2022/02/07

Random mutations and natural selection as basis of the theory of Evolution now collapsing

The theory of evolution has lost its theoretical basis - Mutations organisms need for adaptive purposes are not random


https://www.nature.com/articles/s41586-021-04269-6

Excerpts: "Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution."

"Yet, emerging discoveries in genome biology inspire a reconsideration of classical views. It is now known that nucleotide composition, epigenomic features and bias in DNA repair can influence the likelihood that mutations occur at different places across the genome. At the same time, we have learned that specific gene regions and broad classes of genes, including constitutively expressed and essential housekeeping genes, can exist in distinct epigenomic states."

"These results were further supported by our discovery of reduced mutation rate in genes with lethal knockout effects and broadly expressed genes. Again, these results were consistent with epigenomic profiles. In conclusion, we find that genes with the most important functions experience reduced mutation rate, as predicted by their epigenomic features."


"Our findings reveal adaptive mutation bias that is mediated by a link between mutation rate and the epigenome. This is mechanistically plausible in light of evidence that DNA repair factors can be recruited by specific features of the epigenome."

"Finally, because epigenomic features are plastic, epigenome-associated mutation bias could even contribute to environmental effects on mutation. Our discovery yields a new account of the forces driving patterns of natural variation, challenging a long-standing paradigm regarding the randomness of mutation and inspiring future directions for theoretical and practical research on mutation in biology and evolution."

"We found no evidence of selection on these mutations. The germline mutations had accumulated in randomly chosen single-seed descendants, so very few mutations, only those causing inviability or sterility, should have been removed by selection. Somatic mutations experience even less selection."

Summary and conclusions:

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