Vaishali Katju, Ph.D. - US grants

Gene duplications are the primary source of new genes and novel functions in evolution and contribute to heritable diseases and cancer. Most of the recent progress in elucidating the role of gene duplications in the history of life has been the result of comparative analysis of sequenced genomes. Although these studies can provide a rich record of the history of gene duplications and gene loss, the early evolutionary dynamics and selection pressures on duplicated genes remain poorly understood. In order to measure the genome-wide rate of spontaneous gene duplications and deletions, this project uses Comparative Genome Hybridization to detect spontaneous duplications and deletions in experimental populations of the nematode worm Caenorhabditis elegans that have been subjected to (i) mutation accumulation and (ii) adaptation. Gene duplications and deletions will be independently verified by alternative analytical methods. In addition, the effect of local DNA sequence context on gene duplications and deletions will be investigated. Furthermore, the fitness effects of gene duplications and deletions that are detected in the adapted populations will be tested in competition experiments.

The rate at which new genes appear in populations greatly influences their population dynamics with important consequences for the evolutionary potential of organisms, genetic variation and susceptibility to heritable diseases. Moreover, these results should significantly further our understanding of how new genes evolve. This project will train undergraduate and graduate students and will emphasize significant participation of underrepresented minorities, especially at the undergraduate level.

Mutation induces genetic variation. Genetic variation, in turn, fuels evolutionary change. Experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution and biology. Mutation accumulation (MA) experiments have been instrumental in measuring the rate of origin of deleterious mutations. However, the vast majority of MA studies to date are compromised by two major limitations: (i) the use of phenotypic data to indirectly estimate key mutational parameters, and (ii) the use of experimental lines maintained at a single, minimum effective population size. Although population-genetics theory predicts a wide range of fitness consequences for all classes of spontaneous mutations, their distribution of fitness effects remains obscure. Furthermore, the loss or fixation of mutations and their consequences for population fitness additionally depend upon their individual effect and the efficacy of natural selection, the latter being influenced by the population size. Spontaneous MA lines of the nematode Caenorhabditis elegans were evolved in parallel over 400 generations at three varying effective population sizes to manipulate the efficacy of natural selection in different genomic backgrounds. This represents the most ambitious experiment of its kind within any species. The combination of long-term spontaneous MA lines under varying intensities of selection and use of powerful high-throughput genomic techniques will enable unprecedented insights into (i) the rates of origin of diverse mutations, (ii) their differential accumulation under varying regimes of natural selection, and (iii) a framework to assess the interaction between mutation and selection at the molecular level on a genome-wide scale. The aims are to identify all acquired mutations at the mitochondrial and nuclear level, investigate their differential rates of accumulation under varying population sizes and infer their distribution of fitness effects. Phenotypic fitness-assays will quantify the rate of fitness decay at different population sizes and determine the extent to which larger populations are buffered from mutational degradation. By providing a unified account of the consequences of spontaneous mutations at the genetic and phenotypic levels, this research will yield significant insights into the evolutionary process for several different topics, including the genetic basis of variation, the evolutionary dynamics of mutations under the forces of natural selection and genetic drift, and their range of fitness effects.

Broader Impacts
The experimental lines provide an unprecedented resource to study biological evolution at multiple scales, from phenotype to protein function. The experimental MA lines created as part of this research and the deposition of genome sequences in public databases represent an enormous community resource to be shared with colleagues in the scientific community. In addition to the training projects listed with individual aims, this project will have broad impacts in two areas: academic training/mentorship and public outreach in an environment with a large fraction of underrepresented minorities. Data generated by the research will be (i) disseminated to high school students and the general public via seminars and interactive panel discussions to communicate its evolutionary implications and promote scientific literacy, and (ii) employed in the creation of data sets and mini tutorials for high school students to demystify molecular evolution and introduce them to basic evolutionary computational methods for analyses of genomic sequences. The University of New Mexico is the only research-intensive University that is also Hispanic serving, with two extensive underrepresented student populations comprising Hispanics and Native Americans. This provides a unique opportunity to mentor undergraduate minority students, graduate students and postdocs, and instill in them an appreciation for interdisciplinary research in population-genomics and bioinformatics. Research stemming from this project is expected to greatly enhance our fundamental understanding of the evolutionary process and enable the quantification of several key rate parameters in biology, with implications for all spheres of biology including an understanding of the genetic and phenotypic consequences of maintaining populations at small sizes.

Project Summary Technological advances have enabled biologists to categorize entire omes? genomes, but also transcriptomes, proteomes, metabolomes, etc., down to the level of individual cells. Systems Biology is an ascendant branch of biology, with the goal of understanding the interactions between the molecular components of an organism, and how those interactions function to build, operate, and maintain the organism in the context of its environment. The number of such interactions is vast, but experience suggests that there will be underlying consistent rules. A potential way forward is to scrutinize features of a large system ? a transcriptome, for example ? for consistent signatures of natural selection. A powerful way to reveal the signature of natural selection is to compare the genetic variation introduced by mutation to the standing genetic variation in the population. That is because the standing genetic variation has been scrutinized by natural selection. A consistent discrepancy between the genetic variation introduced by spontaneous mutation and the standing genetic variation present in a species is an unmistakable signature of natural selection. In turn, identifying some feature of an organism that is demonstrably under natural selection is prima facie evidence that the feature has a significant biological function, even if the function is not immediately obvious. The raw material for systems biologists is a (large) set of measures of the abundance of individual transcripts, proteins, metabolites, etc. It seems likely that in most cases the mutational target of an individual transcript, etc., will be small. If the mutational target is small, many genomes must be screened to provide a reliable characterization of the mutational process responsible for producing genetic variation in the trait of interest. The goal of the proposed work is to construct a large set of replicate populations of the model nematode Caenorhabditis elegans that have evolved under minimal natural selection, thereby allowing all but the most highly deleterious mutations to accumulate as if they are invisible to natural selection. Ultimately, the set of mutation accumulation lines are expected to harbor approximately 100,000 spontaneous mutations. C. elegans provides major advantages over other animal models in this context, the most important being that nematodes can be easily and reliably cryopreserved. The resource will therefore be durable, and experiments can be done on the (nearly) exact same genetic stock for decades hence. The genomes of the lines will be sequenced, thereby allowing researchers to associate genotypes with their specific traits of interest. Both the lines themselves and the genome sequences will be made immediately available as a community resource. Systems Biology is inherently concerned with interactions between genes, and between genes and the environment. Model organisms such as C. elegans are especially valuable in that regard because genotypes and environments can be both carefully controlled, neither of which is possible with human subjects.