Current Research Program:

Molecular Evolution and Comparative Genomics of Animal Mitochondrial Genomes.

The Animal Mitochondrial Genome.

The animal mitochondrial genome is a small, compact circular molecule that codes for 13 essential protein coding genes and the minimal translation system required to translate them: 22 tRNA genes and two rRNA genes. Since the same set of genes is present in virtually all animals, homology of these genes is clear. This observation, plus the clonal, maternal pattern of inheritance makes these genomes particularly useful for phylogenetic studies.

Complete Mitochondrial Genomes.

Although we cannot predict in advance what novel features may be uncovered by studying particular genomes, it is clear that the most interesting advances will come from careful analyses of complete genomes. Complete genomes provide the maximum amount of information possible for evolutionary, phylogenetic and genomic analysis. With a complete genome, we can determine whether a particular region of sequence represents the functional gene, or alternatively is a non-functional copy. Without that assurance, it can be difficult to verify unusual features. With a complete genome, we have complete information on the gene arrangement, and can compare it to that of other organisms. With complete genomes and robust phylogenies, we can make strong inferences about the evolutionary changes that have occurred in each lineage, both at the sequence and genome levels.

Our lab is currently focusing on developing complete sequences for mitochondrial genomes of a variety of animals. At present, our emphasis is on insects.

Major Projects:

Mitochondrial Genomics of Insects.

We have developed a set of highly conserved PCR (Polymerase Chain Reaction) primers that allow us to amplify and sequence the entire mitochondrial genomes of most insects in small (0.5 - 1.5 kb) overlapping pieces [Simon et al. 1994; Simon, et al. 2006]. This primer set allows us to develop complete mitochondrial genomes of virtually any insect, regardless of size, and whether or not it can be collected in quantity or cultured in the laboratory. This development allows us to choose taxa for sequencing based on phylogenetic importance, rather than technical convenience.

Over the past few years, we have determined and analyzed the complete mitochondrial genome sequences of a beetle (Stewart and Beckenbach, 2003–only the second beetle sequence available), a Hemipteran (Stewart and Beckenbach, 2005–the first member of suborder Auchenorrhyncha to be sequenced), a stonefly (Stewart and Beckenbach, 2006–the first member this primitive order available), a dobsonfly (unpublished; the first member of order Megaloptera to be sequenced) and an owlfly (unpublished; the first member of order Neuroptera to be sequenced).

Dobsonfly	Owlfly	Stonefly

Even though complete mitochondrial sequences for representatives of all recognized insect orders will soon be available, the real work has only begun. For example, the order Hemiptera is extremely complex, and sequences developed in other laboratories have shown that some groups exhibit enormous sequence diversity that we have not yet begun to understand. Beetles represent the greatest species diversity of any extant order of living organisms. We are currently working on sequences from two more members of this important group. Two of the other “megadiverse” orders, Lepidoptera and Hymenoptera, have hardly been touched. And then there are the flies....

Evolution of the mitochondrial genome in the Order Diptera (true flies).

The Diptera trace back over 250 million years and are one of the most diverse of insect orders. Not only do they have an ancient and complex evolutionary history, but many are of considerable economic importance. Members of this order have long served as model organisms for such fields as genetics, evolution and systematics. I am a major collaborator in a project funded by the National Science Foundation (US) to develop the Dipteran Tree of Life [http://www.inhs.uiuc.edu/cee/FLYTREE]. Our role in the project is to develop a molecular database of mitochondrial genomes representing the earliest divergences of the order, the Nematocera and “Orthorrhaphous” Brachycera, as well as selected outgroups. This data, when combined with other molecular and morphological data, will produce the most detailed representation of the phylogenetic history of this group yet achieved. Equally important, the development of an accurate phylogeny will allow us to use this phylogeny to study the evolution of both nuclear and mitochondrial genomes. We can examine the pattern of nucleotide substitutions and the functional constraints on the evolution of these molecules, as well as the types and frequencies of genome rearrangements that have occurred.

Preliminary results have been quite interesting. Not only are there a number of mitochondrial genome rearrangements among the dipterans, allowing us to re-examine the constraints on these changes, but there is evidence of unexpected features such as truncation of tRNA genes, requiring editing of the RNA products. This work is just underway, and the opportunities virtually limitless.

Novel features of animal mitochondrial genomes.

Careful examination of DNA sequences in a phylogenetic context sometimes leads to unexpected observations. A recent discovery is the presence of single nucleotide frameshift insertions in certain essential mitochondrial genes [Mindell, et al., 1998 and Beckenbach, et al., 2005]. While these observations may seem simply bizarre, in fact they have considerable importance. The understanding of how genes function is challenged by discoveries of exceptions such as these. As well, the use of mitochondrial sequences for phylogenetic reconstruction depends on an understanding of their evolution. We will not fully understand the evolution of these sequences, or the organisms that carry them, until these “exceptions” to normal gene function are well understood.