What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades

<p>Abstract</p> <p>Background</p> <p>The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for <it>Plethodon </it>salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals).</p> <p>Results</p> <p>We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that <it>Plethodon </it>have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled).</p> <p>Conclusions</p> <p>Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like <it>Plethodon</it>, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.</p

Effects of refuges on the evolution of resistance to transgenic corn by the western corn rootworm, \u3ci\u3eDiabrotica virgifera virgifera LeConte\u3c/i\u3e

BACKGROUND: Diabrotica virgifera virgifera LeConte is a major pest of corn and causes over a billion dollars of economic loss annually through yield reductions and management costs. Corn producing toxins derived from Bacillus thuringiensis (Bt) has been developed to help manageD. v. virgifera.However, previous studies have demonstrated the ability of this species to evolve resistance to Bt toxins in both laboratory and field settings. RESULTS: We used an experimental evolution approach to test the refuge strategies for delaying resistance of D. v. virgifera to corn producing Bt toxin Cry34/35Ab1. In the absence of refuges, D. v. virgifera developed resistance to Bt corn after three generations of selection. In some cases, non-Bt refuges reduced the level of resistance compared with the strain selected in the absence of refuges, but refuge strains did show reduced susceptibility to Bt corn compared with the unselected strain. CONCLUSIONS: In this study, non-Bt refuges delayed resistance to Bt corn by D. v. virgifera in some cases but not others. Combining the refuge strategy with pyramids of multiple Bt toxins and applying other pest management strategies will likely be necessary to delay resistance of D. v. virgifera to Bt corn