yudong Qian*, Graham Coop*, Anne C. Stone§, Molly Przeworski*, Norman Arnheim{ddagger} and Anna Di Rienzo*,1

* Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, {dagger} Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, {ddagger} Department of Computational and Molecular Biology, University of Southern California, Los Angeles, California 90089 and § School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287

1 Corresponding author: Department of Human Genetics, University of Chicago, 920 E. 58th St., CLSC Room 507F, Chicago, IL 60637. 
E-mail: dirienzo{at}genetics.uchicago.edu

A previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.


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