Viruses today spread genes among bacteria and humans and other cells, as they always have... We are our viruses — Lynn Margulis, 1998 (1)
May we not feel that in the virus, in their merging with the cellular genome and their re-emerging from them, we observe processes which, in the course of evolution, have created the succesful genetic patterns that underlie all living things? — Salvador Luria, 1959 (2)
The Darwinian paradigm holds that copying mistakes and the shuffling of existing genes are sufficient to write the new genes needed for evolutionary advances. Cosmic Ancestry holds that these processes cannot write useful new genes. Instead, for a species to make evolutionary progress, new genes must first be installed into its genome from outside. We will discuss well-known processes which can install new genes into the genome of a given species. Then we will look at viruses.
RecombinationMutation is the mechanism of genetic change that we hear the most about. Every known example of a single-nucleotide mutation, however, is either adaptive within a narrow range, neutral, or deleterious in its effect. The rare exception is the back-mutation, which merely undoes the damage of a previous mutation and restores the affected strand of DNA to its original condition.
Recombination is a much more powerful mutation way for DNA to change. If an organism's genome were written out as text, single-nucleotide mutations would be single-letter mistakes, whereas recombination takes whole words, sentences, paragraphs, pages or groups of pages and moves them to different locations. These new locations could be elsewhere in the same paragraph, page, bookshelf, or library. Obviously a powerful mechanism like recombination should be incorporated into anyone's understanding of the theory of evolution. There are three kinds of recombination:
- When two strings of similar DNA line up with each other and swap sections, it's called homologous recombination.
- When shorter pieces of similar DNA line up to initiate a swap of longer, dissimilar pieces (of which the shorter pieces can be part), that's called site-specific recombination.
- Transposition enables a piece of DNA to move within the same chromosome, or to a different chromosome, to a location with which it has no similarity.
The Transfer of DNA Across Species BoundariesBacteria trade genes more frantically than a pit full of traders on the floor of the Chicago Mercantile Exchange — Lynn Margulis and Dorion Sagan (3)
While recombination moves whole blocks of genetic instructions within a cell, other processes move whole blocks of genetic information from one bacterium to another bacterium of a different kind. In the analogy between genes and written text, this move is a transfer of paragraphs or pages from one library to another.
One such process is transformation. Here pieces of genetic instructions are released by a bacterium into its environment. Another bacterium, not necessarily of the same strain, picks up the DNA and incorporates it into its own genome. For example, Streptococcus pneumoniae that are not pathogenic can become so by transformation (4). As an illustration of transformation, think of a passenger who jumps overboard from one ship and is later picked up by another one.
Conjugation is the bacterial version of sex. In conjugation, bacterial cells actually connect, and the "male" donates a piece of DNA to the "female." The piece of DNA in this case was excised earlier from the bacterial chromosome. Such excised pieces of DNA are called plasmids. (Plasmids, being able to pass out of one cell and into another, are similar to viruses. But they have no protein coat and no "life cycle" different from that of their host cell; in this respect they resemble small chromosomes.) If the transferred genetic material is a passenger on a ship, in the transfer of plasmids by conjugation, the ships come alongside each other and the passenger walks across a gangplank to the new ship.
Transduction is yet another way for bacteria to exchange genetic material. In transduction, a virus takes up a piece of DNA from its bacterial host and incorporates it into its own viral genome. After the virus has multiplied, many copies of the virus erupt from the infected cell. Depending on the kind of transduction, some or all of the daughter viruses take copies of parts of the bacterial DNA with them. When one of them infects a new cell, it inserts the stolen DNA into the new cell, where the stolen piece becomes integrated into the new cell's DNA. (The stolen piece may be a whole gene with which the cell acquires a new function, as was reported in June, 1996, by two scientists at Harvard Medical School (5).) In transduction, the passenger resorts to hiding inside some freight, hoping to get aboard a different ship that way.
Transduction by viruses works in eukaryotic organisms as well. The discovery that large blocks of genetic instructions can be swapped and transferred among creatures is a clue that the insertion of new genes could be the mechanism behind evolutionary advances. If viruses can transfer eukaryotic genes across species boundaries, and can install their own genes into their hosts, the case for the new mechanism is even stronger. As we will see, viruses do just that.
Viruses are mobile genetic elements (6)
It was an absolutely stunning surprise to us that something as strange as viruses carrying genes from one cell to another can happen — Joshua Lederberg (7)
If your computer suddenly begins to greet you with a vulgar message, you will recognize that the computer has contracted a virus. It might have arrived via the modem, it might have come with a new program on a disk, or someone might have stealthily keyed it in. It might even have been there when you originally acquired the computer. However it got there, it is definitely a computer virus, and your computer did not spontaneously generate it.
Computer viruses are called viruses because they are analogous to biological viruses that infect living cells. Because viruses are simpler than cells, biologists used to think that maybe viruses were the precellular life forms that Darwinism requires. Today however, even Darwinists don't think that viruses are this link. Viruses are not independently capable of metabolism or reproduction. Darwinists now think that viruses evolved after cells. What is a virus?
A virus is a piece of genetic instructions, usually in a protective coat. Virus particles are tiny; a cell can manufacture and contain as many as a thousand of them before breaking open. They were first discovered when biologists observed that some disease-causing agents were able to pass through a filter too fine for bacteria. They can be small because they contain almost none of the machinery of a cell, only a smallish quantity of DNA or RNA.
Viruses are not living things. When they are outside of their host cell, they are just very complex molecular particles that have no metabolism and no way to reproduce. In our computer metaphor, they're like software with no hardware, floppy disks or diskettes without a computer. Having no independent metabolism they can remain viable indefinitely, under the right circumstances. "Some of them can even be crystallized, like minerals. In this state they can survive for years unchanged — until they are wetted and placed into contact with their particular hosts" (8).
The viruses that infect bacteria are more specifically called bacteriophages, or simply phages. The kind and amount of genetic instructions in phages vary from 3,600 RNA nucleotides to 166,000 DNA nucleotide pairs (9). To restate these dimensions in terms of our computer analogy, the computer viruses that infect handheld calculators range in size from 900 bytes to over 40 kilobytes. For comparison, the simplest handheld calculator (a bacterium) has about 200 kilobytes of stored programs.
The viruses that infect eukaryotic cells vary in size also. The poliovirus has 7,600 RNA nucleotides; the vaccinia (cowpox) virus has 240,000 DNA nucleotide pairs (10). To use computer terms again, the computer viruses that infect personal computers range in size from 1.9 kilobytes to 60 kilobytes. For comparison, a very simple personal computer (a yeast cell) has genetic instructions equivalent to about 8 megabytes. An advanced personal computer (a human cell) contains about 1.5 gigabytes of stored information, counting the backup copy and the "silent" DNA.
Herpesvirus by Linda Stannard: All the Virology on the WWW
When a virus attaches to its host cell, the host may take the whole virus into its cytoplasm where the virus's protective coat is removed. However, some bacteriophages use a different invasion method. They remain outside the cell and a chemical trigger causes them to inject their genome into the host's cytoplasm. Either way, the virus's genome enters the cytoplasm of the host cell.
Once inside, the virus causes the machinery of the host cell to enter one of two cycles, the lytic cycle or the lysogenic cycle. In the lytic cycle, which leads to cell degradation, the host begins to carry out the reproductive instructions in the invading virus's genome. Those instructions are, in summary, "make more of me." The host becomes a slave to the invader; it drops everything and begins to manufacture copies of the virus. After many copies have been made, the cell breaks open and dies, and many viruses are released. This is the normal way in which a virus causes symptoms of disease in its host.
In the lysogenic cycle the host cell does not make more viruses, but simply harbors the entire viral genome in the cell, usually by incorporating it into the cell's genome. If the virus is an RNA virus, as many are, the RNA must first undergo "reverse transcription" into DNA. While harboring the viral genes, the cell may grow and multiply normally, carrying the new instructions harmlessly along with it. A virus carried in this manner is said to be latent. Recently scientists have learned that even during latency, some of the virus's genes can be expressed (11).
Sometimes after lysogenic integration of the viral genome into the host's DNA, an "induction event" can cause the viral infection to revert to the lytic cycle, in which the cell makes many copies of the virus and dies. After this happens, the numerous new virus particles can then infect many other cells. If the new infections are lysogenic, the virus's genes may again become integrated into the DNA of the new cells without harm to them. Lytic infection of one host followed by lysogenic infection in another is also called transduction. When we discussed transduction earlier, we said viruses could tranduct a cell's genes to another cell. Here we see that the virus's own genes can also be transducted into cells.
This method of acquiring genes is not in doubt. Among bacteria, for example, "There are some well-documented cases of homologies between viral genes and their host counterparts. ...Some past exchanges have occurred between distantly related phages and between phage and host" (12). Eukaryotes are also known to acquire viral genes, and the phenomenon is not rare. "Endogenous retroviruses and retroviral elements have been found in all vertebrates investigated.... As a general rule, the number of groups of viral sequences found within a given vertebrate species is proportional to the effort spent searching that species" (13).
And it has now been shown that some of the genes that viruses install have a beneficial function for the host. In fact, doctors now use viruses to install genes in the new field of "gene therapy." Even the virus that causes AIDS, if properly disabled, may become useful this way (14, 15).
When the genome of Bacillus subtilis was completely sequenced and published in July, 1997, the sequencers noticed another interesting example of gene transfer. "...Some of the bacteriophages in B. subtilis also appear to contribute genes that aid the host bacterium by helping it resist harmful substances such as heavy metals" (16). This evidence confirms that genes installed by a virus into the genome of the host can be beneficial, even essential, for the evolution of the host.
One example of a benefit conferred by viral genes comes from humans. A sequence installed by a retrovirus regulates the amylase gene cluster, allowing us to produce amylase in our saliva. This sequence that we share with a few other primates enables us to eat starchy foods we otherwise couldn't (17).
In August, 1997, another whole-genome sequencing, of Helicobacter pylori, found that many genes in it are more similar to those of eukaryotes or archaea than other bacteria (18). "Such observations... are often interpreted as evidence of lateral gene transfer in the evolutionary history of an organism," say the sequencers.
Additional evidence that genes can move across species boundaries even in eukaryotes comes in the June 13, 1997, issue of Science. A report there by Frederico J. Gueiros-Filho and Stephen M. Beverley of Harvard describes the "Trans-kingdom Transposition" of a gene-size piece of DNA known as a transposable element (19). The particular transposable element they studied, called mariner, has already been found in planaria, nematodes, centipedes, many insects, and humans (20). Until recently, transposable elements were considered to be functionless, or "junk DNA." But John McDonald, a professor in the department of genetics at the University of Georgia, concludes, "It now appears that at least some transposable elements may be essential to the organisms in which they reside. Even more interesting is the growing likelihood that transposable elements have played an essential role in the evolution of higher organisms, including humans" (21). Another team of biologists has demonstrated that by transformation (discussed above in bacteria) a mariner element can become installed into the inherited genome of zebrafish (22). So viruses are not the only mobile genetic elements.
In conclusion, viruses could easily provide a way for new genes never before encountered by a species to become part of its genome. That viruses install new genes into their hosts is not speculative — it is a well known fact. That transferred genes are important in evolution is becoming well established. According to Cosmic Ancestry, the horizontal transfer of genes by viruses and other means is essential for evolutionary progress.
It is almost certainly the case that some modern-day retrotransposons... are derived from retroviruses that lost their infectivity and are more properly considered as ancient endogenous retroviruses. — J.D. Boeke and J.P. Stoye, 1997 (23)
1. Lynn Margulis, Symbiotic Planet: A New Look at Evolution, Basic Books, 1998. p 64.
2. Salvador E. Luria, Virus Growth and Variation, A. Isaacs and B.W. Lacey, eds., Cambridge University Press, 1959. p 1-10.
3. Lynn Margulis and Dorion Sagan, What Is Life? Simon and Schuster, 1995. p 73.
4. Neil A. Campbell, Biology, 3rd edition. The Benjamin/Cummings Publishing Company, Inc., 1993. p 301.
5. Matthew K. Waldor and John J. Mekalanos, "Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin" p 1910-1914 v 272, Science, June 28, 1996. Also see comments by Nigel Williams, p 1869-1870; and see "Harvard researchers find cholera bacterium may take instruction from a virus," by Misia Landau and Keren McGinity at EurekAlert!, 27 June 27 1996.
6. Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts and James D. Watson, The Molecular Biology of the Cell, 3rd edition. New York: Garland Publishing, Inc., 1994. p 274.
7. Joshua Lederberg, "Interview with Prof. Lederberg, Winner of the 1958 Nobel Prize in Physiology and Medicine" [transcript], conducted by Lev Pevzner, 20 March 1996.
8. Lynn Margulis and Karlene V. Schwartz, Five Kingdoms, 2nd edition. W. H. Freeman and Company, 1988. p 16.
9. T.A. Brown, Genetics: A Molecular Approach, 2nd edition, Chapman and Hall, 1992. p 221.
10. T.A. Brown, Genetics: A Molecular Approach, 2nd edition, Chapman and Hall, 1992. p 234.
11. Susan J. Baserga and Joan A. Steitz, "The Diverse World of Small Ribonucleoproteins," p 359-381, The RNA World, R.F. Gesteland and J.F. Atkins, eds., Cold Spring Harbor Laboratory Press, 1993. p 374.
12. Allan M. Campbell, "Bacteriophage Ecology, Evolution and Speciation," p 81-83, Encyclopedia of Virology, Robert G. Webster and Allan Granoff, eds., Academic Press, 1994.
13. John M. Coffin, Stephen H. Hughes and Harold E. Varmus, eds., Retroviruses, Cold Spring Harbor Laboratory Press, 1997. p 346.
14. Jon Cohen, "A New Role for HIV: A Vehicle For Moving Genes Into Cells" p 195 v 272, Science, 12 April 1996.
15. Andrew Pollack, "Scientists Enlist H.I.V. to Fight Other Ills," The New York Times, 19 January 1999.
16. Nigel Williams, "Gram-Positive Bacterium Sequenced," p 478 v 277, Science, 25 July 1997.
17. John M. Coffin, Stephen H. Hughes and Harold E. Varmus, eds., Retroviruses, Cold Spring Harbor Laboratory Press, 1997. p 403.
18. Jean-F. Tomb et al. (41 others), "The complete genome sequence of the gastric pathogen Helicobacter pylori" p 539-547 v 388, Nature, 7 August 1997.
19. Frederico J. Gueiros-Filho and Stephen M. Beverley, "Trans-kingdom Transposition of the Drosophila Element mariner Within the Protozoan Leishmania," p 1716-1719 v 276, Science, 13 June 1997.
20. Daniel L. Hartl, "Mariner Sails into Leishmania," p 1659-1660 v 276, Science, 13 June 1997.
21. Phil Williams, "Transposable Elements May Have Had A Major Role In The Evolution Of Higher Organisms," EurekAlert!, 9 February 1998.
22. James M. Fadool, Daniel L. Hartl and John E. Dowling. "Transposition of the mariner element from Drosophila mauritiana in zebrafish," p 5182-5186 v 95 n 9, Proc. Nat. Acad. Sci., USA, 28 April 1998.
23. John M. Coffin, Stephen H. Hughes and Harold E. Varmus, eds., Retroviruses, Cold Spring Harbor Laboratory Press, 1997. p 414.
...Bacteria Harpoon and Swallow DNA to Evolve by Rafi Letzter, LiveScience.com, 12 Jun 2018.
13 Jun 2018: Pandora viruses have more than a thousand genes. Some have functions for prokaryotes or eukaryotes. At least two-thirds are completely novel.
05 May 2018: A giant marine virus has 663 predicted genes, 435 of which resemble none previously known.
Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly by Tu Anh Nguyen, Jamie Greig, Asif Khan et al., doi:10.1371/journal.pbio.2004920, PLoS Biol., 24 Apr 2018.
Comparative genomics of bdelloid rotifers... by Chiara Boschetti, Timothy G. Barraclough et al., doi:10.1371/journal.pbio.2004830, PLoS Biol., 24 Apr 2018. ...we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species....
Mineral facilitated horizontal gene transfer: A new principle for evolution of life? by Karina K. Sand and Stanislav Jelavić, doi:10.1101/235531, BioRxiv, preprint online 21 Dec 2017.
Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla by Michael J. Metzger et al., PNAS, online 18 Apr 2018. ...These data suggest that over both short- and long-term evolutionary timescales, Steamer-like retrotransposons, much like retroviruses, can move between organisms and integrate new copies into new host genomes.
Genome evolution across 1,011 Saccharomyces cerevisiae isolates by Jackson Peter et al., Nature, 12 Apr 2018. ...183 ORFs are likely to be the result of horizontal gene transfer (HGT) events from highly divergent yeast species.
Massive lateral transfer of genes ...to the mycoparasitic fungus Trichoderma from its plant-associated hosts by Irina S. Druzhinina et al., PLoS Genet., online 09 Apr 2018.
Transposable elements are the primary source of novelty in primate gene regulation by Marco Trizzino et al., doi:10.1101/gr.218149.116, Genome Res., online 30 Aug 2017.
Destabilizing mutations encode nongenetic variation that drives evolutionary innovation by Katherine L. Petrie et al., Science, 30 Mar 2018. Natural selection, the predominant theory for adaptation, is unable to explain how mutations encode new function
Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere by Jônatas Abrahão et al., Nature Communications, 27 Feb 2018.
Horizontal gene cluster transfer increased hallucinogenic mushroom diversity by Hannah T. Reynolds et al., Evolution Letters, 27 Feb 2018.
"Astrovirology" Chief Ken Stedman Guesses Earth Origins for Viruses, interview with Suzan Mazur, posted on Oscillations, 19 Feb 2018.
11 Feb 2018: A giant virus has genes for eukaryotic histones.
An ancient virus could be responsible for human consciousness: 4-min. facebook video, posted 08 Feb 2018.
07 Feb 2018: Every day, more than 800 million viruses are deposited per square metre above the planetary boundary layer....
20 Jan 2018: The genomes of all vertebrates harbor remnants of ancient retroviral infections.
17 Jan 2018: Viruses Drive Evolution
13 Jan 2018: ...some evolved into genes that let cells communicate.
28 Dec 2017: ...some bacteria inject a toxic cocktail into their competitors. ...the predator cell can acquire antibiotic resistance.
06 Dec 2017: A new study reveals that viruses share genes across the three superkingdoms of life....
Retrotransposons Mimic Germ Plasm Determinants to Promote Transgenerational Inheritance by Bhavana Tiwari et al., Current Biology, 09 Oct 2017.
An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard by Guillaume Cornelis et al., PNAS, online 21 Nov 2017.
24 Oct 2017: A virus carries a gene essential for insect metamorphosis.
A Horizontally Transferred Autonomous Helitron Became a Full Polydnavirus Segment in Cotesia vestalis by Pedro Heringer, Guilherme B. Dias and Gustavo C. S. Kuhn, G3, online 17 Oct 2017. Our results reinforce the idea of parasitoid wasps as frequent agents of horizontal transfers in eukaryotes.
Ancient Viruses Are Buried in Your DNA by Carl Zimmer, The New York Times, 04 Oct 2017.
Effect of the environment on horizontal gene transfer between bacteria and archaea by Clara A. Fuchsman et al., PeerJ, online 29 Sep 2017.
27 Sep 2017: ...multiple waves of LINE retrotransposition and the birth of new mobile elements during primate evolution, and their impact on the evolving human brain.
01 Sep 2017: an interview with Nigel Goldenfeld.
12 Sep 2017: ...that a horizontal gene transfer (HGT) event introduced the reflectin gene into ancient cephalopods.
01 Sep 2017: an interview with Nigel Goldenfeld.
Transposable elements are the primary source of novelty in primate gene regulation by Marco Trizzino et al., doi:10.1101/gr.218149.116, Genome Res., online 30 Aug 2017.
Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer by Frances Tran and James Q. Boedicker, Scientific Reports, online 18 Aug 2017.
Transposable Elements Direct The Coevolution between Plants and Microbes by Michaeil F. Seidl and Bart P.H.J. Thomma, Trends in Genetics, proof online 08 Aug 2017.
Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species by Jesper Bechsgaard et al., doi:10.1534/g3.117.043984, G3, 08 Aug 2017.
More colistin-resistance genes identified in Europe, by Chris Dall, University of Minnesota, 03 Aug 2017. The MCR-1 gene was first identified in China in Escherichia coli from pigs, pork products, and humans in 2015. Since then, the gene has been detected in enteric bacteria from animals and humans in more than 30 countries.... The genes are a particular concern because they are located on plasmids, which are small, highly mobile pieces of DNA that can spread resistance within and between different species of bacteria through horizontal gene transfer.
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses by Ito J, Sugimoto R, Nakaoka H, Yamada S, Kimura T, Hayano T et al., doi:10.1371/journal.pgen.1006883, PLoS Genet, uncorrected proof online 12 Jul 2017. Several studies have suggested that [transposable element] insertions have contributed to the rewiring and evolution of regulatory networks by recruiting multiple genes into the same regulatory circuit.
Tiny Answers to Big Questions by April Pawluk, doi:10.1016/j.cell.2017.06.033, Cell, 13 Jul 2017. Phages remain one of the largest untapped resources of completely novel genetic material, which is sure to contain many surprises.
Origin of magnetotaxis: Vertical inheritance or horizontal transfer? by Sishuo Wang and Youhua Chen, doi:10.1073/pnas.1706937114, PNAS, 27 Jun 2017.
22 May 2017: Retrotransposons often carry long terminal repeats (LTRs) for retroviruslike reverse transcription and integration into the genome....
Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer, by Walter J. Lapadula et al., doi:10.1038/s41598-017-01859-1, Nature Scientific Reports, online 12 May 2017.
17 Apr 2017: Together, our results establish HTT as a major force shaping insect genome.
Integration site selection by retroviruses and transposable elements in eukaryotes, by Tania Sultana et al., doi:10.1038/nrg.2017.7, Nature Reviews Genetics, online 13 Mar 2017. The DNA sequence, chromatin and nuclear context, and cellular proteins cooperate in guiding integration in eukaryotic genomes, leading to a remarkable diversity of insertion site distribution and evolutionary strategies.
07 Apr 2017: ...Klosneuviruses encode an expanded translation machinery....
DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome, by Tuğçe Aktaş et al., doi:10.1038/nature21715, Nature, 06 Apr 2017. Our work uncovers an evolutionarily conserved function of DHX9. We propose that it acts as a nuclear RNA resolvase that neutralizes the immediate threat posed by transposon insertions and allows these elements to evolve as tools for the post-transcriptional regulation of gene expression.
05 Mar 2017: ...hundreds or even more than a thousand predicted HGT regions in the human genome.
31 Mar 2017: ...Oxyphotobacteria acquired the genes for photosynthesis relatively late in cyanobacterial evolution.
What makes bird flu jump species?, Nature, 30 Mar 2017.
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families, by Jemma L. Geoghegan et al., doi: 10.1371/journal.ppat.1006215, PLOS Pathogens, 08 Feb 2017. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species....
Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats..., by Helena Farkašová et al., doi:10.1073/pnas.1621224114, PNAS, 09 Mar 2017. This discovery closes the last major gap in the retroviral fossil record....
09 Mar 2017: ...our results demonstrate that KZFPs partner with transposable elements to build a ...layer of epigenetic regulation.
Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow, by Kerry A. Whittaker and Tatiana A. Rynearson, doi:10.1073/pnas.1612346114, PNAS, 07 Mar 2017. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe....
07 Mar 2017: ...the origin of viral replicative modules seems likely to hark all the way back to the precellular era.
Automated Detection of Lateral Gene Transfer in Fungi, by Pierre-Yves Dupont and Murray P. Cox, doi:10.1534/g3.116.038448, G3, online 24 Feb 2017.
23 Feb 2017: The horizontal transfer of transposable elements ...should be regarded as a pivotal force in eukaryotic genome evolution.
17 Feb 2017: ...giant viruses present an astonishing arsenal of genes not widespread in the virosphere....
Dynamics of genome size evolution in birds and mammals, by Aurélie Kapusta, Alexander Suh, and Cédric Feschotte, doi:10.1073/pnas.1616702114, PNAS, 08 Feb 2017. ...analysis of the amount of genomic DNA gained and lost during eutherian and avian evolution....
11 Jan 2017: 17 Jan 2017: A virus that infects bacteria listens to messages from its relatives when deciding how to attack its hosts.
Novel 'Superspreader' Bacteriophages Promote Horizontal Gene Transfer by Transformation, by Eric C. Keen et al., doi:10.1128/mBio.02115-16, mBio, 17 Jan 2017. Bacteriophages infect an estimated 10^23 to 10^25 bacterial cells each second, many of which carry physiologically relevant plasmids....
The draft genome of whitefly Bemisia tabaci MEAM1..., by Wenbo Chen, Daniel K. Hasegawa et al., doi:10.1186/s12915-016-0321-y, BMC Biology, 14 Dec 2016. The presence of 142 horizontally transferred genes from bacteria or fungi....
Acquisition of Phage Sensitivity by Bacteria through Exchange of Phage Receptors, by Elhanan Tzipilevich et al., doi:10.1016/j.cell.2016.12.003, Cell, 12 Jan 2017. Bacteria sensitive to phage infection can exchange phage receptors with their resistant neighbors by cell-to-cell contact, suggesting a new route for information transfer.
11 Jan 2017: ...they've been around for hundreds of millions of years.
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics, by Jan Janouškovec et al., doi:10.1073/pnas.1614842114, PNAS, 10 Jan 2017. ...the role of horizontal gene transfer in the origin of their unique nuclear architecture.
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution, by Schönknecht G, Weber AP, Lercher MJ, doi:10.1002/bies.201300095, Bioessays, Jan 2014. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg.
Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages, by Charley G. P. McCarthy and David A. Fitzpatrick, doi:10.1128/mSphere.00195-16, mSphere, online 14 Sep 2016.
Redefining the invertebrate RNA virosphere, by Mang Shi et al., doi:10.1038/nature20167, Nature, online 23 Nov 2016....remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements.
In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus, by Xinghong Dai et al., doi:10.1038/nature20589, Nature, online 19 Dec 2016.
Transcriptional regulation of a horizontally transferred gene from bacterium to chordate, by Yasunori Sasakura et al., doi:10.1098/rspb.2016.1712, Proceedings of the Royal Society of London B, 21 Dec 2016; and commentary:
Mechanism of successful horizontal gene transfer between divergent organisms explained, EurekAlert
(+Lab Manager), 20 Dec 2016.
Mycelia as a focal point for horizontal gene transfer among soil bacteria, by Tom Berthold et al., doi:10.1038/srep36390, Scientific Reports, online 04 Nov 2016.
Host genome integration and giant virus-induced reactivation of the virophage mavirus, by Matthias G. Fischer and Thomas Hackl, doi:10.1038/nature20593, Nature, online 07 Dec 2016. Here we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defence system.
06 Dec 2016: ...Thus, bacteria-to-animal horizontal genome transfer represents a remarkable mechanism underpinning the birth of sex chromosomes.
Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria..., by Isabelle R. Gonçalves et al., doi:10.1186/s12862-016-0815-9, BMC Evolutionary Biology, 24 Nov 2016.
30 Nov 2016: These data suggest that eukaryotic hosts are involved in bacterial HGT....
Are viruses alive? by Eugene V. Koonin and Petro Starokadomskyy, doi:10.1016/j.shpsc.2016.02.016, Studies in History and Philosophy of Biological and Biomedical Science, Oct 2016.
Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes, by M. Krupovic and P. Forterre, 1341:41-53 Ann. N. Y. Acad. Sci., Apr (online 11 Feb) 2015.
Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation, by Zhenzhen Yang, Yeting Zhang, et al., doi:10.1073/pnas.1608765113, PNAS, online 24 Oct 2016; and commentary Parasitic plants may form weapons out of genes stolen from hosts by Matt Swayne, Penn State (+ScienceDaily +Virginia Tech), 24 Oct 2016.
LTR retrotransposons create transcribed retrocopies in metazoans, by Shengjun Tan et al., doi:10.1101/gr.204925.116, Genome Res., online 20 Oct 2016. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa and combined with previous work from plants and yeast that it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.
17 Oct 2016: ...here's a bacterium that manipulates animals using animal genes found in a virus.
13 Oct 2016: ...the microbial world ...can move these genes between organisms according to need.
Ancient recombination events and the origins of hepatitis E virus, by Andrew G. Kelly et al., doi:10.1186/s12862-016-0785-y, BMC Evolutionary Biology, 12 Oct 2016. ...we hypothesize that viruses from the alpha-like super-group, which usually infect plants and insects, gain an entirely new structure through recombination to enable tropism into new hosts within the animal world.
Theory of prokaryotic genome evolution, by Itamar Sela, Yuri I. Wolf, and Eugene V. Koonin, doi:10.1073/pnas.1614083113, PNAS, online 04 Oct 2016. ...The relatively small number of genes in prokaryotes is explained by the diminishing return associated with the acquisition of new genes as the genome grows combined with the intrinsic deletion bias.
Bacteria and Humans Have Been Swapping DNA for Millennia, by Kelly Robinson and Julie Dunning Hotopp, The Scientist, 01 Oct 2016.
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses by Simon Roux et al., doi:10.1038/nature19366, Nature, 29 Sep 2016. ...Less than one per cent of observed surface-ocean viruses are 'known'.
Changes in the composition of the RNA virome mark evolutionary transitions in green plants by Arcady Mushegian, Alexey Shipunov and Santiago F. Elena, doi:10.1186/s12915-016-0288-8, BMC Biology, 15 Aug 2016. The broadened repertoire of RNA viruses suggests that colonization of land and growth in anatomical complexity in land plants coincided with the acquisition of novel sets of viruses with different strategies of infection and reproduction.
Genetic Evidence That Captured Retroviral Envelope syncytins Contribute to Myoblast Fusion and Muscle Sexual Dimorphism in Mice by François Redelsperger, Najat Raddi, Agathe Bacquin et al., doi:10.1371/journal.pgen.1006289, PLoS Genet, 02 Sep 2016.
04 Sep 2016: The Kingdom of Speech by Tom Wolfe [review].
Metazoan ribotoxin genes acquired by Horizontal Gene Transfer by Walter Jesus Lapadula et al., doi:10.1101/071340, bioRxiv beta, online 26 Aug 2016.
Unveiled: Earth's Viral Diversity, Lawrence Berkeley National Laboratory via Newswise, 15 Aug 2016. We have increased the number of viral sequences by 50x, and 99 percent of the virus families identified are not closely related to any previously sequenced virus.
Viruses revealed to be a major driver of human evolution, posted on ScienceDaily from Genetics Society of America, 13 Jul 2016.
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities by James P. J. Hall et al., doi:10.1073/pnas.1600974113, PNAS, online 06 Jul 2016. Bacterial adaptation through horizontal gene transfer is central to microbial evolution.... Beneficial [plasmid] genes are captured by the chromosome.
Temperate phages both mediate and drive adaptive evolution in pathogen biofilms by Emily V. Davies, Chloe E. James, David Williams et al., doi:10.1073/pnas.1520056113, PNAS, online 01 Jul 2016.
03 Jun 2016: ...The mutation event giving rise to industrial melanism in Britain was the insertion of a ...transposable element....
Horizontal gene transfer of pectinases from bacteria preceded the diversification of stick and leaf insects by Matan Shelomi et al., doi:10.1038/srep26388, Scientific Reports, 23 May 2016; and commentary:
In the course of evolution, genes of gut microbes "jumped" to their insect host, Max Planck Institute for Chemical Ecology (+ScienceDaily), 31 May 2016.
Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element by François Delavat et al., doi:10.1073/pnas.1604479113, PNAS, online 31 May 2016. Integrative and conjugative elements (ICEs) are frequently detected mobile genome inhabitants. They can contribute to host adaptation by dispersing dozens to hundreds of genes in a single transfer event.... Environmental cues eliciting the "SOS response" or growth on specific carbon substrates can enhance ICE transfer rates.
Extensive horizontal gene transfers between plant pathogenic fungi by Huan Qiu et al., doi:10.1186/s12915-016-0264-3, BMC Biology, 23 May 2016.
13 May 2016: Yeast likely acquired the gene for an essential protein via horizontal gene transfer.
Horizontal transfer beyond genes by Eugene V. Koonin, doi:10.1073/pnas.1418789111, PNAS, 11 Nov 2014.
30 Apr 2016: ...The genetic basis for the evolutionary transition emerges much earlier than anticipated....
Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes by Alexander Suh et al., doi:10.1038/ncomms11396, Nature Communications, 21 Apr 2016.
Surface mutation lets canine parvovirus jump to other species by Tom Fleischman, Cornell University (+Newswise), 14 Apr 2016.
Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients by Jason B. Noon and Thomas J. Baum, doi:10.1186/s12862-016-0651-y, BMC Evolutionary Biology, 12 Apr 2016. ...We also discovered that homologous ancestral bacterial sequences for two of these gene groups ...were likely the subject of very extensive HGT from highly different bacterial donors to many diverse recipient lineages of eukaryotes and archaea.
Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides by William G. Alexander et al., doi:10.1073/pnas.1517242113, PNAS, 12 Apr 2016.
09 Apr 2016: The human reference genome contains over 120 HML-2 [endogenous retrovirus] insertions that are not present in chimpanzees, bonobos, or gorillas.
Multi-host environments select for host-generalist conjugative plasmids by Anastasia Kottara et al., doi:10.1186/s12862-016-0642-z, BMC Evolutionary Biology, 02 Apr 2016.
Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides by William G. Alexander et al., doi:10.1073/pnas.1517242113, PNAS, online 29 Mar 2016.
Discovery of unfixed endogenous retrovirus insertions in diverse human populations by Julia Halo Wildschutte, Zachary H. Williams et al., doi:10.1073/pnas.1602336113, PNAS, online 21 Mar 2016.
Filoviruses are ancient and integrated into mammalian genomes by Derek J Taylor, Robert W Leach and Jeremy Bruenn, doi:10.1186/1471-2148-10-193, BMC Evolutionary Biology, 2010.
17 Mar 2016: ...Viruses likely initiated major evolutionary shifts.
10 Mar 2016: Viruses... have had a significant impact on the evolution of all organisms, from bacteria to humans.
03 Mar 2016: ...These viral fossils probably played a key role in the evolution of our species....
Beg, Borrow and Steal: Three Aspects of Horizontal Gene Transfer in the Protozoan Parasite, Cryptosporidium parvum, Adam Sateriale and Boris Striepen, doi:10.1371/journal.ppat.1005429, PLOS, 03 Mar 2016.
Philosopher of science John Dupré, interviewed by Suzan Mazur, HuffPost Science, 08 Feb 2016.
Integron, from Wikipedia. Integrons are genetic units characterized by their ability to capture and incorporate gene cassettes by site-specific recombination.
04 Feb 2016: The bed bug genome contains more than 800 genes that apparently come from bacteria.
Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility by Pavle Vrljicak et al., doi:10.1534/g3.115.026849, G3, online 27 Jan 2016.
04 Jan 2016: Thousands of human and/or chimpanzee-specific genes are derived from previously silent DNA.
30 Dec 2015: It is even argued that HGT has been highly active and important since the beginning of cellular life and that the complexity of life, as we know it, may not have evolved without HGT.
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes by Alastair Crisp, Chiara Boschetti et al., doi:10.1186/s13059-015-0607-3, Genome Biol. [PubMed abstract], 15 Mar 2015.
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution by Sarah Schaack, Clément Gilbert and Cédric Feschotte, doi:10.1016/j.tree.2010.06.001, Trends Ecol Evol. [PubMed abstract], Sep 2010.
In retrospect: A century of phage lessons by Forest Rohwer and Anca M. Segall, doi:10.1038/528046a, p 46-48 v 528, Nature, 3 Dec 2015.
24 Nov 2015: Approximately one-sixth of the genes in the tardigrade genome were found to have been acquired through horizontal transfer.... (Disputed, 7 Dec 2015 & 3 May 2016.)
23 Nov 2015: Genetic residue from ancient viral infections has been repurposed to play a vital role in acquiring pluripotency....
|Horizontal gene transfer (HGT), the "non-sexual movement of genetic material between two organisms", is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreign DNA must enter the host nucleus, integrate into the genome, and in more complex organisms it must enter the sequestered germline in order to be transmitted to offspring. Once there, it must not experience strong negative selection, despite potential for genetic incompatibility with the host genome and mismatch between the niche of the donor and the host. Over the longer term, foreign DNA may become "domesticated" in the recipient genome and provide novel function. — Eyres et al., 2015|
Horizontal gene transfer in bdelloid rotifers is ancient, ongoing..., Isobel Eyres et al., doi:10.1186/s12915-015-0202-9, BMC Biology, 4 Nov 2015. (Quotation in textbox, right.)
Virus Satellites Drive Viral Evolution and Ecology, Frígols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A, et al., doi:10.1371/journal.pgen.1005609, PLoS Genet, 23 Oct 2015.
Study shows algae virus can infiltrate mammalian cells, Scott Schrage, University of Nebraska-Lincoln (+ScienceDaily), 21 Oct 2015.
9 Oct 2015: [T]he signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor....
27 Sep 2015: Nearly 65% of the proteins encoded by Mollivirus have no known homologs.
Jeanne Ropars, Ricardo C. Rodríguez de la Vega et al., "Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi," doi:10.1016/j.cub.2015.08.025, Current Biology; and commentary in GenomeWeb and The New York Times, 24 Sep 2015.
24 Sep 2015: The nuclear genome is an ever-evolving mosaic of DNA acquired from different sources.
Gasmi L, Boulain H, Gauthier J, Hua-Van A, Musset K, Jakubowska AK et al., "Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses," doi:10.1371/journal.pgen.1005470, 11(9): e1005470, PLoS Genet, 17 Sep 2015; and commentary by David Shultz, "Wasps have injected new genes into butterflies," Science, 17 Sep 2015.
15 Sep 2015: The abundant occurance of lateral gene transfer in all three domains of life.... (book link).
11 Sep 2015: "Giant virus comes back to life," from Robert Temple.
John W. Schoggins, "Viruses carry antiviral cargo," doi:10.1126/science.aad0942, Science, 11 Sep 2015.
Daniel P. Maskell et al., "Structural basis for retroviral integration into nucleosomes" [link], doi:10.1038/nature14495, p 366-369 v523, Nature, 16 Jul 2015.
Chuan Ku et al., "Endosymbiotic origin and differential loss of eukaryotic genes" [abstract], doi:10.1038/nature14963, Nature, online 19 Aug 2015.
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes by Simon Roux et al., eLife 2015;10.7554/eLife.08490, 22 Jul 2015; and commentary:
'Fishing expedition' nets nearly tenfold increase in number of sequenced virus genomes, Ohio State University, (+Newswise), 14 Aug 2015.
16 Aug 2015: ...The virus inserted itself some 650 times or so into the genome — Frank Ryan [book review].
Jianrong Wang et al., "MIR retrotransposon sequences provide insulators to the human genome" [abstract], doi:10.1073/pnas.1507253112, n 32 v 112, PNAS, 11 Aug 2015.
"Ancestral virus for gene therapy" [link], doi:1038/524009e, p 9 v 524, Nature, 6 Aug 2015.
A. Bridgeman et al., "Viruses transfer the antiviral second messenger cGAMP between cells" [abstract], doi:10.1126/science.aab3632, Science, online30 Jul 2015.
30 Jul 2015: ...Dramatic changes such as the complete gain and loss of functional promoters are common.
22 Jul 2015: "All cellular organisms persist and evolve under a perennial onslaught of mobile genetic elements (MGEs)...."
21 Jul 2015: ...The surprising density of the web of life woven through genetic exchange is becoming visible.
Cheng Sun, Cédric Feschotte, Zhiqiang Wu and Rachel Lockridge Mueller, "DNA transposons have colonized the genome of the giant virus Pandoravirus salinus" [abstract], doi:10.1186/s12915-015-0145-1, n 38 v 13, BMC Biology, 12 Jun 2015. "Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses."
9 Jul 2015: We find that the entire basic genome is continually exchanged.... [P]hages ...are likely mediators of most DNA transfers....
Forest Rohwer, Merry Youle, Heather Maughan and Nao Hisakawa, Life in Our Phage World [info], ISBN: 978-0-9904943-0-0, Wholon, San Diego CA, Dec 2014. "Both lytic and lysogenic phage have the capacity to transfer genes horizontally between microbial cells."
22 Jun 2015: How can evolutionary science not be talking about viruses when genomes are so heavily colonized by these entities?
N. Shterzer and I. Mizrahi, "The animal gut as a melting pot for horizontal gene transfer" [abstract], doi:10.1139/cjm-2015-0049, Canadian Journal of Microbiology, 20 Apr 2015.
Charles C Davis and Zhenxiang Xi, "Horizontal gene transfer in parasitic plants" [abstract], doi:10.1016/j.pbi.2015.05.008, p 14-19 v 26, Current Opinion in Plant Biology, Aug 2015.
Savory F, Leonard G, Richards TA, "The Role of Horizontal Gene Transfer in the Evolution of the Oomycetes" [html], doi:10.1371/journal.ppat.1004805, 11(5): e1004805, PLoS Pathog, 28 May 2015.
Michael J. Rosen et al., "Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche" [abstract], doi:10.1126/science.aaa4456, p 1019-1023 v 348, Science, 29 May 2015.
Shlomit Sharoni and Miri Trainic et al., "Infection of phytoplankton by aerosolized marine viruses" [abstract], doi:10.1073/pnas.1423667112, p 6643-6647 v 112, Proc. Natl. Acad. Sci. USA, 26 May 2015. "...Aerosolized viruses can remain infective under meteorological conditions prevailing during E. huxleyi blooms in the ocean, allowing potential dispersal and infectivity over hundreds of kilometers."
Aashiq H. Kachroo et al., "Systematic humanization of yeast genes reveals conserved functions and genetic modularity" [abstract], doi:10.1126/science.aaa0769, Science, 22 May 2015.
Robert Kofler et al., "The recent invasion of natural Drosophila simulans populations by the P-element" [abstract], doi:10.1073/pnas.1500758112, PNAS, 11 May 2015. "This ongoing spread of the P-element in natural populations provides a unique opportunity to understand the dynamics of transposable element spread...."
7 May 2015: Eugene Koonin interviewed by Susan Mazur, Huffington Post.
7 May 2015: An Interview with Ford Doolittle, PLoS Genet.
7 May 2015: Numerous genes for Eukaryotic Signature Proteins (ESPs) have been found in Archaea.
D. Furman, V. Jojic, S. Sharma et al., "Cytomegalovirus infection enhances the immune response to influenza" [abstract], doi:10.1126/scitranslmed.aaa2293, Sci. Transl. Med., 1 Apr 2015.
28 Apr 2015: Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene.
22 Apr 2015: We may owe our survival and complexity to a stowaway virus....
Tina Kyndt, Dora Quispe et al., "The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop" [abstract], doi:10.1073/pnas.1419685112, PNAS, 5 May (online 20 Apr) 2015.
Nikolay Popgeorgiev et al., "Marseillevirus-Like Virus Recovered From Blood Donated by Asymptomatic Humans" [abstract], doi:10.1093/infdis/jit292, J Infect Dis., online 2 Jul 2013.
12 Mar 2015: We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans.... — Crisp, Boschetti et al.
Braham Dhillon, Nicolas Feau et al., "Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen" [abstract], doi:10.1073/pnas.1424293112, PNAS, online 2 Mar 2015.
Mammals Made By Viruses by Carl Zimmer, Discover, 14 Feb 2015.
Hunsperger HM, Randhawa T, Cattolico R, "Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae" [html], doi:10.1186/s12862-015-0286-4, n 16 v 15, BMC Evolutionary Biology, 10 Feb 2015.
Viral Virtuosos by Christopher S. Sullivan, The Scientist, 1 Feb 2015. "...virus-encoded miRNAs...."
Julie A. Schwartz et al., "FISH Labeling Reveals a Horizontally Transferred Algal ...Nuclear Gene on a Sea Slug ...Chromosome" [pdf], p 300-312 v 227, Biol. Bull., Dec 2014; and commentary:
Sea Slug has Taken Genes from the Algae it Eats, Allowing it to Photosynthesize Like a Plant... by Diana Kenney, Marine Biological Laboratory, 3 Feb 2015.
30 Jan 2015: I guess we owe the evolution of pregnancy to what are effectively genomic parasites — Vincent Lynch
19 Jan 2015: ...Deliberate killing of nonimmune cells ...releases DNA and makes it accessible for HGT.
13 Jan 2015: ...Inherited viruses that are millions of years old play an important role in building up the complex networks that characterise the human brain.
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, et al., "Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress" [html], doi:10.1371/journal.pgen.1004915, 11(1): e1004915, PLoS Genet, 8 Jan 2015.
7 Jan 2015: When a mobile genetic element inserts into the host genome, it inevitably modifies that genome.... — Koonin and Krupovic
Viruses & HGT: What'sNEW continued