Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name



Biological Sciences

First Advisor

Markus Friedrich


The value of mitochondrial versus nuclear gene sequence data in phylogenetic analysis has received much attention without yielding definitive conclusions. Theoretical arguments and empirical data suggest a lower phylogenetic utility than equivalent nuclear gene sequences, but there are also many examples of important progress made using mitochondrial sequences. We therefore undertook a systematic performance analysis of mitochondrial and nuclear sequence partitions taken from a representative sample of dipteran species. For phylogenetic tree reconstruction, mitochondrial genes performed generally inferior to nuclear genes. However, the mitochondrial genes resolved branches for which nuclear genes failed. Moreover, the combined use of mitochondrial and nuclear sequences produced superior results without artifacts for nodes where mitochondrial and nuclear gene data sets on their own generated conflicting topologies. These findings strongly advocate the inclusion of mitochondrial sequences even in deep phylogeny reconstruction. The comparison of tree support between our and previous analyses identified robustly supported high confidence clades in the Diptera but also a number of problematic groupings in need of further analysis. For divergence time estimation, we show widespread convergence of clade age estimates from both mitochondrial and nuclear gene sources under a wide variety of data preparation and model paradigms. Our results indicate slightly superior performance of nuclear gene derived ages for nodes for several clades in the tree ranging in age from approximately 30 to 160 myo. We further find that third codon position inclusion negatively affects our ability to resolve ages under many circumstances. Increasing model complexity and granularity of data partitioning offered little benefit in terms of final results while increasing the computational complexity. Finally, we produce high confidence age estimates for cyclorrhaphan divergences in agreement with previous literature, and provide the first timeline for major divergences within the calyptrate flies.