The distribution of fitness effects (DFE) of new mutations is of fundamental importance in evolutionary biology and has practical applications in biomedicine, including complex disease and cancer. Several methods exist by which the DFE can be estimated, each of which has limitations. Indirect estimates derived from standing genetic variation provide information about the DFE of mutations under very weak to moderate selection but provide little information about strongly selected mutations. Conversely, estimates of the DFE from experimental data provide information about relatively strongly selected mutations but can only provide information about weakly selected mutations in aggregate. A comprehensive characterization of the full DFE must integrate both kinds of information. Importantly, in humans the fitness effects of all but the mos highly deleterious mutations cannot be estimated directly. Direct estimates of the DFE from model organisms can inform efforts to model human population genetic processes, as well as advance our understanding of evolution in general. The nematode C. elegans provides the ideal model system to in which to experimentally characterize the DFE: its short generation time, unparalleled genetic resources and ease with which stocks can be cryopreserved make it unique among multicellular organisms.
In Aims 1 and 2, stocks of C. elegans that have accumulated mutations for 250 generations under minimal natural selection will be employed to estimate the DFE, combining the methods of classical quantitative genetics with high-throughput genotyping and phenotyping. The goals of Aim 1 are (1) characterize the genome-wide mutation rate by sequencing a set of mutation accumulation (MA) lines, and (2) obtain an accurate estimate of the decline in fitness with MA by large-particle flow cytometry (aka a worm sorter) to measure lifetime reproduction of a very large number of individuals. MA lines will be mated to the unmutated ancestor to generate F1 heterozygotes, which will be similarly characterized for fitness.
In Aim 2, a large panel of Recombinant Inbred Advanced Intercross Lines (RIAILs) will be constructed from a cross of two fully-sequenced MA lines. Each RIAIL will be genotyped at each mutant locus and individual mutations can be treated as quantitative trait loci (QTL), from which the homozygous DFE can be inferred statistically. To estimate the heterozygous DFE, each RIAIL will be mated to the ancestor of the MA lines and fitness determined in the F1 offspring. Further, it will be apparent if overdominant mutations (i.e., heterozygote advantage) are present; unambiguous evidence for true overdominance is almost non-existent. In both Aims 1 and 2, fitness will be assessed under several relevant environmental conditions.
In Aim 3, the DFE will be determined statistically from the site-frequency spectrum in a set of 162 wild isolates of C. elegans. The proposed work will provide the most comprehensive characterization of the DFE in any multicellular organism, and will inform any study in applied population genetics.
Mutation is of fundamental importance in several arenas of public health, including complex heritable disease, cancer, aging, and genetic counseling, and many studies investigating these topics employ models in which the statistical distribution of 'mutational effects' - i.e., the effet that a specific mutation has on a trait of interest - is a key parameter. There are now very detailed estimates of the rate and molecular properties of mutations in humans, but the full distribution of mutational effects cannot be directly measured in humans, and indirect methods are subject to several unavoidable sources of potential bias. Experimental data from tractable model organisms provide the best opportunity to determine the distribution of mutational effects in an unbiased way.
|Evans, Kathryn S; Brady, Shannon C; Bloom, Joshua S et al. (2018) Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses. Genetics 210:1509-1525|
|Johnson, Lindsay M; Chandler, Luke M; Davies, Sarah K et al. (2018) Network Architecture and Mutational Sensitivity of the C. elegans Metabolome. Front Mol Biosci 5:69|
|Yeh, Shu-Dan; Saxena, Ayush Shekhar; Crombie, Timothy A et al. (2018) The mutational decay of male-male and hermaphrodite-hermaphrodite competitive fitness in the androdioecious nematode C. elegans. Heredity (Edinb) 120:1-12|
|Zdraljevic, Stefan; Andersen, Erik C (2017) Natural diversity facilitates the discovery of conserved chemotherapeutic response mechanisms. Curr Opin Genet Dev 47:41-47|
|Cook, Daniel E; Zdraljevic, Stefan; Roberts, Joshua P et al. (2017) CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res 45:D650-D657|
|Laricchia, K M; Zdraljevic, S; Cook, D E et al. (2017) Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species. Mol Biol Evol 34:2187-2202|
|Lee, Daehan; Yang, Heeseung; Kim, Jun et al. (2017) The genetic basis of natural variation in a phoretic behavior. Nat Commun 8:273|
|Reed, Laura K; Baer, Charles F; Edison, Arthur S (2017) Considerations when choosing a genetic model organism for metabolomics studies. Curr Opin Chem Biol 36:7-14|
|Cook, Daniel E; Andersen, Erik C (2017) VCF-kit: assorted utilities for the variant call format. Bioinformatics 33:1581-1582|
|Teotónio, Henrique; Estes, Suzanne; Phillips, Patrick C et al. (2017) Experimental Evolution with Caenorhabditis Nematodes. Genetics 206:691-716|
Showing the most recent 10 out of 20 publications