Evolution · 2007 · 166 citations · 94 references
Life SciencesBiologyGeneticsMitochondrial GeneticsMolecular EvolutionPhylogeneticsBayesian PhylogeneticsCoalescent-based PhylogeneticsInsect PhylogeneticsInsect PhylogenyPhylogenetic PatternsPhylogenetic Tree ReconstructionCoalescenceHybridization InferenceLineage SortingMitochondrial Genome PhylogeneticsMitochondrial IntrogressionNuclear Gene PhylogeneticsNuclear Gene PhylogenyPhylogenetic Character Analysis
We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively.
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MODELTEST: testing the model of DNA substitution.
David Posada, Keith A. Crandall · Bioinformatics · 1998 · 20.1K citations