New insights into evolution: why genes appear to move around

Scientists at Uppsala University have proposed an addition to the theory of evolution that can explain how and why genes move on chromosomes. The hypothesis, called the SNAP Hypothesis, is presented in the scientific journal PLOS Genetics.

Life originated on earth almost four billion years ago and diversified into a vast array of species. How has this diversification occurred? The Theory of Evolution together with the discovery of DNA and how it replicates provide an answer and a mechanism. Mutations in DNA occur from generation to generation and can be selected if they help individuals to adapt better to their environment. Over time, this has led to the separation of organisms into the different species that now inhabit all the different ecosystems of the planet.

Current theory (that evolution involves mistakes made when replicating a gene) explains how genes can mutate over time and acquire new meanings. However, a mystery in biology is that the relative locations of genes on chromosomes also changes over time. This is very obvious in bacteria, where different species often have the same genes in very different relative locations. Since the origin of life, genes have apparently been changing location. The questions are, how and why do genes move their relative locations?

Now, scientists at Uppsala University have proposed an addition to the theory of evolution that can explain how and why genes move on chromosomes. The hypothesis, called the SNAP Hypothesis, is based on the observation that tandem duplications of sections of chromosome occur very frequently in bacteria (more than a million times more frequently than most mutations). These duplications are lost spontaneously unless they are selected. Selection to maintain a duplication can occur whenever bacteria find themselves in a sub-optimal environment, where having two copies of a particular gene could increase fitness (for example, if the duplicated region includes a gene that increases growth rate on a poor nutrient).

Duplications typically contain hundreds of genes, even if only one is selected. The scientists Gerrit Brandis and Diarmaid Hughes argue that mutations can quickly accumulate in the hundreds of non-selected genes, including genes that are normally essential when there is only a single copy in the chromosome. Once two different essential genes are inactivated, one in each copy of the duplication, the duplication can no longer be lost. From this point on, the bacteria will have many genes unnecessarily duplicated, and mutations to inactivate or delete them will be positively selected because they increase fitness.

Over time, all of the unnecessary duplicated genes may be lost by mutation, but this will happen randomly in each copy of the duplication. By this process of random loss of unnecessary duplicated genes in each copy of the duplication, the relative order of the remaining genes can be completely changed. The SNAP process can rearrange gene order very rapidly and it may contribute to separating different species.

Brandis G, Hughes D (2020) The SNAP hypothesis: Chromosomal rearrangements could emerge from positive Selection during Niche Adaptation. PLOS Genet 16(3): e1008615. https://doi.org/10.1371/journal.pgen.1008615

For more information, please contact Diarmaid Hughes, professor at the Department of Medical Biochemistry and Microbiology, Uppsala University.
Tel: + 46 18 471 4507, email: diarmaid.hughes@imbim.uu.se