D be consistent with the theory proposed here and not withD be consistent with the

D be consistent with the theory proposed here and not with
D be consistent with the theory proposed here and not with the traditional one. With regards to parallelism in general, note that even though the theory presented here is thoroughly in agreement with the widely accepted notion that the number of independent evolutionary events should be considered as a cost in the construction of phylogenetic trees, it allows much more molecular parallelism than the traditional theory. This is because, according to the theory proposed here, similar selection pressures as well as similar writing phenotypes in related species support parallelism. However, hypothesized parallelism still needs to go “with the direction of the phylogenetic tree” rather than against it. In other words, independent evolutionary events do not all have the same cost in phylogeny construction but are more likely to occur the closer the species under consideration are, because both the writing phenotype and the performing phenotype (and hence natural selection) are more similar there. Thus, we may expect some molecular parallelism in the construction of de novo genes, even though, like traditional theory, we doLivnat Biology Direct 2013, 8:24 http://www.biology-direct.com/content/8/1/Page 22 ofnot expect parallel dysfunctionalization of an originally functional gene. Second, if the writing of mutations can write regulatory information into the evolving de novo locus while using information from elsewhere and thus drive evolution toward a functioning product before transcription and/or translation take place, then we also need to consider the possibility PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27488460 that it can move coding sequence information into the de novo locus from elsewhere before transcription and/or translation. The PIPSL gene (Akiva et al. 2006)–a new gene transcribed in the testis of humans and chimpanzees [202]–provides an example of the kind of empirical evidence that would be relevant here. Zhang et al. [203] found evidence of strong Pan-RAS-IN-1MedChemExpress Pan-RAS-IN-1 positive selection (evolution of the amino acid sequence) in PIPSL in the lineage leading to humans and chimpanzees, even though the gene appears not to be translated in either species. They furthermore argued against the idea that the gene has been dysfunctionalized and that such dysfunctionalization is the reason it appears not to be translated [203]. But because, from the traditional perspective, one does not expect to see a high dN/dS ratio with no translation, the authors proposed that the protein is there and that we just have not found it yet–perhaps it is translated during some brief time-window that has so far escaped observation. While they may be right in saying that there is both a signal of selection and a protein, the theory presented here brings up an additional possibility: that there is a signal of selection yet there is no protein. If the protein is searched for thoroughly and is not found, it would be an intriguing negative finding, because it would be understandable from the new theory but not from the traditional one. That is, although it does not necessarily follow from the new theory that there should be sequences currently undergoing positive evolution that are not yet expressed, because for all we know, the transfer of coding information does not lend itself to a dN/dS > 1 read, the possibility that it does may be pursued as a potential distinguishing factor between the new theory and the traditional one, in the PIPSL gene and in other examplesf .Epistatic capture amplifies the issue of de novo genesDe nov.