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Genetics, Vol. 166, 1783-1794, April 2004, Copyright © 2004

Nucleotide Variation and Recombination Along the Fourth Chromosome in Drosophila simulans

Wen Wanga,c, Kevin Thorntonb, J. J. Emersona, and Manyuan Longa,b
a Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
b The Committee on Genetics, University of Chicago, Chicago, Illinois 60637
c CAS-Max Planck Junior Scientist Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China

Corresponding author: Manyuan Long, University of Chicago, 1101 East 57th St., Chicago, IL 60637., mlong{at}midway.uchicago.edu (E-mail)

Communicating editor: L. HARSHMAN

The fourth chromosome of Drosophila melanogaster and its sister species are believed to be nonrecombining and have been a model system for testing predictions of the effects of selection on linked, neutral variation. We recently examined nucleotide variation along the chromosome of D. melanogaster and revealed that a low average level of recombination could be associated with considerably high levels of nucleotide variation. In this report, we further investigate the variation along the fourth chromosome of D. simulans. We sequenced 12 gene regions evenly distributed along the fourth chromosome for a worldwide collection of 11 isofemale lines and 5 gene regions in a local population of 10 isofemale lines from South America. In contrast to predictions for regions of very low recombination, these data reveal that the variation levels in many gene regions, including an intron region of the ci gene, vary considerably along the fourth chromosome. Nucleotide diversity ranged from 0.0010 to 0.0074 in 9 gene regions interspersed with several regions of greatly reduced variation. Tests of recombination indicate that the recombination level is not as low as previously thought, likely an order of magnitude higher than that in D. melanogaster. Finally, estimates of the recombination parameters are shown to support a crossover-plus-conversion model.




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