Gene Copy‐Number Changes in Evolution

Abstract

Abstract High‐throughput genomics have revealed widespread copy‐number differences within and among populations of species belonging to diverse taxonomic groups. Experimental evolution in model organisms with minimal natural selection demonstrates that genome‐wide empirical estimates of the spontaneous rates of gene duplication and deletion are extremely high and contribute to the abundance of copy‐number variation (CNV). CNVs are, on average, deleterious with respect to fitness, but their high spontaneous rates of origin can also facilitate rapid adaptation to novel environmental challenges. Duplications and deletions constitute opposing forces that shape genome complexity and size. Gene duplications are the ultimate source of new genes that confer novel phenotypes, whereas deletions remove superfluous genetic material. Furthermore, CNVs can contribute to the evolution of genetic incompatibility and speciation. Future challenges for understanding the evolutionary potential of CNVs include elucidating the relative roles of genetic drift and natural selection for the maintenance of CNVs in populations. Key Concepts Gene duplications are naturally occurring mutations within genomes wherein genic material is duplicated, resulting in additional copies of the duplicated gene. Gene deletions are mutations where genic material has been deleted, thereby reducing the number of copies of the deleted gene. Gene duplications and deletions have resulted in extensive gene copy‐number variation (CNV) in populations across all domains of life. The evolution of gene content and genome size is the net result of duplications adding new genetic material and contributing to the evolution of new genes, and deletions, which are continuously removing genetic information. The study of copy‐number variants at single loci has a long history in population genetics, but a systematic analysis of CNVs across whole genomes became possible only after technical breakthroughs in DNA microarray technology and whole‐genome sequencing. The rates of spontaneous gene duplication and deletion per gene are extraordinarily high and usually much higher than the nucleotide substitution rates. Most CNVs in natural populations are deleterious. Both duplications and deletions can contribute to adaptive genetic variation in natural and experimental populations. The long‐term maintenance of duplicated genes, which contribute to the evolution of novel genes, can be achieved by both positive selection on gene copy‐number and subfunctionalisation resulting from the loss of partial functions of complementary gene copies. Gene duplication and subfunctionalisation can contribute to reproductive isolation and speciation. A comprehensive understanding of how CNVs contribute to the evolution of genomes will require a combination of high‐throughput genomics with analysis of the functional and fitness consequences of CNVs in experimental and natural populations.