Phylogenetic incongruence in the Drosophila melanogaster species group.

@article{wong07, abstract = {Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) the node joining the Drosophila erecta-Drosophila orena, Drosophila melanogaster-Drosophila simulans, and Drosophila yakuba-Drosophila teissieri lineages, and (2) the node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii, and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection.}, address = {Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA. aw246@cornell.edu}, author = {Wong, A. and Jensen, J. D. and Pool, J. E. and Aquadro, C. F. }, citeulike-article-id = {2937879}, doi = {http://dx.doi.org/10.1016/j.ympev.2006.09.002}, issn = {1055-7903}, journal = {Molecular phylogenetics and evolution}, keywords = {congruence, phylogenetics}, month = {June}, number = {3}, pages = {1138--1150}, posted-at = {2008-06-27 19:23:40}, priority = {2}, title = {Phylogenetic incongruence in the Drosophila melanogaster species group.}, url = {http://dx.doi.org/10.1016/j.ympev.2006.09.002}, volume = {43}, year = {2007} }

TY - JOUR ID - wong07 L3 - citeulike-article-id:2937879 N2 - Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) the node joining the Drosophila erecta-Drosophila orena, Drosophila melanogaster-Drosophila simulans, and Drosophila yakuba-Drosophila teissieri lineages, and (2) the node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii, and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection. IS - 3 JF - Molecular phylogenetics and evolution SN - 1055-7903 AD - Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA. aw246@cornell.edu EP - 1150 TI - Phylogenetic incongruence in the Drosophila melanogaster species group. VL - 43 SP - 1138 KW - congruence KW - phylogenetics AU - Wong, A AU - Jensen, JD AU - Pool, JE AU - Aquadro, CF PY - 2007/June// UR - http://dx.doi.org/10.1016/j.ympev.2006.09.002 ER -