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POTASSIUM CHANNELS. “The viral K+ channels are small and basically consist of the pore module shared by all K+ channels. Our analyses indicate that viral-encoded K+ channel proteins do not have a close phylogenetic relationship with their host-encoded K+ channel proteins. A similar scenario was recently discovered for a chlorovirus encoded cation transporter which occurs in different virus species independent of their host.” https://lnkd.in/dsexZC2 View in LinkedIn

VIRAL GENE SWAPS. “Hence their ancestor probably exchanged vast pools of genetic elements horizontally and generated a reticulated network of genes at an early stage of their evolution. This view is consistent with the genetics of phycodnavirus evolution as these viruses have both prokaryotic and eukaryotic homologs in addition to many other genes with no cellular homologs.” https://lnkd.in/dsexZC2 View in LinkedIn

STILL CONSIDERED NEUTRAL. "Synonymous variation is therefore still often thought to lack any major functional or evolutionary importance." https://lnkd.in/dU2Q65U View in LinkedIn

HORIZONTAL NOT VERTICAL. “Comparative genomics studies further suggest that virus evolution can best be understood in terms of reticulated ‘trees’ and mosaic evolution. This means that large DNA viruses fundamentally have a network-based history that does not trace back to a single gene or set of genes.” https://lnkd.in/dsexZC2 View in LinkedIn

PREFERRED CODONS. "Such codons are translated more accurately and more efficiently because they are recognized by more abundant tRNA molecules with more specific anti-codon binding. While this kind of selection acting on synonymous mutations is widely accepted, it is generally estimated to be weak - nearly, if not quite, neutral." https://lnkd.in/dU2Q65U View in LinkedIn

NEW IDEAS. “If the viral channel proteins are simplified versions of cellular proteins recently acquired from their hosts, then we would expect to see a high level of sequence similarity between the viral and host homologs. However, this traditional view of virus evolution has been challenged by recent phylogenetic studies of genes in large eukaryotic viruses and prokaryotic viruses.” https://lnkd.in/dsexZC2 View in LinkedIn

CODON BIAS. "Highly expressed genes and codons encoding functionally important amino acids generally display particularly biased patterns of codon usage. This observation led to the theory that selection for translation optimization generates higher levels of codon bias. In other words, it is thought that the speed and accuracy of mRNA translation is higher for a subset of codons, referred to as “optimal” (“preferred”) codons." https://lnkd.in/dU2Q65U View in LinkedIn

MOLECULAR PIRACY? “The fact that K+ channels from all eukaryotes contain a common pore structure that resembles the viral K+ channels is consistent with the traditional assumption that viruses are mere ‘gene pick pockets’ and frequently acquire genes from their host via molecular piracy.” https://lnkd.in/dsexZC2 View in LinkedIn

HISTORICAL DOGMA. "Synonymous sites are then the collection of potential synonymous mutations present in a gene. Predicated on the assumption that the coding sequences of a gene is simply the recipe for making the protein, synonymous mutations were long thought to have no functional effect, in other words to be “silent” and thus selectively neutral." https://lnkd.in/dU2Q65U View in LinkedIn

NEW PARADIGM. "Asserting the core importance of persistent virus to host survival thus presents a big break from historic views in evolutionary biology and adds a process of selection that stems from the horizontal transmission of persistent virus. As the virosphere provides no ‘virus-free' habitat for any life form, all living forms have adapted to their own viral habitat." https://lnkd.in/etdQ9rN View in LinkedIn