Genetic innovation mediated by viruses

Readers have wondered
about the literature connecting viruses to the genome. Here are a few examples related to mammals and humans I found today.

Apologies for the delay. Turns out I had to ask the right question to get these answers.

The takeaway remains the same:
trust trait analyses = phenomics, which include fossils. Don’t trust deep time genomic studies, which can be and frequently are affected by endemic viruses, producing false positive results that link cats, bats and horses, or link ducks with chickens, or link grebes and flamingos, or link elephants with golden moles.

Broeker and Moelling 2019 wrote:
“We describe mechanisms of genetic innovation mediated by viruses and related elements that, during evolution, caused major genetic changes beyond what was anticipated by Charles Darwin. Viruses and related elements introduced genetic information and have shaped the genomes and immune systems of all cellular life forms. None of these mechanisms contradict Darwin’s theory of evolution but extend it by means of sequence information that has recently become available. Not only do small increments of genetic information contribute to evolution, but also do major events such as infection by viruses or bacteria, which can supply new genetic information to a host by horizontal gene transfer. Thereby, viruses and virus‐like elements act as major drivers of evolution.”

“The conventional definition of a species assumes that any organism acquires its set of genes solely from its parents (subject to minor variations in each generation due to imperfect copying mechanisms). However, mechanisms like HGT= horizontal gene transfer can introduce genetic material even from distantly related species, including viruses or smaller genetic agents such as transposable elements.”

“The human genome contains up to two‐thirds of sequences originating from retroviruses and transposable elements, and at least 145 genes (of a total of 21,000) are likely derived from bacteria, archaea, fungi, protists, and plants.”

Meyerson and Sawyer 2011 reported,
“Recent studies have identified ancient virus genomes preserved as fossils within diverse animal genomes.”

Van Blerkom 2003 reported,
“Some viruses show evidence of long‐standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic.”

References
Broeker F and Moellng K 2019. What viruses tell us about evolution and immunity: beyond Darwin? Ann NY Acad Sc 447(1):53–68. doi: 10.1111/nyas.14097
Meyerson NR and Sawyer SL 2011. Two-stepping through time: mammals and viruses. Trends in Microbiology 19(6):286–294. doi: 10.1016/j.tim.2011.03.006
Van Blerom LM 2003. Role of viruses in human evolution. American Journal of Physical Anthropology 122(Suppl):14–46. doi: 10.1002/ajpa.10384

Publicity
PBS Nova: The viruses that made us human

“Unlike most viruses, which infect, replicate, and then leave their host, retroviruses elbow their way into their host’s genome where they are copied and passed on to daughter cells for the life of the host. This retrovirus, however, managed to sneak its way into one of our ancestor’s sperm or egg cells, able to be passed on to every cell in every subsequent generation. Virus and host had become one.”

“Early mammals used the spare viral parts left in the junk drawers of the genome to use a viral gene to help create the placenta, and other symbiotic viruses help turn us from a ball of cells into a fully-formed squalling infant and protect us from pathogens.”

“Humans are, in a very real sense, part virus.”

“Retroviruses use a slower, stealthier approach. After entering the cell, the retrovirus uses an enzyme called reverse transcriptase to turn its RNA into DNA before making its way to the nucleus. Once in the nucleus, it inserts its DNA into the host’s genome.”

“Sometimes a virus will infect a sperm or egg cell. If fertilization occurs, the offspring will have a copy of the viral genome in every single one of its cells. It can pass the hybrid genome on to its offspring, creating what scientists call a fully endogenous retrovirus—a fancy term for a virus that comes from within.”

“The process requires an astonishingly rare set of circumstances be met, Katzourakis says. “Although endogenous retroviruses make up a pretty large proportion of our genome, in terms of the number of times they’ve infiltrated our genome over the past sixty or so million years, it only comes down to about 30 or 40 distinct occasions,” he says.”

Source: https://pterosaurheresies.wordpress.com/2025/10/10/genetic-innovation-mediated-by-viruses/