Genome complexity: mutation rate study in prokaryotes (Introduction)

by David Turell , Thursday, August 06, 2020, 20:13 (1358 days ago) @ David Turell

Results are not clear at all:

https://phys.org/news/2020-08-faster-evolution-linked-tiny-genomes.html

scientists have found a link between mutation rate—how quickly the DNA sequence changes—and genome size.

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"'This was a really surprising result," said Professor Tom Bourguignon, co-first author of the study and head of the Evolutionary Genomics Unit at OIST. "Currently, the most accepted idea is that population size is the main factor that determines genome size in prokaryotes, particularly in endosymbionts, but our research challenges this view."

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"'At small population sizes, natural selection is much less effective, and evolution is driven more strongly by chance," said Dr. Yukihiro Kinjo, co-first author and a postdoctoral scholar from the Evolutionary Genomics Unit. "Without enough selection pressure to maintain specific genes, mutations can arise that inactive and erode these genes, eventually leading to their total loss from the genome."

"While population size as a driving force for genome reduction may be an attractive idea, many free-living prokaryotes that live in larger populations have also evolved smaller genomes, suggesting that it's only part of the story. Additional explanations have also been proposed but, until now, the mutation rate—or the speed at which evolution occurs—has been overlooked.

"In the study, the scientists collected genome data from a diverse range of prokaryotes, including strains from two endosymbiotic lineages and seven free-living lineages.

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"Surprisingly, the scientists did not find a clear link between estimated population size and rate of gene loss. Instead, they found a relationship between mutation rate and gene loss for seven out of the nine lineages studied, with higher mutation rates associated with faster rates of gene loss, resulting in smaller genomes.

"'Although we haven't established a cause, there is a theoretical prediction that explains this observation; if the rate of mutation outweighs a selection pressure to maintain a gene, the gene will be lost from the genome," said Dr. Kinjo.

"The scientists also found clues as to how the gene loss occurred, as strains with smaller genomes had lost genes involved in repairing DNA.

"DNA repair genes fix damaged DNA, so when they are lost the mutation rate of a strain can quickly increase. Most mutations are harmful, so this can quickly inactivate other genes and drive their loss from the genome. If some of these inactivated genes are also involved in DNA repair, this can further accelerate mutation rate and gene loss," explained Professor Gaku Tokuda, from the University of the Ryukyus.

"Although the answers to how gene loss occurs are becoming clearer, whether there are evolutionary reasons behind why prokaryotes increase their rate of mutation to shrink their genome, and if so, what these reasons are, remains an open question.

"'Figuring out the evolutionary explanation for what we see is really complicated. It could be that an increased rate of mutation occurs to provide an adaptive advantage, such as the removal of unwanted or unnecessary genes. But we still can't rule out the possibility that the increased rate of mutation is non-adaptive and due to chance," said Dr. Kinjo.

"Overall, their findings shed new light on the evolution of small genomes, prompting a re-think of the current dominant idea of genome reduction being driven by small population sizes."

Comment: I think part of the misunderstood results is from trying to apply Darwin theory. The causer may not be evolutionary selection pressure. Natural selection is a passive event.