Our main research interests are the evolution of major groups of animals and their genomes.  Our favorite animals are marine non-bilaterian taxa, including Porifera (sponges), Cnidaria (corals, jellyfishes), and Ctenophora (comb jellies). It is rarely appreciated that from the phylogenetic perspective each group of these animals forms at least an equal-status taxon to all bilaterian animal (from flatworms to humans) and thus should harbor a large portion of animal genomic diversity that we only now are beginning to explore.  Ongoing projects include:

Comparative mitochondrial genomics of non-bilaterian animals.

Mitochondrial DNA of bilaterian animals is typically a small, circular-mapping molecule that encodes 37 tightly packed genes.  MtDNA of the choanoflagellate Monosiga brevicollis, the closest unicellular out-group, is four times larger and contains 1.5 times as many genes.  Comparative genomic studies can provide valuable insights into the mechanisms responsible for this remarkable transition in mtDNA evolution, but the scarcity of data from non-bilaterian animals (phyla Placozoa, Porifera, Ctenophora, and Cnidaria) severely limits these studies.  My group aims to sample and analyze mitochondrial genomes from all major groups of non-bilaterian animals.  Currently, we are working on the mitochondrial genomes of multiple sponges (see below), representatives of all major lineages in Cnidaria and Ctenophora.  Our analyses revealed a large extent of mitochondrial diversity in these groups.  We discovered such unusual features as mitochondrial introns, putative transposable elements, translational frameshifting, fragmented ribosomal RNA (rRNA) genes, transfer RNA (tRNA) gene recruitment, and tRNA editing.  We also found several cases of parallel evolution in mitochondrial genome organization in different groups.  Such cases can help to elucidate molecular and evolutionary forces responsible for unusual features in animal mtDNA, some of which have been implicated in human diseases.  

Porifera Tree of Life.

This is a large, collaborative project involving researchers from Dartmouth College, Harbor Branch Oceanographic Institution at Florida Atlantic University, Iowa State University, Nova Southeastern University, the Smithsonian Institution, the University of Alabama at Birmingham, and the University of Richmond, as well as the Museo Marino Margarita, Venezuela, Queensland Museum, Australia, and the University of Göttingen, Germany.  My group is responsible for sequencing and analyzing mitochondrial genomes from representatives of all families of sponges and for the combined phylogenetic analysis.  The goal of the whole project is to generate a well-supported molecular and morphological phylogeny of the Porifera that will improve understanding of all aspects of sponge biology, allow the interpretation of existing sponge data in a proper evolutionary context, and serve as a catalyst for future interdisciplinary research involving sponges.  By the end of the project, we expect not only to elucidate the phylogeny of sponges but also to gain a comprehensive picture of mitochondrial genome evolution in this group of animals. This project will also allow us to make important methodological advances in the field of mitochondrial genomics, both in optimizing laboratory procedures and in developing analytical tools.

Phylogeny and evolution of Baikal sponges.

Lake Baikal, the oldest and the most voluminous lake on the planet, has exceptionally high faunal diversity and level of endemicity.  However, the questions of the number of endemic species, their age, and their evolutionary histories, are still hotly debated.  In collaboration with my colleagues at the Limnological Institute in Irkutsk, Russia, I began to investigate some of these questions on an endemic group of freshwater sponges (family Lubomirskiidae).  These sponges dominate the benthic community of the lake, play an essential role in its ecology, and represent the most spectacular example of endemic radiation in freshwater sponges in the world.  To date we determined complete mitochondrial sequences for representatives from four endemic genera present in the lake as well as partial sequences of several mitochondrial and nuclear genes from most recognized species.

Evolution of mitochondrial proteome.

In the 30 years since the first animal mtDNA has been published, we have learned a great deal about the evolution of mitochondrial genomes. However, because mtDNA encodes only a tiny fraction of mitochondrial proteins, the evolution of mitochondrial proteome remains largely unexplored. From the evolutionary viewpoint, this proteome represents an interesting system as it is made out of interacting components encoded by two genomes with different rates and modes of evolution and because some analogous molecules (e.g., components of the translation machinery) are encoded in both nuclear and mitochondrial DNA. We began to explore the evolution of mitochondrial proteome by investigating the fate of nuclear-encoded aminoacyl-tRNA synthetases (aa-RS) in animals, where mitochondrial-encoded tRNAs are lost. We found that the loss of such tRNA genes in the sea anemone Nematostella and a ctenophore Mnemiopsis had lead to a loss of all but two nuclear-encoded aaRS in both organisms. We intend to test the universality of this observation by analyzing publically available mitochondrial and nuclear genomes in other eukaryotes, especially those that lost some or all mitochondrial tRNAs. We are also interested in exploring the evolution of other elements of mitochondrial proteome in animals.