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.
Gene duplication is the primary source of novel genes. Moreover, duplications and deletions of genes contribute to genetic variation in populations, which can both contribute to biological adaptations and disease. The frequency of gene copy-number differences in populations, as well as the rate that gene duplications and deletions are fixed in genomes, is determined by a combination of (i) the spontaneous duplication/deletion rates, and (ii) the probabilities of preservation or elimination of these changes by evolutionary forces such as natural selection and random genetic drift. The rate at which new gene copies arise or are lost from genomes is therefore fundamental to our understanding of (i) the maintenance of genetic variation in gene copy-number in populations, and (ii) how new genes evolve. This project had two major goals: (i) to measure the rate of gene duplications and deletions in a model organism, and (ii) to test if duplications and deletions are a common form of genetic change during adaptation. Mutation accumulation lines of the nematode Caenorhabditis elegans were analyzed for gene copy-number changes. The rate of gene duplication in these experiments was 5 x 10-6 duplications/gene/generation. This rate is three orders of magnitude greater than the spontaneous rate of point mutation per nucleotide site in this species and also greatly exceeds an earlier estimate derived from the frequency distribution of extant gene duplicates in the sequenced C. elegans genome. The discrepancy between these direct measurements of the genome-wide gene duplication rate and previous estimates that were based on analyzing sequenced genomes, suggests that the vast majority of gene duplications are detrimental and removed by natural selection. The gene deletion rate was likewise high, or 4 x 10-7 deletions/gene/generation. The high rates of spontaneous gene duplications and deletions suggest that this type of genetic variation is also important for genetic adaptation, for example when there is selection for an increase or decrease in gene dosage. We tested this in experimental population of C. elegans that were adapting following reduced fitness during mutation accumulation. The second goal of this grant was to investigate whether gene duplications and deletions constitute a common mechanism of adaptive genetic change. Populations of C. elegans were evolved for >200 generations and the frequencies of duplications and deletions in these populations analyzed. Multiple duplications and deletions were detected in intermediate to high frequencies. Several lines of evidence suggest that the changes in frequency were adaptive: Many copy-number changes reached high frequency, near fixation or were fixed in a short time. Many independent duplications and deletions in high frequency harbor overlapping regions which likely include genes that are under selection for either higher or lower rates of expression. The size spectrum of duplications in the adaptive recovery populations is significantly larger than that of spontaneous duplications in mutation accumulation experiments. This is expected if larger duplications are more likely to encompass genes that are being selected for increased dosage. These results validate the great potential borne by gene copy-number changes for evolutionary adaptation. The grant provided opportunities for training of undergraduates and graduate students in genetics, genomics and experimental evolution in a designated Hispanic- and minority-serving institution. The experiments have also resulted in lines and populations of C. elegans that can be shared with the scientific community for further studies on the consequences of mutations and adaptation.
