title: Genome Evolution in Three Species of Cactophilic Drosophila.
abstract: We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.
authors.affiliation: Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, 62210 Mexico.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sanchez-Flores
authors.affiliation: Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, 62210 Mexico.
authors.forename: Fernando
authors.initials: F
authors.lastname: Peñaloza
authors.affiliation: Laboratorio Nacional de la Genomica Para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, 36821 Mexico Department of Biology, University of Maryland, College Park, Maryland 20742.
authors.forename: Javier
authors.initials: J
authors.lastname: Carpinteyro-Ponce
authors.affiliation: Laboratorio Nacional de la Genomica Para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, 36821 Mexico.
authors.forename: Nestor
authors.initials: N
authors.lastname: Nazario-Yepiz
authors.affiliation: Laboratorio Nacional de la Genomica Para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, 36821 Mexico.
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
authors.affiliation: Department of Biology, University of Maryland, College Park, Maryland 20742 machado@umd.edu tmarkow@ucsd.edu.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Machado
authors.affiliation: Laboratorio Nacional de la Genomica Para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, 36821 Mexico Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 machado@umd.edu tmarkow@ucsd.edu.
authors.forename: Therese Ann
authors.initials: TA
authors.lastname: Markow
mesh_terms: D000818:Animals; D007446:Chromosome Inversion; D059006:Chromosomes, Insect; D019295:Computational Biology / Q000379:methods; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D063990:Gene Ontology; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D012641:Selection, Genetic; D013045:Species Specificity
keywords: Drosophila; cactophilic; evolution; genome; inversions