Overall Research Interests

I study the origins of biological diversity, particularly how abrupt genomic events such as polyploidy (genome duplication), chromosomal change, and hybridization have contributed to evolution and diversification. Biologists have long been fascinated by these processes because they create unique opportunities for the evolution of novelty with the potential for relatively rapid speciation. While assessing the roles of these genomic changes in evolution has historically been a difficult task, advances in genomics and computational biology have created new opportunities for addressing these longstanding questions. My research program integrates new computational and evolutionary genomic tools with traditional approaches such as molecular evolution, phylogenetics, mathematical modeling, and experimental work to better understand the origins of biological diversity. I use a combination of publicly available genomic data and new data generated by myself and my collaborators from a diverse set of study systems. Below I describe several themes of my research and outline how I expect this work will progress in the future.


Polyploidy & Plant Evolution

Polyploidy, or whole genome duplication, results in rapid reproductive isolation and speciation, alters patterns of gene expression, and potentially yields novel phenotypes. Botanists have long debated the relevance of polyploidy to plant evolution with some authors proclaiming it the key to plant adaptation and diversification and others dismissing it as an evolutionary dead end. However, recent analyses of plant genomes have revealed that many apparent diploids are in fact ancient polyploids that over time have returned to a genetic diploid state, a process known as diploidization. By exploiting the fact that polyploidization doubles every gene in the genome, evolutionary genomic analyses are able to track these events in plant history and clarify their role in evolution.

By developing new bioinformatic tools and approaches to analyze the phylogenetically diverse genomic data on public databases, I have found evidence for more than 50 ancient genome duplications throughout plant history. Some of these paleopolyploidizations have occurred prior to critical nodes in the land plant phylogeny, and suggest that polyploidy did indeed play a significant role in the evolution and diversification of plants. Much of my current work is focussed on sorting out exactly how these genome duplications have impacted plant evolution. For example, I am working to date each of these duplication events to determine if they are distributed randomly or clustered in time. I am also using a variety of tests to assess the contribution of paleologs to plant adaptation. To better understand the biased retention and loss of paleologs, I am beginning to apply models of network evolution to elucidate the forces behind the evolution of these duplicate gene networks. Finally, I am exploring whether increased speciation or decreased extinction rates have accompanied these paleopolyploidizations, and searching for the mechanisms behind the rate changes (e.g., reciprocal gene loss).


Evolution of Chromosome Number & Genome Organization

An outstanding feature of plant genome evolution is the wide range of chromosome numbers distributed across the plant phylogeny. Despite nearly 100 years of cytological study, we still do not fully understand the forces and mechanisms that drive chromosome number evolution, a fundamental feature of plant genetics. An overall trend of increasing chromosome numbers might be expected in plants because of the numerous rounds of genome duplication that most plants have experienced. However, many lineages have apparently undergone significant chromosome loss following paleopolyploidy. By combining evolutionary genomic analyses with cytological data to calculate the rates of polyploidy and aneuploidy, it is possible to provide insight into genome evolution across the plant phylogeny.

Among eukaryotes, homosporous ferns are the undisputed kings of chromosome numbers with the largest chromosome count for any species (Ophioglossum reticulatum, n = 1440) and an overall average of n = 62.87,more than three times the angiosperm average. Researchers have long hypothesized that ferns must have experienced many more rounds of polyploidy than angiosperms to explain their high numbers. My evolutionary genomic analyses of Sanger and 454 EST data for four species of ferns indicates that they are indeed ancient polyploids. Surprisingly, my results suggest their rate of paleopolyploidization is actually half the angiosperm rate, and that contrary to conventional wisdom, angiosperm polyploids have been much more successful than fern polyploids on average. Combined with other analyses, my data strongly suggest that fern genomes retain their chromosomes at a much higher rate than angiosperms. I am currently working to collect additional data and develop new tools to evaluate this hypothesis. Ultimately, I hope to characterize and test whether the inferred changes in plant genome organization have been key elements of seed plant diversification.


The Role of Hybridization in Evolution

Like polyploidy, hybridization has long held a special place in the minds of evolutionary biologists. However, hybridization has historically been difficult to detect, especially if the parental taxa are missing or if the hybridization is ancient. To resolve these classic problems, I have developed a novel test for hybridization - the "introlog test" - that leverages the broad genomic data to test for hybridization and introgression. Not surprisingly, my new analyses suggest that hybridization is more common in plants and animals than previous estimates, and provides the first broadly genomic estimate of hybridization frequency. Further, I have also developed an unambiguous test for allopolyploidization and a similarly novel estimate of the frequency of allo- versus autopolyploidy. Using this new tool, I am exploring the contribution of intrologs (genes of hybrid origin) to adaptation across a wide range of eukaryotes, as well as the timing of ancient hybridization events.


Other Interests

In addition to the above work, I am researching a variety of related questions. In collaboration with Katrina Dlugosch, I am exploring the evolutionary genomics of invasiveness. Together with Nolan Kane, I am exploring the evolutionary biology of genes that are rapidly evolving in green plants. Nolan and I are also leveraging the considerable resources of the Compositae Genome Project to assess differences in macro and micro evolution in the Compositae, the largest family of flowering plants. With Hannes Dempewolf I am studying the genomics of plant domestication. In addition to applied questions such as identifying candidate genes associated with domestication, we are interested in whether some plants are more apt to be domesticated and how artificial and natural selection differ. My interests in polyploidy also extent to their contemporary ecology, and I am exploring polyploid biogeography using GIS with Marc Bogonovich, as well as patterns of cross cytotype asymmetric reproductive isolation with Renee Lopez-Smith. I also spend time exploring how to best handle and analyze new sources of data, such as 454 and Solexa sequences, and writing Perl or other scripts to integrate these data into our analyses. Most of the products of my bioinformatic efforts are available at evopipes.net.