Molecular Variation at the In(2L)t Proximal Breakpoint Site in Natural Populations of Drosophila melanogaster and D. simulans

Corresponding author: Peter Andolfatto, Institute of Cell, Animal and Population Biology, Ashworth Labs, Kings Bldgs., University of Edinburgh, Edinburgh, EH9 3JT Scotland, United Kingdom., peter.andolfatto{at}ed.ac.uk (E-mail)

Communicating editor: A. G. CLARK

A previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the number of haplotypes near the proximal breakpoint of In(2L)t, a common inversion polymorphism in this species. Another striking feature of the data was a window of unusually high nucleotide diversity spanning the breakpoint site. To distinguish between selective and neutral demographic explanations for the observed patterns in the data, we sample alleles from three additional populations of D. melanogaster and one population of D. simulans. We find that the strength of associations among sites found at the breakpoint varies between populations of D. melanogaster. In D. simulans, analysis of the homologous region reveals unusually elevated levels of nucleotide polymorphism spanning the breakpoint site. As with American populations of D. melanogaster, our D. simulans sample shows a marked reduction in the number of haplotypes but not in nucleotide diversity. Haplotype tests reveal a significant deficiency in the number of haplotypes relative to the neutral expectation in the D. simulans sample and some populations of D. melanogaster. At the breakpoint site, the level of divergence between haplotype classes is comparable to interspecific divergence. The observation of interspecific polymorphisms that differentiate major haplotype classes in both species suggests that haplotype classes at this locus are considerably old. When considered in the context of other studies on patterns of variation within and between populations of D. melanogaster and D. simulans, our data appear more consistent with the operation of selection than with simple demographic explanations.

This article has been cited by other articles:

				A. Bhutkar, S. W. Schaeffer, S. M. Russo, M. Xu, T. F. Smith, and W. M. Gelbart Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes Genetics, July 1, 2008; 179(3): 1657 - 1680. [Abstract] [Full Text] [PDF]

				T. L. Turner, M. T. Levine, M. L. Eckert, and D. J. Begun Genomic Analysis of Adaptive Differentiation in Drosophila melanogaster Genetics, May 1, 2008; 179(1): 455 - 473. [Abstract] [Full Text] [PDF]

				M. T. Levine and D. J. Begun Evidence of Spatially Varying Selection Acting on Four Chromatin-Remodeling Loci in Drosophila melanogaster Genetics, May 1, 2008; 179(1): 475 - 485. [Abstract] [Full Text] [PDF]

				A. Sanchez-Gracia and J. Rozas Unusual Pattern of Nucleotide Sequence Variation at the OS-E and OS-F Genomic Regions of Drosophila simulans Genetics, April 1, 2007; 175(4): 1923 - 1935. [Abstract] [Full Text] [PDF]

				M. Kirkpatrick and N. Barton Chromosome Inversions, Local Adaptation and Speciation Genetics, May 1, 2006; 173(1): 419 - 434. [Abstract] [Full Text] [PDF]

				J. E. Pool, V. B. DuMont, J. L. Mueller, and C. F. Aquadro A Scan of Molecular Variation Leads to the Narrow Localization of a Selective Sweep Affecting Both Afrotropical and Cosmopolitan Populations of Drosophila melanogaster Genetics, February 1, 2006; 172(2): 1093 - 1105. [Abstract] [Full Text] [PDF]

				L. M. Matzkin, T. J. S. Merritt, C.-T. Zhu, and W. F. Eanes The Structure and Population Genetics of the Breakpoints Associated With the Cosmopolitan Chromosomal Inversion In(3R)Payne in Drosophila melanogaster Genetics, July 1, 2005; 170(3): 1143 - 1152. [Abstract] [Full Text] [PDF]

				E. Baudry, B. Viginier, and M. Veuille Non-African Populations of Drosophila melanogaster Have a Unique Origin Mol. Biol. Evol., August 1, 2004; 21(8): 1482 - 1491. [Abstract] [Full Text] [PDF]

				P. Andolfatto and J. D. Wall Linkage Disequilibrium Patterns Across a Recombination Gradient in African Drosophila melanogaster Genetics, November 1, 2003; 165(3): 1289 - 1305. [Abstract] [Full Text] [PDF]

				J. L. Feder, J. B. Roethele, K. Filchak, J. Niedbalski, and J. Romero-Severson Evidence for Inversion Polymorphism Related to Sympatric Host Race Formation in the Apple Maggot Fly, Rhagoletis pomonella Genetics, March 1, 2003; 163(3): 939 - 953. [Abstract] [Full Text] [PDF]

				G. A. Gomez and E. Hasson Transpecific Polymorphisms in an Inversion Linked Esterase Locus in Drosophila buzzatii Mol. Biol. Evol., March 1, 2003; 20(3): 410 - 423. [Abstract] [Full Text] [PDF]

				W. A. Odgers, C. F. Aquadro, C. W. Coppin, M. J. Healy, and J. G. Oakeshott Nucleotide Polymorphism in the Est6 Promoter, Which Is Widespread in Derived Populations of Drosophila melanogaster, Changes the Level of Esterase 6 Expressed in the Male Ejaculatory Duct Genetics, October 1, 2002; 162(2): 785 - 797. [Abstract] [Full Text] [PDF]

				J. Parsch, C. D. Meiklejohn, and D. L. Hartl Patterns of DNA Sequence Variation Suggest the Recent Action of Positive Selection in the janus-ocnus Region of Drosophila simulans Genetics, October 1, 2001; 159(2): 647 - 657. [Abstract] [Full Text] [PDF]

				J. Rozas, M. Gullaud, G. Blandin, and M. Aguade DNA Variation at the rp49 Gene Region of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure Genetics, July 1, 2001; 158(3): 1147 - 1155. [Abstract] [Full Text] [PDF]

				A. Takahashi, S.-C. Tsaur, J. A. Coyne, and C.-I Wu The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster PNAS, March 16, 2001; (2001) 61465098. [Abstract] [Full Text]

				M. Kovacevic and S. W. Schaeffer Molecular Population Genetics of X-Linked Genes in Drosophila pseudoobscura Genetics, September 1, 2000; 156(1): 155 - 172. [Abstract] [Full Text]

				P. Andolfatto and M. Przeworski A Genome-Wide Departure From the Standard Neutral Model in Natural Populations of Drosophila Genetics, September 1, 2000; 156(1): 257 - 268. [Abstract] [Full Text]

				A. Takahashi, S.-C. Tsaur, J. A. Coyne, and C.-I Wu The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster PNAS, March 27, 2001; 98(7): 3920 - 3925. [Abstract] [Full Text] [PDF]