Katju Lab Research Overview
 
Research Interests We seek to understand the genetic factors contributing to the origin of phenotypic diversity. The contribution of gene duplication to novel gene function and adaptive phenotypes are of special interest. Our research focuses on several fundamental questions regards the phenomenon of gene duplication, namely What mechanisms are responsible for the creation of new genes via duplication? To what extent does a newly created gene resemble its progenitor locus and consequently, what are the implications for sequence and functional diversification between the two paralogs? What evolutionary forces promote the spread of a gene duplicate from its original state as a single-copy in one individual to fixation at the population- and species-level? Are there any discernible features (genomic location or some other structural feature) that enhance their probability of fixation? 
 Early Stages of Duplicate Gene Evolution:
Gene duplication is widely regarded as one of the major contributing factors to the origin of novel biochemical processes and adaptive evolution.  The direct examination of large, unbiased samples of young gene duplicates in the early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. In the past, we have investigated a large sample of newborn gene duplicates in the genome of the nematode Caenorhabditis elegans, with respect to their structural classes and genomic features. We are currently employing a comparative genomic approach to elucidate the early evolutionary features of gene duplicates via a reciprocal analysis of six closely related species/subspecies pairs. These analyses will provide an opportunity to test key predictions of gene-duplication theory as well as determine if any general patterns of gene duplication unite genomes across a diverse assemblage of species. Evaluation of the Future Evolutionary Potential of Gene Duplicates via Patterns of Molecular Evolution and Gene Expression Data: The patterns of paralog sequence divergence are key to understanding the evolutionary forces that promote functional divergence between gene duplicates. However, the influence of diverse evolutionary forces in different phases of a duplicate's life can obscure the key mutational events that initiate functional divergence. These challenges can be circumvented by comparing paralogs of relatively recent origin. The patterns and rates of molecular evolution of evolutionarily young paralogs will be compared to determine if (i) paralogs exhibit asymmetric rates of sequence divergence, (ii) determine the degree of functional constraints and (iii) identify the type of substitutional changes. Finally, rapidly emerging data from expression profile studies and genetic interaction networks will be utilized to test additional hypotheses regarding functional diversification of paralogs namely the relationship between (i) coding sequence divergence and functional divergence and (ii) the type of duplication event and expression divergence between paralogs. Role of Compensatory Change in the Origin of Reproductive Incompatibility: The maintenance of populations at small sizes can lead to the accumulation of deleterious mutations. Conditionally beneficial mutations at other loci can epistatically interact with the deleterious alleles and compensate for their negative effects, thereby leading to the formation of unique coadapted gene complexes within a specific genetic background. We are currently testing the role of such beneficial mutations in the evolution of reproductive incompatibility in experimental lines of the nematode C. elegans.
Research in the lab has been facilitated by generous support from the National Science Foundation and start-up funds from the University of New Mexico.