Nucleotide Variation and Recombination Along the Fourth Chromosome in Drosophila simulans

doi:10.1534/genetics.166.4.1783

Nucleotide Variation and Recombination Along the Fourth Chromosome in Drosophila simulans

Wen Wang^a,c, Kevin Thornton^b, J. J. Emerson^a, and Manyuan Long^a,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 sisterspecies are believed to be nonrecombining and have been a modelsystem for testing predictions of the effects of selection onlinked, neutral variation. We recently examined nucleotide variationalong the chromosome of D. melanogaster and revealed that alow average level of recombination could be associated withconsiderably high levels of nucleotide variation. In this report,we further investigate the variation along the fourth chromosomeof D. simulans. We sequenced 12 gene regions evenly distributedalong the fourth chromosome for a worldwide collection of 11isofemale lines and 5 gene regions in a local population of10 isofemale lines from South America. In contrast to predictionsfor regions of very low recombination, these data reveal thatthe variation levels in many gene regions, including an intronregion of the ci gene, vary considerably along the fourth chromosome.Nucleotide diversity ranged from 0.0010 to 0.0074 in 9 generegions interspersed with several regions of greatly reducedvariation. Tests of recombination indicate that the recombinationlevel is not as low as previously thought, likely an order ofmagnitude higher than that in D. melanogaster. Finally, estimatesof the recombination parameters are shown to support a crossover-plus-conversionmodel.

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