Phylogenetic utility of mitochondrial and nuclear genes: a case study in the diptera (true flies)

PHYLOGENETIC UTILITY OF MITOCHONDRIAL AND NUCLEAR GENES:A CASE STUDY IN THE DIPTERA (TRUE FLIES)byJASON CARAVASMay 2012Advisor: Dr. Markus FriedrichMajor: Biological SciencesDegree: Doctor of Philosophy The value of mitochondrial versus nuclear gene sequence data in phylogeneticanalysis has received much attention without yielding definitive conclusions. Theoreticalarguments and empirical data suggest a lower phylogenetic utility than equivalent nucleargene sequences, but there are also many examples of important progress made usingmitochondrial sequences. We therefore undertook a systematic performance analysis ofmitochondrial and nuclear sequence partitions taken from a representative sample ofdipteran species. For phylogenetic tree reconstruction, mitochondrial genes performedgenerally inferior to nuclear genes. However, the mitochondrial genes resolved branchesfor which nuclear genes failed. Moreover, the combined use of mitochondrial andnuclear sequences produced superior results without artifacts for nodes wheremitochondrial and nuclear gene data sets on their own generated conflicting topologies.These findings strongly advocate the inclusion of mitochondrial sequences even in deepphylogeny reconstruction. The comparison of tree support between our and previousanalyses identified robustly supported high confidence clades in the Diptera but also a