title: The causes of phylogenetic conflict in a classic Drosophila species group.
abstract: Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related species. However, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. Here, we show that the history of three well-known closely related species, Drosophila pseudoobscura, D. persimilis and D. p. bogotana, is not well represented by a bifurcating phylogenetic tree. The phylogenetic relationships among these species vary widely between different genomic regions. Much of this phylogenetic variation can be explained by the potential of different genomic regions to introgress between species, as measured in laboratory studies. We argue that the utility of multiple markers in species-level phylogenetic studies can be greatly enhanced by knowledge of genomic location and, in the case of hybridizing species, by knowledge of the functional or linkage relationships among the markers and regions of the genome that reduce hybrid fitness.
authors.affiliation: Department of Genetics, Rutgers University, 604 Allison Road, Nelson Biological Laboratories, Piscataway, NJ 08854-8082, USA. cmachado@email.arizona.edu
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Machado
authors.forename: Jody
authors.initials: J
authors.lastname: Hey
mesh_terms: D000818:Animals; D005075:Biological Evolution; D004330:Drosophila / Q000145:classification* / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D016678:Genome; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D013045:Species Specificity
chemical_list: D005819:Genetic Markers