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Originally published as Genetics Published Articles Ahead of Print on March 17, 2006.
Genetics, Vol. 173, 779-791, June 2006, Copyright © 2006
doi:10.1534/genetics.105.054585
Rates and Patterns of Chromosomal Evolution in Drosophila pseudoobscura and D. miranda
Carolina Bartolomé1 and Brian Charlesworth
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
1 Corresponding author: Grupo de Medicina Xenómica (USC), Unidad de Medicina Molecular, Hospital Clínico Universitario de Santiago, Edificio Consultas, planta -2, 15706 Santiago de Compostela, Spain.
E-mail: cbhusson{at}usc.es
Comparisons of gene orders between species permit estimation of the rate of chromosomal evolution since their divergence from a common ancestor. We have compared gene orders on three chromosomes of Drosophila pseudoobscura with its close relative, D. miranda, and the distant outgroup species, D. melanogaster, by using the public genome sequences of D. pseudoobscura and D. melanogaster and 
50 in situ hybridizations of gene probes in D. miranda. We find no evidence for extensive transfer of genes among chromosomes in D. miranda. The rates of chromosomal rearrangements between D. miranda and D. pseudoobscura are far higher than those found before in Drosophila and approach those for nematodes, the fastest rates among higher eukaryotes. In addition, we find that the D. pseudoobscura chromosome with the highest level of inversion polymorphism (Muller's element C) does not show an unusually fast rate of evolution with respect to chromosome structure, suggesting that this classic case of inversion polymorphism reflects selection rather than mutational processes. On the basis of our results, we propose possible ancestral arrangements for the D. pseudoobscura C chromosome, which are different from those in the current literature. We also describe a new method for correcting for rearrangements that are not detected with a limited set of markers.
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