Adaptive Evolution Of Yeast Ohnology Genes

Gene duplication. and subsequent divergence, has long been thought to be the principal engines powering the evolution of new gene function.What mechanism drives duplicate genes acquiring novelty functionally is essential for understanding the evolution of complexity of higher organisms. It is generally believed that adaptive evolution is the only mechanism of novel function evolution of genes.Two models, namely new functionalization (NEO-F) model and escape from adaptive conflict (EAC)model,have been proposed to explain adaptive evolution of duplicate genes.Although there have been case studies to support these two models, respectively, evaluation of the relative importance of these two models has not been performed at genomic level.Brewer's yeast Saccharomyces cerevisiae has undergone whole-genome duplication (WGD) event about 100 million years ago. through a long time evolution.approximate 10% of the duplicate genes created by WGD were retained in the genome.Have these retained duplicate genes undergone adaptive evolution? If some of them have experienced adaptive evolution.which of the new functionalization (NEO-F) model and escape from adaptive conflict (EAC) model is more popular than the other? To answer these questions,we used phylogeny-based maximum likelihood methods and the sequence data from various yeast species to detect the evidence of adaptive evolution (having experienced positive selection) in duplicate genes.We analyzed 223 balance data sets and obtained the following results:1.A number of ohnologs in S. cerevisiae have undergone positive selection.We applied the branch-site model A and its null model that was widely used in the aspect of positive selection detection to construct likelihood ratio test (LRT).Among the 223 ohnologs. we found that 108 of 223 genes (48%) had the evidence of positive selection either in one branch right after WGD or in both.This suggested that adaptive evolution was primary mechanism facilitating retention of ohnologs after WGD experienced by S. cerevisiae. Then,we used these genes against those without positive selection evidence to undertake GO analysis.The result showed that the genes with evidence of positive selection had a certain proportion in the function of anti-oxidation, molecular transducer and biological adhesion,while those without evidence of positive selection were none in these three aspects.This indicated that these three functional groups were important to adaptive evolution in yeast. 2.EAC model is one of adaptive evolution mechanisms of the yeast ohnology genesWe used strict standards to distinguish the two adaptive evolution models of duplicate genes. That is. theω(nonsynonymous substitution vs.synonymous substitution ratio)values along the branches right after WGD were used to classify EAC and NEO-F models.Under the model B.there were 38 genes identified as EAC model and 87 genes as NEO-F model:but under the model A.the numbers of EAC and NEO-F models were 43 and 65.respectively.When the combination of both the two models A and B was applied.the numbers of EAC and NEO-F reduced to 5 and 17 respectively.These results implied that although the NEO-F model was more popular than EAC model.the EAC model was also a major mechanism of adaptive evolution of yeast duplicate genes.We could make two conclusions from the above results:Firstly,although the yeast WGD event occurred about 100 million years ago. nearly half (48%)of the duplicate genes were found to have evidence of adaptive evolution when focusing on post-duplication branches followed WGD using maximum likelihood method to detect positive selection sites.This showed that adaptive evolution has an extremely important role to retain duplicate genes.Secondly,although the proportion of duplicate genes consistent with EAC model is smaller than that of those consistent with NEO-F model. the importance of EAC model could not been ignored because of its special role in new function evolution of genes.