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)
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:
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.
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).
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.
William P Hanage, "Fuzzy species revisited" [html], doi:10.1186/1741-7007-11-41, n41 v11, BMC Biology, 15 Apr 2013. Few now disagree that the movement of genetic material between lineages is an essential source of evolutionary innovation, and that bacteria tend towards a 'plug and play' strategy that allows genes specific for quite narrow segments of niche space to be shared among multiple species.
Andrew T. Carter et al., "The type F6 neurotoxin gene cluster locus of Group II Clostridium botulinum has evolved by successive disruption of two different ancestral precursors" [Open Access abstract], doi:10.1093/gbe/evt068, Genome Biol Evol, 3 May 2013; and commentary: Mining the botulinum genome, Institute of Food Research (also Science Codex), 14 May 2013.
11 May 2013: ...TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage....
Dami Song, Won Kyong Cho et al., "Evolution of and Horizontal Gene Transfer in the Endornavirus Genus" [html], doi:10.1371/journal.pone.0064270, 8(5): e64270, PLoS ONE, 7 May 2013.
Rafael Contreras-Galindo et al., "HIV Infection Reveals Wide-Spread Expansion of Novel Centromeric Human Endogenous Retroviruses" [abstract], doi:10.1101/gr.144303.112, Genome Research, online 8 May 2013.
Geoffrey S Diemer and Kenneth M Stedman, "A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses" [html], doi:10.1186/1745-6150-7-13, n13 v7, Biology Direct, 11 Jun 2012.
Aurélie Kapusta, Zev Kronenberg, Vincent J. Lynch et al., "Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs" [html], doi:10.1371/journal.pgen.1003470, 9(4): e1003470, PLoS Genet, 25 Apr 2013.
Bo Wu, Jacopo Novell1, Jeremy M. Foster, Barton E. Slatko et al., "Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes" [abstract], doi:10.1073/pnas.1304049110, p7748-7753 v110, Proc. Natl. Acad. Sci. USA, 7 May (online 22 Apr) 2013. "Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function."
David Alvarez-Ponce et al., "Gene similarity networks provide tools for understanding eukaryote origins and evolution" [abstract], doi:10.1073/pnas.1211371110, Proc. Natl. Acad. Sci. USA, online 1 Apr 2013. "Connected components with prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes."
Esnault C, Cornelis G, Heidmann O, Heidmann T, "Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation" [html], doi:10.1371/journal.pgen.1003400, 9(3): 1003400, PLoS Genet., online 28 Mar 2013. "Syncytins are 'new' genes encoding the envelope protein of captured endogenous retroviral elements.... These genes are remarkable, as they are 'necessary' for a basic function in placental mammals and yet they were acquired 'by chance' on multiple occasions and independently in diverse mammalian species."
Guy L, Nystedt B, Toft C, Zaremba-Niedzwiedzka K, Berglund EC et al., "A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella" [html], doi:10.1371/journal.pgen.1003393, 9(3): e1003393, PLoS Genet., online 28 Mar 2013.
Digging Down Below the Tree of Life by Michael Schirber, Astrobiology Magazine, 28 Mar 2013.
Hans-Jörg Frasch et al., "Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice" [abstract], Current Opinion in Biotechnology, online 27 Mar 2013.
Gerald Schönknecht, Wei-Hua Chen, Chad M. Ternes, Guillaume G. Barbier, Roshan P. Shrestha et al., "Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote" [abstract], doi:10.1126/science.1231707, p1207-1210 v339, Science, 8 Mar 2013; and two commentaries:
Eduardo P. C. Rocha, "With a Little Help from Prokaryotes" [summary], doi:10.1126/science.1234938, p1154-1155 v339, Science, 8 Mar 2013; and
Algae Get Help to Go to Extremes by Sabrina Richards, The Scientist, 7 Mar 2013.
Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, et al., "Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade" [html], doi:10.1371/journal.pgen.1003265, 9(2): e1003265, PLoS Genet, 14 Feb 2013."...Although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher."
Cecilia Alsmark et al., "Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes" [abstract], doi:10.1186/gb-2013-14-2-r19, R19 v14, Genome Biology, 25 Feb 2013.
28 Feb 2013: We discovered massive transfers of a DNA transposon... between multiple teleost fishes and lampreys....
Kimberley D. Seed et al., "A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity" [abstract], doi:10.1038/nature11927, p489-491 v494, Nature, 28 Feb 2013; and commentary:
...Viruses Can Have Immune Systems, Tufts University, (also Newswise.com), 27 Feb 2013.
Stéphanie Bedhomme et al., "Genotypic but not phenotypic historical contingency revealed by viral experimental evolution" [abstract], doi:10.1186/1471-2148-13-46, v13 n46, BMC Evolutionary Biology, 19 Feb 2013. "...Our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re)emergence is not evolutionarily constrained."
16 Feb 2013: Viruses are notorious for their role in disease, but only about 1% are actually pathogenic....
Zhenxiang Xi, Yuguo Wang et al., "Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade" [html], doi:10.1371/journal.pgen.1003265, 9(2): e1003265, PLoS Genet., 14 Feb 2013. "Strikingly, our phylogenetic analyses conservatively indicate that 24%–41% of these gene sequences show evidence of HGT...."
Sarah C. P. Williams, "The other microbiome" [pdf], doi:10.1073/pnas.1300923110, Proc. Natl. Acad. Sci. USA, 5 Feb 2013.
Alexandre Martinière, Aurélie Bak et al., "A virus responds instantly to the presence of the vector on the host and forms transmission morphs" [html], doi:10.7554/eLife.00183, eLife 2013;2:e00183, elifesciences.org, 22 Jan 2013.
Sandeep P Kishore et al., "Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans" [abstract], doi:10.1186/1471-2148-13-37, v13 n37, BMC Evolutionary Biology, 11 Feb 2013.
Xianghong Li et al., "A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture" [abstract], doi:10.1073/pnas.1121543109, E478-E487 n6 v110, Proc. Natl. Acad. Sci. USA, 5 Feb 2013.
Cowley M and Oakey RJ, "Transposable Elements Re-Wire and Fine-Tune the Transcriptome" [html], doi:10.1371/journal.pgen.1003234, 9(1): e1003234, PLoS Genet., 24 Jan 2013.
Hywel T P Williams, "Phage-induced diversification improves host evolvability" [abstract], doi:10.1186/1471-2148-13-17, v13 n17, BMC Evolutionary Biology, 22 Jan 2013.
Pascal-Antoine Christin et al., "Anatomical enablers and the evolution of C4 photosynthesis in grasses" [abstract], doi:10.1073/pnas.1216777110, p1381-1386 v110, Proc. Natl. Acad. Sci. USA, 22 Jan 2013. "Despite its complexity, it evolved more than 62 times independently in flowering plants. However, C4 origins are absent from most plant lineages and clustered in others...."
Mukul S. Bansal et al., "Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes" [abstract], doi:10.1093/bioinformatics/btt021, Bioinformatics, online 17 Jan 2013.
Martin F. Polz et al., "Horizontal gene transfer and the evolution of bacterial and archaeal population structure" [abstract], doi:10.1016/j.tig.2012.12.006, Trends in Genetics, online 15 Jan 2013.
Rupak Mitra, Xianghong Li et al., "Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon" [abstract], doi:10.1073/pnas.1217548110, Proc. Natl. Acad. Sci. USA, online 17 Dec 2012. "Our study suggests that some DNA transposons are still actively shaping some mammalian genomes and reveals an unprecedented opportunity to study the mechanism, regulation, and genomic impact of cut-and-paste transposition in a natural mammalian host"; and commentary:
Rare form of active 'jumping genes' found in mammals, Johns Hopkins University, (also PhysOrg.com), 3 Jan 2013.
1 Jan 2013: A retrotransposon was transferred at least nine times, providing a major component to the genomes of some ruminants, marsupials, squamates, monotremes and African mammals.
H. Deborah Chen et al., "An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product" [html], doi:10.1371/journal.pgen.1003060, 8(12): e1003060, PLoS Genet., online 27 Dec 2012.
Böttger A, Doxey AC, Hess MW, Pfaller K, Salvenmoser W, et al., "Horizontal Gene Transfer Contributed to the Evolution of Extracellular Surface Structures: The Freshwater Polyp Hydra Is Covered by a Complex Fibrous Cuticle Containing Glycosaminoglycans and Proteins of the PPOD and SWT (Sweet Tooth) Families" [html], doi:10.1371/journal.pone.0052278, 7(12): e52278, PLoS ONE, online 27 Dec 2012. "PPODs are taxon-specific proteins which appear to have entered the Hydra genome by horizontal gene transfer from bacteria."
Damon Lisch, "How important are transposons for plant evolution?" [abstract], doi:10.1038/nrg3374, p49-61 v14, Nature Reviews Genetics, Jan 2013. "On the basis of what we know now, it is clear that TEs are capable of causing many kinds of genetic variation, and it is also clear that they have had important effects on the course of plant evolution. Doubtlessly, many more examples of TE involvement in the evolution of new adaptive traits will emerge over the next few years."
20 Dec 2012: Evolution: A View from the 21st Century by James A. Shapiro
Jeudy S, Abergel C, Claverie J-M, Legendre M, "Translation in Giant Viruses: A Unique Mixture of Bacterial and Eukaryotic Termination Schemes" [html], doi:10.1371/journal.pgen.1003122, 8(12): e1003122, PLoS Genet., 13 Dec 2012. "These giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. The presence of those genes, thought to be hallmarks of cellular organisms, revived fundamental interrogations on the evolutionary origin of these viruses and the link they might have with the emergence of eukaryotes.... An increasing number of studies support the idea that giant viruses have ancient origins, possibly predating the radiation of eukaryotes."
Phuong Thi Le et al., "An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales" [abstract], doi:10.1186/1471-2148-12-243, BMC Evolutionary Biology, 12 Dec 2012.
11 Dec 2012: James Shapiro points to his web article about HGT from eukaryotes to bacteria.
9 Dec 2012: The well-established molecular details of horizontal transfer in the evolution of bacterial antibiotic resistance are difficult to reconcile with neo-Darwinism — James A. Shapiro
2 Dec 2012: More than 1,000 genes in choanoflagellates appear to have arrived by transfer....
28 Nov 2012: Archaea acquired more than 1,000 genes by transfer from eubacteria.
Céline Petitjean et al., "Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea" [abstract], doi:10.1186/1471-2148-12-226, BMC Evolutionary Biology, 26 Nov 2012.
17 Nov 2012: Bdelloid rotifers have acquired genes from more than 500 species including fungi, bacteria, and plants.
Caroline Ash, "Rivers of Gene Flow" [abstract], doi:10.1126/science.338.6109.864-a, Science, 16 Nov 2012. "...identifying environmental sources of antibiotic resistance genes in one river system...."
Nina V. Fedoroff, "McClintock’s challenge in the 21st century" [abstract], doi:10.1073/pnas.1215482109, Proc. Natl. Acad. Sci. USA, online 13 Nov 2012. "Today we know that transposon and retrotransposon sequences constitute an astounding two-thirds of our own genome and 85% of the corn genome. We know, too, that the fingerprints of transposable elements and transposition are everywhere in eukaryotic genomes."
7 Nov 2012: 910 genes apparently transferred from prokaryotes, fungi or viruses provide essential or plant-specific activities....
7 Nov 2012: Diverse bacteriophages carry genes for proteins "targeting the eukaryotic nucleus."
George R. Young et al., "Resurrection of endogenous retroviruses in antibody-deficient mice" [abstract], doi:10.1038/nature11599, Nature, online 24 Oct 2012.
Eric Bapteste et al., "Evolutionary analyses of non-genealogical bonds produced by introgressive descent" [abstract], doi:10.1073/pnas.1206541109, Proc. Natl. Acad. Sci. USA, online 22 Oct 2012. "...An important step to a more realistic pluralist treatment of evolutionary complexity."
Jumping Gene Enabled Key Step in Corn Domestication by Nicole Miller, re: John Doebley, University of Wisconsin-Madison, 25 Sep 2011.
Genomic hitchhikers in birds shed light on evolution of viruses by Jim Sliwa, EurekAlert!, 16 Oct 2012. "The genomes of birds are riddled with DNA sequences from viruses...."
Manuel A. Merlo et al., "Evidence for 5S rDNA Horizontal Transfer in the toadfish Halobatrachus didactylus (Schneider, 1801) based on the analysis of three multigene families" [abstract], doi:10.1186/1471-2148-12-201, v12 n201 BMC Evolutionary Biology, 7 Oct 2012.
Gergely J. Szollosi et al., "Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations" [abstract], doi:10.1073/pnas.1202997109, Proc. Natl. Acad. Sci. USA, online 4 Oct 2012.
Laurie A Graham et al., "Smelt was the likely beneficiary of an antifreeze gene laterally transferred between fishes" [abstract], doi:10.1186/1471-2148-12-190, n190 v12, BMC Evolutionary Biology, 25 Sep 2012.
16 Sept 2012: Very large viruses coexisted with or preceded the first primordial cells.
Chris Creevey and James McInerney, "Horizontal gene transfer drives extreme physiological change in Haloarchaea" [abstract | PDF], arXiv:1209.2455 [q-bio.GN], arXiv.org, 11 Sep 2012. "We found that almost half the genes, about which we can make strong statements, have bacterial ancestry and are likely a result of multiple horizontal transfer events."
13 Sept 2012: "...the horizontal flow of genes is a part of the story of life."
Schmitt I, Lumbsch HT, "Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi" [html], doi:10.1371/journal.pone.0004437, 4(2): e4437, PLoS ONE, 2009.
McDaniel LD, Young EC, Ritchie KB, Paul JH, "Environmental Factors Influencing Gene Transfer Agent (GTA) Mediated Transduction in the Subtropical Ocean" [html], doi:10.1371/journal.pone.0043506, 7(8): e43506, PLoS ONE, 15 Aug 2012.
Liu L, Chen X, Skogerbø G, Zhang P, Chen R, He S, Huang DW, "The Human Microbiome: A Hot Spot of Microbial Horizontal Gene Transfer" [PubMed abstract], Genomics, online 25 Jul 2012.
Maria Hoffmann et al., "Genetic and phylogenetic evidence for horizontal gene transfer among ecologically disparate groups of marine Vibrio" [abstract], doi:10.1111/j.1096-0031.2012.00416.x, Cladistics, 26 Jul 2012.
Jean-François Pombert, Mohammed Selman et al., "Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites" [abstract], doi:10.1073/pnas.1205020109, Proc. Natl. Acad. Sci. USA, online 16 Jul 2012. "...All these genes ...appear to have originated by several independent HGT events from different eukaryotic and prokaryotic donors."
League GP, Slot JC, Rokas A., "The ASP3 Locus in Saccharomyces cerevisiae Originated by Horizontal Gene Transfer from Wickerhamomyces" [PubMed abstract], doi:10.1111/j.1567-1364.2012.00828.x, FEMS Yeast Res., online 9 Jul 2012. ("Originated"?)
Kristen S. Swithers et al., "Vitamin B12 synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales" [abstract], doi:10.1093/gbe/evs057, Genome Biol Evol, online 12 Jul 2012.
5 Jul 2012: The evolution of RNA viruses is more promiscuous than we knew. (References Koonin & Dolja (2012); and Liu et al. (2012))
28 Jun 2012: ...A muscle protein core set... was already present in unicellular organisms before the origin of multicellular animals.
Vadim Mozhayskiy and Ilias Tagkopoulos, "Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution" [abstract], doi:10.1186/1471-2105-13-S10-S13, v13(Suppl 10):S13, BMC Bioinformatics, online 25 Jun 2012.
24 Jun 2012: miRNAs from plants can enter animal cells and regulate their metabolic processes....
Huiquan Liu et al., "Evolutionary genomics of mycovirus-related dsRNA viruses reveals cross-family horizontal gene transfer and evolution of diverse viral lineages" [abstract], doi:10.1186/1471-2148-12-91, v12 n91, BMC Evolutionary Biology, 20 Jun 2012.
Andrew S. Lang et al., "Gene transfer agents: phage-like elements of genetic exchange" [link], doi:10.1038/nrmicro2802, p472-482 v10, Nature Reviews Microbiology, Jul 2012.
Zhenxiang Xi et al., "Horizontal transfer of expressed genes in a parasitic flowering plant" [abstract], doi:10.1186/1471-2164-13-227, v13 n227, BMC Genomics 2012, online 8 Jun 2012; and commentary at Harvard Gazette | PhysOrg.com | Scientific American | Stony Brook University.
Victor Satler Pylro et al., "Detection of Horizontal Gene Transfers from Phylogenetic Comparisons" [7-page html], doi:10.1155/2012/813015, International Journal of Evolutionary Biology, 2012.
Horizontal gene transfer maintains chloroplasts stolen from prey in the algae Dinophysis acuminata by Jennifer Wisecaver, IGERT.org, 21 May 2012.
Geoffrey S Diemer and Kenneth M Stedman, "A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses" [abstract], doi:10.1186/1745-6150-7-13, Biology Direct, online 19 Apr 2012.
Roberto Ferrari et al., "Reorganization of the host epigenome by a viral oncogene" [abstract], doi:10.1101/gr.132308.111, Genome Research, online 12 Apr 2012.
Christina Tobin Kåhrström, "Evolution: Converging on divergence" [abstract], doi:10.1038/nrg3247, p380 v13, Nature Reviews Genetics, Jun 2012. "...The impact of HGT on ecological differentiation is controversial... but the spread of individual genes and alleles through populations (gene-specific sweeps) is frequently observed."
Chang Fu Tian et al., "Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations" [abstract], doi:10.1073/pnas.1120436109, Proc. Natl. Acad. Sci. USA, online 14 May 2012. "Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process."
Ellie Harrison and Michael A. Brockhurs, "Plasmid-mediated horizontal gene transfer is a coevolutionary process" [abstract], doi:10.1016/j.tim.2012.04.003, Trends in Microbiology, online 7 May 2012.
Gkikas Magiorkinis et al., "Env-less endogenous retroviruses are genomic superspreaders" [Open Access abstract], doi:10.1073/pnas.1200913109, p7385-7390 v109, Proc. Natl. Acad. Sci. USA, 8 May (online 23 Apr) 2012.
Michael E D'Angelo, "Perforin evolved from a gene duplication of MPEG1, followed by a complex pattern of gene gain and loss within Euteleostomi" [abstract], doi:10.1186/1471-2148-12-59, n59 v12, BMC Evolutionary Biology, 2 May 2012.
Leeches provide traces of DNA from other species by Ewen Callaway, Nature.com, 23 Apr 2012.
C Calderón et al., "Detecting lateral genetic material transfer" [abstract | PDF], arXiv:1204.2601v1 [cs.NE], arXiv.org, 12 Apr 2012.
Andrew R Francis and Mark M Tanaka, "Evolution of variation in presence and absence of genes in bacterial pathways" [abstract], doi:10.1186/1471-2148-12-55, n55 v12, BMC Evolutionary Biology, 20 Apr 2012. "...The role of horizontal gene transfer is probably the initial introduction of a complete novel pathway...."
Catherine A. Lee et al., "The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions" [abstract], doi:10.1128/JB.00301-12, JB.00301-12, Journal of Bacteriology, Apr 2012.
Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso M-L, et al., "A Natural System of Chromosome Transfer in Yersinia pseudotuberculosis" [html], doi:10.1371/journal.pgen.1002529, 8(3): e1002529, PLoS Genet, Mar 2012.
Robert HS Kraus et al., "Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks" [Open Access abstract], doi:10.1186/1471-2148-12-45, v12 n45, BMC Evolutionary Biology, 2 Apr 2012.
Chan CX, Reyes-Prieto A, Bhattacharya D, "Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution" [html], doi:10.1371/journal.pone.0029138, PLoS ONE 6(12): e29138, online 14 Dec 2012. And authors' commentary:
Cheong Xin Chan et al., "Endosymbiotic and horizontal gene transfer in microbial eukaryotes: Impacts on cell evolution and the tree of life" [html], v2 n2, Mobile Genetic Elements, Mar/Apr 2012.
24 Mar 2012: ...The contribution of EVEs to cellular function... is exceeding even the boldest predictions. — Cédric Feschotte and Clément Gilbert
Pervasive horizontal gene transfer in Chlamydia by James McInery, Bioinformatics and Molecular Evolution Unit of NUI, Maynooth, Ireland, 17 Mar 2012.
Yehu Moran et al., "Recurrent horizontal transfer of bacterial toxin genes to eukaryotes" [abstract], doi:10.1093/molbev/mss089, Mol. Biol. Evol., online 12 Mar 2012.
Dana C. Price et al., "Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants" [abstract], doi:10.1126/science.1213561, p843-847 v335, Science, 17 Feb 2012. "Plantae share many genes with an EGT or HGT origin that have essential functions such as photosynthesis, starch biosynthesis, plastid protein import, plastid solute transport, and alcohol fermentation."
9 Mar 2012: ...Fundamental elements of the C4 pathway ...were acquired via a minimum of four independent lateral gene transfers....
Catherine Mary, "Giant Viruses Revive Old Questions About Viral Origins" (Didier Raoult Profile) [summary], doi:10.1126/science.335.6072.1035, p1035 v335, Science, 2 Mar 2012.
29 Feb 2012: An insect species acquired a beneficial gene from bacteria by horizontal gene transfer.
Jingfeng Li et al., "Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance" [abstract], doi:10.1101/gr.130740.111, Genome Res., online 23 Feb 2012.
Sandra Stegemann et al., "Horizontal transfer of chloroplast genomes between plant species" [abstract], doi:1073/pnas.111407610, Proc. Natl. Acad. Sci. USA, online 30 Jan 2012.
Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, et al., "Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments" [html], doi:10.1371/journal.pgen.1002430, 7(12): e1002430, PLoS Genet, online 24 Dec 2011. "The majority of genes encoding functions critical for association with plants are among horizontally transferred genes."
Allison M. Barbaglia1 et al., "Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize" [abstract], doi:10.1534/genetics.111.136176, Genetics, online 14 Dec 2011. "Helitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. ...Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription read through and capture of nearby exons."
13 Dec 2011: ...Our results imply that pathogens may be advantageous to ...hosts through effective HGT events at a large evolutionary scale.
11 Dec 2011: ...Different rare species living in freshwater ...all leave DNA traces in their environment....
19 Nov 2011: Where do new genes come from?
Derek J. Taylor et al., "Evolutionary maintenance of filovirus-like genes in bat genomes" [Open Access abstract], doi:10.1186/1471-2148-11-336, v11 n336, BMC Evolutionary Biology, online 17 Nov 2011. "Our results indicate that filovirus-like elements have significance beyond genomic imprints of prior infection. That is, there appears to be, or have been, functionally maintained copies of such genes in mammals."
Anne Dupressoir et al., "A pair of co-opted retroviral envelope syncytin genes is required for formation of the two-layered murine placental syncytiotrophoblast" [abstract], doi:10.1073/pnas.1112304108, Proc. Natl. Acad. Sci. USA, online 27 Oct 2011. "These findings establish that both endogenous retrovirus-derived syncytin genes contribute independently to the formation of the two syncytiotrophoblast layers during placenta formation, demonstrating a major role of retroviral gene capture, through convergent evolution, to generate multiple placental structures."
Anthony Studer et al., "Identification of a functional transposon insertion in the maize domestication gene tb1" [abstract], doi:10.1038/ng.942, p1160-1163 v43, Nature Genetics, Nov 2011. "Here we show that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor, teosinte. Molecular dating indicates that the Hopscotch insertion predates maize domestication by at least 10,000 years, indicating that selection acted on standing variation rather than new mutation."
26 Oct 2011: transposable retroviral elements responsible for most of the morphological differences between chimps and humans — Hans-Peter Wheeler sends email with a link.
Satyanarayana Tatineni et al., "A plant virus evolved by acquiring multiple nonconserved genes to extend its host range" [abstract], doi:10.1073/pnas.1113227108, p17366-17371 v108, Proc. Natl. Acad. Sci. USA, 18 Oct 2011. "These findings suggest that CTV acquired multiple nonconserved genes ...and, as a result, gained the ability to interact with multiple hosts, thus extending its host range during the course of evolution."
Eugene V Koonin et al., "The ancient Virus World and evolution of cells" [abstract | html], doi:10.1186/1745-6150-1-29, v1 n29, Biology Direct, 19 Sep 2006. "The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life.... Viruses actively move between biomes and are thought to be major agents of evolution by virtue of their capacity to operate as vehicles of horizontal gene transfer (HGT)."
27 Sep 2011: Single-stranded circular DNA viruses have entered eukaryotic genomes many times. Over 300 examples were recently found....
Richard P. Bonocora, Qinglu Zeng et al., "A homing endonuclease and the 50-nt ribosomal bypass sequence of phage T4 constitute a mobile DNA cassette" [abstract], doi:10.1073/pnas.1107633108, p16351-16356 v108, Proc. Natl. Acad. Sci. USA, 27 Sep 2011.
26 Sep 2011: More than 1500 genes necessary for the evolution of pregnancy in placental mammals were recruited into service....
John W Stiller, "Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer" [abstract], doi:10.1186/1471-2148-11-259, n 259 v11, BMC Evolutionary Biology, 11 Sep 2011.
Kelli Hoover, Michael Grove et al., "A Gene for an Extended Phenotype" [abstract], doi:10.1126/science.1209199, p1401 v333, Science, 9 Sep 2011. "Gypsy moths infected by a baculovirus climb to the top of trees to die, liquefy, and 'rain' virus on the foliage below to infect new hosts. The viral gene that manipulates climbing behavior of the host was identified...."
Allan C. Spradling, "Drosophila P elements preferentially transpose to replication origins" [abstract], doi:10.1073/pnas.1112960108, Proc. Natl. Acad. Sci. USA, online 6 Sep 2011; and commentary:
A "Jumping Gene's" preferred targets may influence genome evolution, Carnegie Institution of Washington, 6 Sep 2011.
Dong-Dong Wu and Ya-Ping Zhang, "Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer" [abstract], doi:10.1016/j.ygeno.2011.08.006, Genomics via Science Direct, accepted manuscript, Aug 2011.
Gwyneth Dickey Zakaib, "...From giant viruses to unexplained marine DNA..." [html], doi:10.1038/476020a, p20-21 v476, Nature, 4 Aug 2011.
Lucía F. Franchini, Rodrigo López-Leal et al., "Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons" [abstract], doi:10.1073/pnas.1104997108, Proc. Natl. Acad. Sci. USA, online 29 Aug 2011.
Thomas A. Richards et al., "Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes" [abstract], doi:10.1073/pnas.1105100108, Proc. Natl. Acad. Sci. USA, online 30 Aug 2011.
Henry L. Levin and John V. Moran, "Dynamic interactions between transposable elements and their hosts" [abstract], doi:10.1038/nrg3030, p615-627 v12, Nature Reviews Genetics, Sep 2011.
Chu-Chun Huang et al., "...Implications for a plasmid origin of a chromosome centromere" [abstract], doi:10.1073/pnas.1101944108, Proc. Natl. Acad. Sci. USA, online 1 Aug 2011.
2 Aug 2011: ...Ancestral genes can control the ability of horizontally acquired genes to confer species-specific traits upon different organisms.
Jaret P Bilewitch and Sandie M Degnan, "A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function" [abstract], doi:10.1186/1471-2148-11-228, n228 v11, BMC Evolutionary Biology, 29 Jul 2011. "...These findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve."
23 Jul 2011: Transposable Elements (TEs) appear to have installed genetic programs implicated in 99 different primate-specific traits.
New Virus Jumps From Monkeys to Lab Worker by Michael Price, ScienceNow, 14 Jul 2011.
Matthew E Rhodes et al., "Differences in lateral gene transfer in hypersaline versus thermal environments" [abstract], doi:10.1186/1471-2148-11-199, n199 v11, BMC Evolutionary Biology, online 8 Jul 2011.
Joel L. Sachs et al., "Evolutionary transitions in bacterial symbiosis" [abstract], doi:10.1073/pnas.1100304108, Proc. Natl. Acad. Sci. USA, online 20 Jun 2011.
6 Jul 2011: A 10-minute video about viruses and evolution....
15 Jun 2011: The evolutionary transition from single-celled green algae to multicellular land plants required the acquisition of 3006 genes.
27 May 2011: ...C4 and CAM photosynthesis; ...few, if any, of their essential components are completely new....
13 May 2011: Many scientists now argue that viruses contain a genetic archive that's been circulating the planet for billions of years.
Shinichiro Maruyama et al., "Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids" [abstract], doi:10.1186/1471-2148-11-105, v11 n105, BMC Evolutionary Biology, 18 Apr 2011.
Yao-Wu Yuan and Susan R. Wessler, "The catalytic of all eukaryotic cut-and-paste transposase superfamilies" [abstract], doi:10.1073/pnas.1104208108, Proc. Natl. Acad. Sci. USA, online 25 Apr 2011.
20 Apr 2011: Did transposons come from viruses?
17 Apr 2011: How important is lateral gene transfer? (Jerry Coyne's blog)
12 Apr 2011: Endogenous retroviruses... — our review of Virolution by Frank Ryan.
Anna G. Himler et al., "Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias" [abstract], doi:10.1126/science.1199410, p254-256 v332, Science, 8 Apr 2011; and commentary:
Francis M. Jiggins and Gregory D. D. Hurst, "Rapid Insect Evolution by Symbiont Transfer" [summary], doi:10.1126/science.1205386, p185-186 v332, Science, 8 Apr 2011.
19 Mar 2011: ...Scientists now appreciate that viruses contain perhaps the largest collection of unknown genes on earth.
Gyanendra P. Dubey and Sigal Ben-Yehuda, "Intercellular Nanotubes Mediate Bacterial Communication" [abstract], doi:10.1016/j.cell.2011.01.015, p590-600 v144, Cell, 18 Feb 2011; and commentary: Molecular mail by nanotube, doi:10.1038/470438c, p438 v471, Nature, 24 Feb 2011. (photo shows bacterial conjugation)
Zoltán Ivics and Zsuzsanna Izsvák, "The expanding universe of transposon technologies for gene and cell engineering" [html], doi:10.1186/1759-8753-1-25, v1 n25, Mobile DNA, 7 Dec 2010. "Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion."
...ALS could be caused by a retrovirus that inserted itself into the human genome thousands of years ago, Johns Hopkins Medical Institutions, 2 Mar 2011.
27 Feb 2011: Industrial yeasts contain genes and clusters of genes not found in laboratory reference strains.
18 Feb 2011: A virus integrated into the genomes of humans and great ape males helps to eliminate defective germline cells.
14 Feb 2011: A 23-gene cluster was horizontally transferred among fungi.
13 Feb 2011: First evidence of gene transfer from human host to bacterial pathogen
Genes Older Than Earth? is a related new webpage, posted 8 Feb 2011.
Chris R. Smith, Christopher D. Smith et al., "Draft genome of the red harvester ant Pogonomyrmex barbatus" [abstract], doi:10.1073/pnas.1007901108, Proc. Natl. Acad. Sci. USA, online 31 Jan 2011. "...Ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor."
Treangen TJ, Rocha EPC, "Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes" [html], doi:10.1371/journal.pgen.1001284, PLoS Genet 7(1): e1001284, 27 Jan 2011; and commentary: Gene 'Relocation' Key to Most Evolutionary Change in Bacteria, The University of Maryland Center for Bioinformatics and Computational Biology, 27 Jan 2011.
14 Jan 2011: Nematodes digest cellulose using genes acquired from prokaryotes.
2 Jan 2011: Horizontal gene transfer, or HGT, is a ubiquitous feature of genome evolution....
Noah K. Whiteman and Andrew D. Gloss, "...Nematode debt to bacteria" [html], doi:10.1038/468641a, p641-642 v468, Nature, 2 Dec 2010. "...Over deep evolutionary time, these nematodes have incorporated into their genomes at least six distinct types of bacterial genes...."
11 Dec 2010: ...Class I RNRs [ribonucleotide reductases] have spread to archaea and eukaryotes via transfers from the bacterial domain....
Michael Syvanen and Michael Ducore, "Whole Genome Comparisons Reveals a Possible Chimeric Origin for a Major Metazoan Assemblage" [abstract | 15-page PDF], doi:10.1142/S0218339010003408, p261-275 v18, Journal of Biological Systems, Jun 2010. "We would like to point out that the underappreciated evolutionary mechanism of horizontal gene transfer can provide insight into this taxon sampling problem."
...35 hitherto unknown families of endogenous retroviruses, BasqueResearch, 29 Nov 2010.
Upending Conventional Wisdom, Certain Virus Families Are Ancient, ScienceDaily, 17 Nov 2010.
21 Nov 2010: The human genome contains about 1.8 million recognizable Alu sequence residues.... They are now seen as having much structural and evolutionary significance — Roy Britten
19 Nov 2010: ...Genetic material derived from all known viral genome types and replication strategies can enter the animal germ line....
Interesting article HGT is the subject of email and a link from Jeff Krolick, 5 Nov 2010.
2 Nov 2010: The software problem for the origin of life is not ignored, for once....
26 Oct 2010: We're finding suites of genes that you would really never expect to find in viral life, but would expect to find in cellular organisms.
Yong E. Zhang et al., "Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome" [html], doi:10.1371/journal.pbio.1000494, PLoS Biol 8(10): e1000494, 5 Oct 2010.
1 Oct 2010: Their only function seems to be transferring genes.
Clément Gilbert and Cédric Feschotte, "Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses" [html], doi:10.1371/journal.pbio.1000495, PLoS Biol 8(9): e1000495, Sep 2010. Also see commentary: Ancient Virus Found Hiding Out in Finch Genome by Cassandra Willyard, Science Now, 28 Sep 2010. "A newly uncovered 'viral fossil' buried deep in the genome of the zebra finch indicates that the hepatitis B family of viruses—known as hepadnaviruses—originated at least 19 million years ago. Together with recent findings on other viruses, the work suggests that all viruses may be much older than thought."
28 Sep 2010: Far from being negligible, these LGT events certainly have radically remolded evolutionary trends in recipient organisms, and similar roles in other animals can be expected to be discovered.
Yuyu Niu, Yang Yu, Agnieszka Bernat et al., "Transgenic rhesus monkeys produced by gene transfer into early-cleavage-stage embryos using a simian immunodeficiency virus-based vector" [abstract], doi:10.1073/pnas.1006563107, Proc. Natl. Acad. Sci. USA, online 24 Sep 2010.
Rice study examines how bacteria acquire immunity by Jade Boyd, Rice News & Media Relations, 15 Sep 2010. Bacteria get attacked by viruses called phages, and the CRISPR contain genetic sequences from phages. The CRISPR system is both inheritable and programmable, meaning that some sequences may be there when the organism is first created, and new ones may also be added when new phages attack the organism during its life cycle, says Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering.
13 Sep 2010: Origins, evolution, and phenotypic impact of new genes
Daniel W. Bellott et al., "Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition" [abstract], doi:10.1038/nature09172, p612-616 v466, Nature, 29 Jul 2010. "We conclude that both the Z chromosome and the X chromosome experienced substantial net gene gain."
Claudia P. Marquez and Ellen J. Pritham, "Phantom, a New Subclass of Mutator DNA Transposons Found in Insect Viruses and Widely Distributed in Animals" [abstract], doi:10.1534/genetics.110.116673, p1507-1517 v185, Genetics, Aug 2010. "Here we describe a previously uncharacterized group of DNA transposons designated Phantom identified in the genomes of a wide range of eukaryotic taxa, including many animals.... Interestingly three Phantom proteins were also identified in two insect viruses and phylogenetic analysis suggests horizontal movement from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals."
Sylvia Schaffer et al., "Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the 'Higher Oribatida' (Acari), conflicting with current classification schemes" [abstract], doi:10.1186/1471-2148-10-246, v10 n246, BMC Evolutionary Biology, 11 Aug 2010. "Character histories of six morphological traits indicate that their evolution followed a rather complex pattern of multiple independent gains (and losses)."
4 Aug 2010: Sponges have many genes that are used only by more advanced animals for encoding organs, nerves and muscles.
30 Jul 2010: Nineteen of the species... had RNA viral sequences embedded in their DNA.
23 Jul 2010: The cell, and indeed evolution, can dial up these microRNAs very flexibly in different cells to address various targets, and they only need one protein complex to come and do the job.
The gut's 'friendly' viruses revealed, doi:10.1038/news.2010.353, by Amy Maxmen, NatureNews, online 14 Jul 2010. "The team found genes encoding proteins never detected before in bacterial viruses. When in bacteria, these proteins are part of pathways responsible for carbohydrate metabolism and amino-acid synthesis. Viruses carrying such genes might alter them and insert them into gut bacteria, potentially changing a person's metabolism."
A Viral Wonderland in the Human Gut by Gisela Telis, ScienceNow, 14 Jul 2010.
Adam D. Ewing and Haig H. Kazazian Jr, "High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes" [abstract], doi:10.1101/gr.106419.110, Genome Research, online 20 May 2010. "...We estimate that the rate of L1 retrotransposition in humans is between 1/95 and 1/270 births."
Elizabeth J. Duncan and Peter K. Dearden, "Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex" [abstract], doi:10.1101/gr.104794.109, p917-928 v20, Genome Research, Jul (online 10 May) 2010. "Such capture of a sequence into a signaling pathway due to a local chromatin domain may be a general mechanism whereby novel genes are recruited into ancient cell signaling pathways."
Maynard ND, Birch EW, Sanghvi JC, Chen L, Gutschow MV, et al., "A Forward-Genetic Screen and Dynamic Analysis of Lambda Phage Host-Dependencies Reveals an Extensive Interaction Network and a New Anti-Viral Strategy" [html], doi:10.1371/journal.pgen.1001017, 6(7): e1001017, PLoS Genet., online 8 Jul 2010. "Our results demonstrate a highly integrated network between lambda and its host...."
Sohini Ghoshroy et al., "Molecular evolution of glutamine synthetase II: Phylogenetic evidence of a non-endosymbiotic gene transfer event early in plant evolution" [abstract], doi:10.1186/1471-2148-10-198, v10 paper 198, BMC Evolutionary Biology, 25 Jun 2010.
4 Jul 2010: ...[A] new mechanism for how mammals acquire genes, from The University at Buffalo.
29 Jun 2010: One of the most dramatic possibilities is that elements of DNA have entered the germline from viruses — excerpted from an online review of What Darwin Got Wrong.
"Jumping Genes" Find New Homes in Humans More Often Than Previously Estimated by Vincent Dollard, Emory University (also Physorg.com), 25 Jun 2010.
...New Theory on Aging, The George Washington University Medical Center, 23 Jun 2010. "...A new theory states that within the DNA itself, are archaic retroviruses...."
The Independent Evolution of Multicellularity, a new webpage, mentions an instance of HGT by a DNA virus, 23 Jun 2010.
Cheryl P. Andam, David Williams and J. Peter Gogarten, "Biased gene transfer mimics patterns created through shared ancestry" [abstract], doi:10.1073/pnas.1001418107, Proc. Natl. Acad. Sci. USA, online 21 May 2010. "...The signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer."
Satoko Yoshida et al., "Horizontal Gene Transfer by the Parasitic Plant Striga hermonthica" [abstract], doi:10.1126/science.1187145, p1128 v238, Science, 28 May 2010. "...Suggesting that nuclear genes can be captured by parasitic weeds in nature."
Yoav Raz and Emmanuel Tannenbaum, "The Influence of Horizontal Gene Transfer on the Mean Fitness of Unicellular Populations in Static Environments" [abstract], doi:10.1534/genetics.109.113613, p327-337 v185, Genetics, May 2010. "...We conclude that HGT does not confer a selection advantage in static environments. Rather, its advantage must lie in its ability to promote faster adaptation in dynamic environments, an interpretation that is consistent with the observation that HGT can be promoted by environmental stresses on a population."
Jumping Elements, Some of Which Cause Genetic Diseases, Become Incorporated in the Genome at Different Stages of Human Development, Pennsylvania State University, 28 Apr 2010.
Claudia P. Marquez and Ellen J. Pritham, "Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals" [abstract], doi:10.1534/genetics.110.116673, Genetics, online 10 May 2010. Phantom elements found in dsDNA viruses adds to the growing body of evidence... that dsDNA viruses may act as vectors for horizontal movement of TEs between eukaryotes.
2 May 2010: Transposable elements spread between disparate species by hitch-hiking in the genomes of parasites shared by these species.
1 May 2010: Phylogenetic analyses imply the ancestral transfer of these genes from a fungus to an ancestor of numerous modern aphid species.
1 May 2010: A dual-function gene is very old according to a pair of German microbiologists.
28 Apr 2010: The conserved gene systems revealed by the plant-vertebrate phenologs illustrate a more ancient homology than the 'deep homology' of metazoans that is currently a focus of evolutionary developmental biology (evo-devo).
Wenheng Zhang et al., "Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism" [abstract], doi:10.1073/pnas.0910155107, Proc. Natl. Acad. Sci. USA, 6 Apr 2010. "Several studies from phylogenetically diverse species indicate that zygomorphy has evolved independently via the repeated recruitment of CYC2-like genes."
Thomas A. Richards et al., "...a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi..." [abstract], doi:10.1105/tpc.109.065805, p1897-1911 v21, The Plant Cell, Jul 2009.
15 Apr 2010: Germs we eat may supply genes to the microbes in our guts.
Matthieu Legendre et al., "mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus" [abstract], doi:10.1101/gr.102582.109, Genome Research, online 1 Apr 2010.
3 Apr 2010: Whole chromosomes can be horizontally transferred into reproductively isolated strains of fungi.
11 Mar 2010: Hans-Peter Wheeler points to an article about a virus in the human germ line.
5 Mar 2010: Genes in the microbes in our guts are 150 times more numerous than human genes.
Virginie Doceul, Michael Hollinshead et al., "Repulsion of Superinfecting Virions: A Mechanism for Rapid Virus Spread" [abstract], doi:10.1126/science.1183173, p873-876 v327, Science, 12 Feb 2010. "Here, we show that vaccinia virus spreads... fourfold faster than its replication cycle would permit."
Yoav Raz and Emmanuel David Tannenbaum, "The Influence of Horizontal Gene Transfer on the Mean Fitness of Unicellular Populations in Static Environments" [Open Access abstract], doi:10.1534/genetics.109.113613, Genetics, online 1 Mar 2010. "...[HGT's] advantage must lie in its ability to promote faster adaptation in dynamic environments, an interpretation that is consistent with the observation that HGT can be promoted by environmental stresses on a population."
Nikoh N, McCutcheon JP, Kudo T, Miyagishima S, Moran NA, et al., "Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host" [html], PLoS Genet 6(2): e1000827, doi:10.1371/journal.pgen.1000827, 26 Feb 2010.
17 Feb 2010: We suggest that both ...were derived from ancestral bacterial proteins....
Herpin A, Braasch I, Kraeussling M, Schmidt C, Thoma EC, et al., "Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements" [html], PLoS Genet 6(2): e1000844, doi:10.1371/journal.pgen.1000844, 12 Feb 2009. "Our study therefore provides strong evidence for the important role of transposable elements in the rewiring of gene regulatory networks."
8 Feb 2010: Such lateral gene transfers between bacteria and animals could be an important source of evolutionary innovation.
Frank Ryan, "I, virus: Why you're only half human" [link], New Scientist, 29 Jan 2010.
4 Feb 2010: Our results imply that natural selection has favored both the movement and fixation of these exceptional invasive alleles.
16 Jan 2010: The chimpanzee and human Y chromosomes have undergone wholesale renovation since the species diverged.
Helen M. Rowe et al., "KAP1 controls endogenous retroviruses in embryonic stem cells" [abstract], doi:10.1038/nature08674, p237-240 v463, Nature, 14 Jan 2010. "More than forty per cent of the mammalian genome is derived from retroelements, of which about one-quarter are endogenous retroviruses (ERVs)."
13 Jan 2010: A sea slug acquired photosynthesis from algae — Sidney K. Pierce
7 Jan 2010: A gene from a non-retroviral virus has been integrated into various mammalian genomes, including our own.
Dongying Wu et al., "A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea" [abstract], doi:10.1038/nature08656, p1056-1060 v462, Nature, 24 Dec 2009. "This is the first time that a version of this 'textbook' eukaryotic gene has been discovered in bacteria."
Yongming Wang, František Líška et al., "A novel active endogenous retrovirus family contributes to genome variability in rat inbred strains" [abstract], doi:10.1101/gr.100073.109, p 19-27 v 20, Genome Research, 20 Jan 2010 (online 3 Nov 2009).
26 Dec 2009: ...The protein... is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon.
16 Dec 2009: The giant [Marseillevirus] adopts genes from the other organisms, including eukaryotes, bacteria and other viruses....
13 Dec 2009: Some microorganisms can survive interplanetary journeys cocooned inside rocks blasted off planets by comet and asteroid impacts. [Pertains to research at ASU about photosynthesis.]
11 Dec 2009: ...the percentage of genes transferred ...could be close to 100%.
25 Nov 2009: Butterflies and caterpillars were once separate species, brought together by hybridization?
Bethan V. Lowder et al., "Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus" [abstract], doi:10.1073/pnas.0909285106, Proc. Natl. Acad. Sci. USA, online 2 Nov 2009. "The poultry ST5 clade has undergone genetic diversification from its human progenitor strain by acquisition of novel mobile genetic elements from an avian-specific accessory gene pool, and by the inactivation of several proteins important for human disease pathogenesis."
Luis Boto, "Horizontal gene transfer in evolution: facts and challenges" [Open Access abstract], doi:10.1098/rspb.2009.1679, Proc. R. Soc. B, online 28 Oct 2009. "These studies show that the transfer can occur not only among but also between domains in all possible directions.... [T]here is a need for a new paradigm in evolution that includes horizontal gene transfer...."
MB Gogarten, JP Gogarten and L Olendzenski, eds., Horizontal Gene Transfer: Genomes in Flux [publisher's promo], Humana Press (Springer), 2009.
CJ Huang et al., "Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences" [abstract], 10:74, BMC Mol Biol, 25 Jul 2009. And commentary —
Keren Vaknin et al., "TEs or not TEs? That is the evolutionary question" [html], doi:10.1186/jbiol188, 8:83, Journal of Biology, online 23 Oct 2009.
Aris Katzourakis et al., "Macroevolution of Complex Retroviruses" [abstract], doi:10.1126/science.1174149, p1512 v325, Science, 18 Sep 2009. "Our analysis highlights the role of evolutionary constraint in maintaining viral genome structure and indicates that accessory genes and mammalian mechanisms of innate immunity are the products of macroevolutionary conflict played out over a geological time scale."
Druin Burch, "The Virus Within" [transcript at findarticles.com], p14-16&42 n8 v118, Natural History, Oct 2009. "We've got past theorizing that retroviruses could jump into a species' genome: we've shown they actually do."
If only the weeds would keep their genes to themselves, EurekAlert.com, 6 Oct 2009.
6 Oct 2009: There are now compelling documentations of horizontal gene transfer in eukaryotes....
29 Sep 2009: ...HGT from multiple sources is shown to be able to generate and optimize novel evolutionary characters in eukaryotes....
Naomi Siew and Daniel Fischer, "Unravelling the ORFan Puzzle" [abstract], doi:10.1002/cfg.311, p432–441 v4(4), Comparative and Functional Genomics, Jul 2003. "ORFans are open reading frames (ORFs) with no detectable sequence similarity to any other sequence in the databases."
Vincent Daubin and Howard Ochman, "Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli" [abstract], doi:10.1101/gr.2231904, p1036-1042 v14, Genome Research, Jun 2004. "...ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions."
Maite Novo et al., "Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118" [abstract], doi:1073/pnas.0904673106, p16333-16338 v106, Proc. Natl. Acad. Sci. USA, 22 Sep 2009. "...These data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes."
21 Sep 2009: Nearly half of the human genome is derived from transposable elements (TEs).
17 Sep 2009: The gain and loss of exons has contributed to the evolution of new features.
Kerry M. Oliver et al., "Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism" [abstract], doi:10.1126/science.1174463, p 992-994 v 325, Science, 21 Aug 2009. And commentary—
Virus benefits insect hosts, TheScientist.com, 20 Aug 2009.
Maite Novo et al., "Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118" [OA abstract], doi:10.1073/pnas.0904673106, Proc. Natl. Acad. Sci. USA, online 9 Sep 2009.
Itai Sharon, Ariella Alperovitch et al., "Photosystem I gene cassettes are present in marine virus genomes" [abstract], doi:10.1038/nature08284, p 258-262 v 461, Nature, 10 Sep 2009. "...The oceanic virome could be an almost unlimited source of naturally bioengineered gene cassettes."
Jongsik Chun et al., "Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae" [abstract], doi:10.1073/pnas.0907787106, p 15442-15447 v 106, Proc. Natl. Acad. Sci. USA, 8 Sep 2009. "...It is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer...."
Dawit Kidane, Begoña Carrasco et al., "Evidence for Different Pathways during Horizontal Gene Transfer in Competent Bacillus subtilis Cells" [article], doi:10.1371/journal.pgen.1000630, e1000630, v 5 n 9, PLoS Genet, online 4 Sep 2009.
Jerry Chancellor replies with a link to an interesting article about sea squirts, 4 Sep 2009.
Thomas A. Richards et al., "Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi" [abstract], doi:10.1105/tpc.109.065805, The Plant Cell, online 7 Jul 2009.
24 Aug 2009: Most of our genes... were transferred from an endosymbiont. — Carl Zimmer
21 Aug 2009: I find it fascinating that this prokaryotic symbiosis could so profoundly shape the evolution of life....
Weilong Hao and G. Brian Golding, "Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?" [abstract], doi:10.1534/genetics.109.104216, p 1365-1375 v 182, Genetics, Aug 2009.
Anthrax bacteria conspire with viruses to stay alive, The Rockefeller University, 12 Aug 2009.
Vincent J. Lynch and Günter P. Wagner, "Did Egg-laying Boas Break Dollo's Law? Phylogenetic Evidence for Reversal to Oviparity in Sand Boas (Eryx: Boidae)" [abstract], doi:10.1111/j.1558-5646.2009.00790.x, Evolution, online 30 Jul 2009. "Re-evolution of lost complex morphological characters...."
25 Jul 2009: Spermatozoa of all species can take up exogenous DNA or RNA molecules and internalize them into nuclei.
Anne Dupressoir et al., "Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene" [abstract], doi:10.1073/pnas.0902925106, p 12127-12132 v 106, Proc. Natl. Acad. Sci. USA, 21 Jul 2009. Also see commentary:
Jonathan P. Stoye, "Proviral protein provides placental function" [extract], doi:10.1073/pnas.0906295106, p 11827-11828 v 106, Proc. Natl. Acad. Sci. USA, 21 Jul 2009.
23 Jul 2009: Primate-specific genes were inserted de novo, not generated by gradual divergence from non-primate genes.
Carla J. Cohen et al., "Endogenous retroviral LTRs as promoters for human genes: A critical assessment" doi:10.1016/j.gene.2009.06.020, Gene, online 3 July.
Eva C. Berglund et al., "Run-Off Replication of Host-Adaptability Genes Is Associated with Gene Transfer Agents in the Genome of Mouse-Infecting Bartonella grahamii" [article], doi:10.1371/journal.pgen.1000546, e1000546, v 5 n 7, PLoS Genet, online 3 Jul 2009.
27 Jun 2009: More than 20% of diatom genes were apparently recruited from red and green algae.
Josefa González and Dmitri A. Petrov, "The adaptive role of transposable elements in the Drosophila genome" [Science Direct abstract], doi:10.1016/j.gene.2009.06.008, Gene, online 23 Jun 2009.
Takeshi Kawashima et al., "Domain shuffling and the evolution of vertebrates" [abstract], doi:10.1101/gr.087072.108, Genome Research, online 14 May 2009.
Peter Simmonds, "Virus evolution" [PDF], p 96-99, Microbiology Today, May 2009. "...[Mimiviruses] adopt a phylogenetic position ancestral to the split of the animal, plant and other component kingdoms of eukaryotes, implying an extraordinarily long evolutionary existence, possibly reaching back as far as the origin of life."
Hiroki Kano et al., "L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism" [abstract], doi:10.1101/gad.1803909, p 1303-1312 v 23, Genes & Development, 1 Jun 2009. "...The integration events usually occur in embryogenesis rather than in germ cells and are not heritable." Also see commentary: Jumping genes discovery 'challenges current assumptions', EurekAlert!, 11 Jun 2009. "Jumping genes do most of their jumping, not during the development of sperm and egg cells, but during the development of the embryo itself."
Elizabeth Pennisi, "The Bug and the Bacterium: Interdependent Genomes" [summary], doi:10.1126/science.324_1253, p 1253 v 324, Science, 5 Jun 2009. "...A long history of give-and-take between the genomes of the bug and a tiny bacterium...."
2 Jun 2009: Ken Jopp points us to a news item about bacteria that can capture DNA.
Matti Jalasvuori et al., "On the astrobiological relevance of viruses in extraterrestrial ecosystems" [abstract], doi:10.1017/S1473550409004479, International Journal of Astrobiology, online 12 May 2009.
30 May 2009: For prokaryotes, entire metabolic pathways ...could be added by the virtue of horizontal gene transfer (HGT).
28 May 2009: This "adaptive" arm ...may be the serendipitous outcome of invading DNA introduced by a virus or microbe infecting a fishlike creature.
Yaniv Brandvain and Michael J. Wade, "The Functional Transfer of Genes From the Mitochondria to the Nucleus: The Effects of Selection, Mutation, Population Size and Rate of Self-fertilization" [abstract], doi:10.1534/genetics.108.100024, Genetics, online 27 May 2009.
Weilong Hao and G. Brian Golding, "Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?" [abstract], doi:10.1534/genetics.109.104216, Genetics, online 27 May 2009. "Lateral gene transfer (LGT) and gene rearrangement are essential for shaping bacterial genomes during evolution."
Venigalla B. Rao, "A virus DNA gate: Zipping and unzipping the packed viral genome" [extract], doi:10.1073/pnas.0903670106, p 8403-8404 v 106, Proc. Natl. Acad. Sci. USA, 26 May 2009. "The internal capsid pressure... >10 times that of bottled champagne, provides a driving force for delivery of viral genome into host cell. ...The efficiency of delivery in some phages reaches the theoretical limit."
Adam Monier et al., "Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus" [abstract], doi:10.1101/gr.091686.109, p 1441-1449 v 19, Genome Research, Aug (online 18 May) 2009.
18 May 2009: Viral infections can augment the metabolism, immunity, distribution and evolution of their hosts in many unexpected and potentially positive ways.
Jonathan L. Gordon et al., "Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome" [article], doi:10.1371/journal.pgen.1000485, 5(5): e1000485, PLoS Genet. 15 May 2009. "We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, ...and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD."
Mariusz Nowacki et al., "A Functional Role for Transposases in a Large Eukaryotic Genome" [abstract], doi:10.1126/science.1170023, p 935-938 v 324, Science, 15 May 2009.
6 May 2009: ...The existence of a unique vertex in Mimivirus, possibly for genome delivery....
Geoffrey J Faulkner et al., "The regulated retrotransposon transcriptome of mammalian cells" [abstract], doi:10.1038/ng.368, p 563-571 v 41, Nature Genetics, May (online 19 Apr) 2009. "We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome."
12 Apr 2009: Two single-celled eukaryotes have apparently used horizontal gene transfer extensively to evolve and diverge.
Ancient crenarchaeal viruses are described in an Astrobiology article to which Cody Bennett points us in an email, 5 Apr 2009.
Xudong Cheng et al., "A New Family of Ty1-copia-Like Retrotransposons Originated in the Tomato Genome by a Recent Horizontal Transfer Event" [abstract], doi:10.1534/genetics.108.099150, p 1183-1193 v 181, Genetics, Apr (online 19 Jan) 2009. "The possible hijacking of nuclear genes by retrotransposons could transfer them between organisms...."
28 Mar 2009: Bacteria rapidly acquire whole metabolic pathways by the horizontal transfer of multiple genes.
19 Mar 2009: ...Lateral transfer among eukaryotes and between eukaryotes and bacteria appears to be an on-going and not too infrequent process.
10 Mar 2009: ...The gene has been 'dead' for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages.
8 Mar 2009: HGT also turns out to be the rule rather than the exception in the third great domain of life, the eukaryotes.
Gennady Churakov et al., "Mosaic Retroposon Insertion Patterns in Placental Mammals" [abstract], doi:10.1101/gr.090647.108, Genome Research, online 4 Mar 2009.
28 Feb 2009: We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.
27 Feb 2009: It is well documented that genes of viral origin are used by eukaryotes to ensure physiological functions....
Mark J. Mandel et al., "A single regulatory gene is sufficient to alter bacterial host range" [abstract], doi:10.1038/nature07660, Nature, online 1 Feb 2009. Also see commentary: Single gene lets bacteria jump from host to host, by Terry Devitt, University of Wisconsin, Madison, 1 Feb 2009. "The regulatory gene entered the bacterium's lineage and allowed it to expand its host range into the squid."
Bryan R. Cullen, "Viral and cellular messenger RNA targets of viral microRNAs" [abstract], doi:10.1038/nature07757, p 421-425 v 457, Nature, 22 Jan 2009.
Elena Khazina and Oliver Weichenrieder, "Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame" [abstract], doi:10.1073/pnas.0809964106, p 731-736 v 106, Proc. Natl. Acad. Sci. USA, 20 Jan 2009. Also see Parasites in the genome, Max Planck Institute for Developmental Biology, 19 Jan 1009.
19 Jan 2009: Nonretroviral RNA viruses may have contributed more substantially and directly to the evolution of mammalian genomes than has been assumed so far.
NYU Scientists Discover Dangerous New Method for Bacterial Toxin Transfer, NYU Langone Medical Center, 6 Jan 2009. "We have found that a bacteriophage can transfer genetic elements, or DNA, between unrelated bacterial species in a way that was really not expected."
Marco Minoia et al., "Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas" [abstract], doi:10.1073/pnas.0806164106, p 20792-20797 v 105, Proc. Natl. Acad. Sci. USA, 30 Dec 2008.
Siyang Sun et al., "The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces" [abstract], doi:10.1016/j.cell.2008.11.015, p 1251-1262 v 135, Cell, 26 Dec 2008.
24 Dec 2008: Retroviral genome invasions... have occurred throughout the evolution of vertebrates and continue to the present day.
23 Dec 2008: Maybe heat-loving prokaryotes are not the oldest form of life.
Marco Minoia et al., "Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas" [abstract], doi:10.1073/pnas.0806164106, Proc. Natl. Acad. Sci. USA, online 19 Dec 2008. "...HGT rates can be modulated by external environmental conditions provides an explanation as to why selective conditions can promote DNA exchange."
18 Nov 2008: ...Borrowing a couple of genes....
Mary E. Rumpho et al., "Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica" [abstract], doi:10.1073/pnas.0804968105, Proc. Natl. Acad. Sci. USA, online 11 Nov 2008. "We demonstrate that foreign organelle retention generates metabolic novelty ("green animals") and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer."
4 Nov 2008: Only a Theory, by Kenneth R. Miller
30 Oct 2008: Horizontal transfer (HT) of DNA transposons has apparently produced evolutionary innovation in mammals.
21 Oct 2008: Hundreds of genes from bacteria are found in diatom genomes.
'Space invader' DNA infiltrated mammalian genomes, by Jessica Griggs, NewScientist.com news service, 20 Oct 2008.
Mathieu Brochet et al., "Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae" [abstract], doi:1073/pnas.0803654105, Proc. Natl. Acad. Sci. USA, online 2 Oct 2008. "We demonstrate that large DNA segments of up to 334 kb ...can be transferred through conjugation from multiple initiation sites."
30 Sep 2008: Horizontal gene transfer with the animals is going to turn out to be more widespread than anybody believes now.
18 Sep 2008: The virophage could be a vehicle mediating lateral gene transfer between giant viruses.
11 Sep 2008: ...Multiple independently acquired genes are able to generate and optimize key evolutionary novelties in major eukaryotic groups.
Hiroyuki Ogata and Jean-Michel Claverie, "How to Infect a Mimivirus" [summary], doi:10.1126/science.1164839, p 1305-1306 v 321, Science, 5 Sep 2008. "Large DNA viruses such as the giant Mimivirus can be infected by smaller viruses."
Virus weaves itself into the DNA transferred from parents to babies, University of Rochester Medical Center, 3 Sep 2008.
Chris Pointing, "The functional repertoires of metazoan genomes" [PubMed abstract], doi:10.1038/nrg2413, p 689-698 v 9, Nature Reviewes Genetics, Sep (online 29 Jul) 2008. "If turn-over of functional sequence is so pervasive then where does the new functional sequence materialize from?"
17 Aug 2008: The origin of new genes in well-documented species of fruitflies....
Wei Wei et al., "Ancient, recurrent phage attacks and recombination shaped dynamic sequence-variable mosaics at the root of phytoplasma genome evolution" [Open Access abstract], doi:10.1073/pnas.0805237105, p 11827-11832 v 105, Proc. Natl. Acad. Sci. USA, 19 Aug (online 13 Aug) 2008.
Guillaume Bourque et al. "Evolution of the mammalian transcription factor binding repertoire via transposable elements" [abstract], doi:10.1101/gr.080663.108, Genome Research, online 5 Aug 2008.
1 Aug 2008: ...On average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer.... — geneticists from Düsseldorf and Tel Aviv.
20 Jul 2008: The number of cases of HGT involving eukaryotes is now so great....— Patrick Keeling and Jeffrey Palmer.
25 Jun 2008: Vertebrate and jellyfish eyes use similar genes.
Keiko Akagi1, Jingfeng Li, Robert M. Stephens et al., "Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition" [abstract], doi:10.1101/gr.075770.107, p 869-880 v 18, Genome Research, Jun (online 7 May) 2008. "...Recent endogenous L1 retrotransposition has diversified genomic structures and transcripts extensively, distinguishing mouse lineages and driving a major portion of natural genetic variation."
Zauberman N, Mutsafi Y, Halevy DB, Shimoni E, Klein E, et al. "Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus" [open access article], doi:10.1371/journal.pbio.0060114, e114 v 6 n 5, PLoS Biology, 13 May 2008; and press release:
...Invasion Strategy of the World's Largest Virus, Weizmann Institute, 29 May 2008.
Yong-beom Lim et al. "Filamentous Artificial Virus from a Self-Assembled Discrete Nanoribbon" [abstract | press release], doi:10.1002/anie.200800266, p 4525-4528 v 47, Angewandte Chemie International Edition, 2 Jun (online 7 May) 2008. "Viruses are true experts at importing genetic material into the cells of an infected organism."
Megha Ghildiyal et al., "Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells" [abstract], doi:10.1126/science.1157396, p 1077-1081 v 320, Science, 23 May (online 10 Apr) 2008.
20 May 2008: How a virus became a retroposon is detailed in a report by French virologists and genetecists.
Ryoma Kamikawa et al., "Direct phylogenetic evidence for lateral transfer of elongation factor-like gene" [abstract], doi:10.1073/pnas.0711084105, Proc. Natl. Acad. Sci. USA, online 5 May 2008. "...The first case in which the donor–recipient relationship was clarified."
Bacteriophages: The Most Common Life-Like Form on Earth, Astronomy Picture of the Day, 21 Apr 2008.
11 Apr 2008: Earth's first animal... was probably significantly more complex than previously believed.
3 Apr 2008: What is the origin of eukaryotic RNA polymerases?
Ben Field and Anne E. Osbourn, "...Independent Assembly of Operon-Like Gene Clusters in Plants" [abstract], doi:10.1126/science.1154990, Science, online 20 Mar 2008. "...Recent assembly of operon-like gene clusters for triterpene synthesis has occurred independently in divergent plant lineages...."
Baruch S. Blumberg, "Obituary: Joshua Lederberg (1925–2008)" [html], doi:10.1038/452422a, p 422 v 452 Nature, 27 Mar 2008. "...He discovered that viruses that infect bacteria can transfer genetic information between their hosts."
14 Mar 2008: Viruses serve as gene banks for ecosystems?!
David A Ray et al., "Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus" [abstract], doi:10.1101/gr.071886.107, Genome Research, online 13 Mar 2008. "Together these data suggest that there has been tremendous recent activity of various DNA transposons in the bat lineage that far exceeds those previously reported for any mammalian lineage."
Ludivine Sinzelle et al., "Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes" [abstract], doi:10.1073/pnas.0707746105, Proc. Natl. Acad. Sci. USA, online 13 Mar 2008. "The reconstructed ...transposon shows efficient cut-and-paste transposition in human cells and preferentially inserts into a 15-bp consensus target sequence."
Ana Babić et al., "Direct Visualization of Horizontal Gene Transfer" [abstract], doi:10.1126/science.1153498, p 1533-1536 v 319, Science, 14 Mar 2008.
Han Xiao et al., "A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit" [abstract], doi:10.1126/science.1153040, p 1527-1530 v 319, Science, 14 Mar 2008. "Our discovery demonstrates that retrotransposons may be a major driving force in genome evolution and gene duplication, resulting in phenotypic change in plants."
Christelle Desnues et al., "Biodiversity and biogeography of phages in modern stromatolites and thrombolites" [html], doi:10.1038/nature06735, Nature, online 2 Mar 2008. "The high percentage of unknown sequences recovered from the three metagenomes...." also commentary:
Biologists surprised to find parochial bacterial viruses, EurekAlert!, 4 Mar 2008.
Haruhiko Siomi and Mikiko C Siomi, "Interactions between transposable elements and Argonautes have (probably) been shaping the Drosophila genome throughout evolution" [abstract], doi:10.1016/j.gde.2008.01.002, Current Opinion in Genetics & Development, corrected proof online 4 Mar 2008.
24 Feb 2008: An intuitively unlikely evolutionary event has, in fact, occurred at least twice in primates.
William J.Broad, "Joshua Lederberg, 82, a Nobel Winner, Dies [2 Feb]" [html], The New York Times, 5 Feb 2008.
Victoria P. Belancio et al., "Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health" [abstract], doi:10.1101/gr.5558208, Genome Research, online 6 Feb 2008.
Hugh P. Cam et al., "Host genome surveillance for retrotransposons by transposon-derived proteins" [abstract | Editor's Summary], doi:10.1038/nature06499, p 431-436; also commentary by Daniel F. Voytas, "Fighting fire with fire," p 412-413; v 451 Nature, 24 Jan 2008.
Wenfeng Qian and Jianzhi Zhang, "Evolutionary dynamics of nematode operons: Easy come, slow go" [abstract], doi:10.1101/gr.7112608, Genome Research, online 24 Jan 2008. "...The rate of operon gain is ~3.3 times that of operon loss."
Naruo Nikoh et al., "Wolbachia genome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes" [abstract], doi:10.1101/gr.7144908, p 272-280 v 18, Genome Research, online 11 Dec 2007. "...~30% of Wolbachia genes... are present on the insect nuclear genome. ...Molecular evolutionary and other lines of evidence indicated that the transferred genes are probably derived from a single lateral transfer event."
Anuphap Prachumwat and Wen-Hsiung Li, "Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes" [abstract], doi:10.1101/gr.7046608, p 221-232 v 18, Genome Research, online 14 Dec 2007. "...A substantial proportion of vertebrate genes (~22%) cannot be found in the nonvertebrate genomes studied."
Yoichi Sekita et al., "Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta" [abstract], doi:10.1038/ng.2007.51, p 243-248 v 40, Nature Genetics, Feb (online 6 Jan) 2008. "...Retrotransposon-derived Rtl1... is essential for maintenance of the fetal capillaries...."
26 Dec 2007: Do thawing glaciers speed up evolution?
Larry Klaes wrote an article mentioning transposases as the source for light-responding proteins in plants, 23 Dec 2007.
10 Dec 2007: When eukaryotes are included..., the phylogeny of life seems better represented by a network than a tree....
6 Dec 2007: A flood of new information,... [including] greater appreciation of the importance of lateral gene transfer, is transforming 21st century biology — National Science Foundation
4 Dec 2007: If Charles Darwin reappeared today, he might be surprised to learn that humans are descended from viruses as well as from apes — Robin Weiss
Transposons recycled into transcription factors to sense light! is the subject of email from Cédric Feschotte, 28 Nov 2007.
29 Nov 2007: Surprises come from a comparison of twelve fruitfly genomes.
Arnaud Le Rouzic et al., "Long-term evolution of transposable elements" [abstract], doi:10.1073/pnas.0705238104, p 19375-19380 v 104, Proc. Natl. Acad. Sci. USA, 4 Dec (online 26 Nov) 2007. "...Integration of an adaptive TE-derived sequence in the host genome... seem even more frequent than previously thought, and a significant proportion of genes, including promoters and regulatory sequences, indeed appears to derive from former TE insertions...."
19 Nov 2007: Ancient retroviruses spurred evolution of gene regulatory networks in humans and other primates.
Thomas Hohn, "Plant virus transmission from the insect point of view" [login link], doi:10.1073/pnas.0709178104, p 17905-17906 v 104, Proc. Natl. Acad. Sci. USA, 13 Nov 2007.
Guillaume Blanc et al., "Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome" [abstract], doi:10.1101/gr.6742107, p 1657-1664 v 17, Genome Research, online 4 Oct 2007. "Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought."
25 Oct 2007: You can think of the genome as a revolving door—genes keep coming and going — Matthew W. Hahn
Transgenics Transformed: Maize Mini-chromosomes Can Add Stacks of Functional Genes to Plants, newswise.com, 11 Oct 2007. "A new method of constructing artificial plant chromosomes from small rings of naturally occurring plant DNA can be used to transport multiple genes at once into embryonic plants where they are expressed, duplicated as plant cells divide, and passed on to the next generation...."
Camila M. Romano et al., "Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys" [text], doi:10.1371/journal.pone.0001026, PLoS Biol 2(10): e1026 (Public Library of Science), published 10 Oct 2007.
Guillaume Blanc et al., "Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome" [abstract], doi:10.1101/gr.6742107, Genome Research, online 4 Oct 2007.
Marc Bailly-Bechet et al., "Causes for the intriguing presence of tRNAs in phages" [abstract], doi:10.1101/gr.6649807, p 1486-1495 v 17, Genome Research, Oct (online 4 Sep) 2007.
Debbie Lindell et al., "Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution" [abstract], doi:10.1038/nature06130, p 83-86 v 449, Nature, 6 Sep 2007. "Phages infecting marine cyanobacteria encode a number of host-like genes including photosynthesis...."
Elizabeth Pennisi, "Jumping Genes Hop Into the Evolutionary Limelight" [summary], doi:10.1126/science.317.5840.894, Science, 17 Aug 2007. "...Many conserved elements burst onto the scene between the emergence of lampreys and sharks."
14 Sep 2007: Lateral gene transfer... may happen much more frequently between bacteria and multicellular organisms than scientists previously believed.....
29 Jul 2007: The Limits of Organic Life in Planetary Systems
28 Jul 2007: Evolution is recycling — Tarjei Mikkelsen
Oliver Piskurek and Norihiro Okada, "Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals" [abstract], doi:10.1073/pnas.0700531104, Proc. Natl. Acad. Sci. USA, online 10 Jul 2007.
1 Jun 2007: Modern mammals, ...evolved ...with a surprising assist from genetic elements usually derided as mere junk.
Erik S. Barton et al., "Herpesvirus latency confers symbiotic protection from bacterial infection" [abstract], doi:10.1038/nature05762; and commentary by Matt Kaplan, "Herpesviruses might have benefits" [text], doi:10.1038/news070514-13, Nature, online 16 May 2007.
16 May 2007: ...The focus has shifted towards analysing flows of gene populations... into eukaryotes— James A. Lake.
10 May 2007: E.O. Wilson thinks panspermia is likely.
In-Geol Choi and Sung-Hou Kim, "Global extent of horizontal gene transfer" [(Open Access) abstract], doi:10.1073/pnas.0611557104, p 4489-4494 v 104, Proc. Natl. Acad. Sci. USA, 13 Mar (online 7 Mar) 2007.
Fasélli Coulibalay et al., "The molecular organization of cypovirus polyhedra" [abstract], doi:10.1038/nature05628, p 97-101.... "The resulting ultrastable and sealed crystals shield the virus particles from environmental damage"; and commentary by Felix A. Rey, "Holed up in a natural crystal," p 35 v 446, Nature, 1 Mar 2007.
29 Mar 2007: I felt sick to my stomach.... — Jonathan Eisen
Marie Touchon and Eduardo P. C. Rocha, "Causes of Insertion Sequences Abundance in Prokaryotic Genomes" [abstract], doi:10.1093/molbev/msm014, p 969-981 v 24, Molecular Biology and Evolution, Apr (online 23 Jan) 2007. "HGT seems necessary for the presence of [insertion sequences]...."
M. Cosentino Lagomarsino et al., "Hierarchy and feedback in the evolution of the Escherichia coli transcription network" [abstract], doi:10.1073/pnas.0609023104, p 5516-5520 v 104, Proc. Natl. Acad. Sci. USA, 27 Mar 2007. "...Horizontally transferred genes are mainly added at the bottom, as new target nodes."
Yaniv Brandvain et al., "Gene Co-Inheritance and Gene Transfer" [abstract], doi:10.1126/science.1134789, p 1685 v 315, Science, 23 Mar 2007.
20 Mar 2007: ...The movement of plant genes... involves a complex web....
20 Mar 2007: All retroviruses are very old.... — John Coffin.
Raul Alvarez-Venegas et al., "Origin of the Bacterial SET Domain Genes: Vertical or Horizontal?" [abstract], doi:10.1093/molbev/msl184, p 482-497 v 24, Molecular Biology and Evolution, Feb 2007 (online 5 Dec 2006).
Michael G. Giacomelli et al., "The Conversion of 3' UTRs into Coding Regions" [abstract], doi:10.1093/molbev/msl172, p 457-464 v 24, Molecular Biology and Evolution, Feb 2007 (online 10 Nov 2006).
12 Mar 2007: More about gene transfer comes from two new articles.
No Missing Link? Evolutionary Changes Occur Suddenly, Professor Says, ScienceDaily.com, 12 Feb 2007.
12 Feb 2007: The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as ...evolution itself.
Luis M. Márquez et al., "A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance" [abstract], doi:10.1126/science.1136237, p 513-515 v 315, Science, 26 Jan 2007.
Marie Doyle et al., "An H-NS-like Stealth Protein Aids Horizontal DNA Transmission in Bacteria" [abstract], doi:10.1126/science.1137550, p 251-252 v 315, Science, 12 Jan 2007. "This stealth strategy seems to be used widely to aid horizontal DNA transmission and has important implications for bacterial evolution."
Tal Dagan and William Martin, "Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution" [abstract], doi:10.1073/pnas.0606318104, Proc. Natl. Acad. Sci. USA, online 9 Jan 2007. "The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LGT at some time in their evolutionary past."
31 Dec 2006: Many genes once thought to be unique to humans have been in the tree of life for over a half billion years.
Angly F, Felts B, Breitbart M, Salamon P, Edwards R et al., "The marine viromes of four oceanic regions" [text], doi:10.1371/journal.pbio.0040368, PLoS Biol 4(11): e368 (Public Library of Science), published 7 Nov 2006. "On average, >91% of the sequences were not significantly similar to those in the extant databases."
Xiaoyun Qiu, Aditi U. Gurkar, and Stephen Lory, "Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa" [abstract], doi:10.1073/pnas.0606810104, Proc. Natl. Acad. Sci. USA, online 18 Dec 2006. "...A cluster of 108 genes ...can exist in an extrachromosomal circular form. ...The PAPI-1-containing strains are able to transfer it into ...recipient strains that do not harbor this island naturally."
5 Dec 2006: Almost all human genes contain duplicated sequences.
28 Nov 2006: Did the acquisition of an advantageous gene improve human brains?
Kazumi Matsubara et al., "Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes" [abstract], doi:10.1073/pnas.0605274103, Proc. Natl. Acad. Sci. USA, online 16 Nov 2006. "...suggesting that the sex chromosomes of snakes, mammals, and birds were all derived from different autosomal pairs of the common ancestor."
13 Nov 2006: The eyeless, earless [sea urchin] has genes that, in us, are involved in detecting sight and sound — Nature.
Xavier Didelot et al., "A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination" [abstract], doi:10.1101/gr.5512906, Genome Research, online 7 Nov 2006. "Several of the recombination events transferred novel genes in addition to homologous sequences, resulting in similar gene content in the two lineages."
João P. Gomes et al., "Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspot" [abstract], doi:10.1101/gr.5674706, Genome Research, online 7 Nov 2006. "Frequent recombination contrasts with a low level of point substitution...."
Sven B. Gould et al., "Nucleus-to-Nucleus Gene Transfer and Protein Retargeting into a Remnant Cytoplasm of Cryptophytes and Diatoms" [abstract], doi:10.1093/molbev/msl113, p 2413-2422 v 23, Molecular Biology and Evolution, Dec (online 13 Sep) 2006.
Viral Fossil Brought Back to Life, by Martin Enserink, ScienceNOW Daily News, 1 Nov 2006. "...Researchers have resurrected a retrovirus that infected our ancestors millions of years ago and now sits frozen in the human genome."
Marie Dewannieux et al., "Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements" [abstract], doi:10.1101/gr.5565706, Genome Research, online 31 Oct 2006.
6 Oct 2006: Once dismissed ...'jumping genes' are now regarded as major players ....
26 Sep 2006: What [rhodopsin] is doing in so many bacteria is not known....
Norbert Bannert and Reinhard Kurth, "The Evolutionary Dynamics of Human Endogenous Retroviral Families" [abstract], doi:10.1146/annurev.genom.7.080505.115700, p 149-173 v 7, Annual Review of Genomics and Human Genetics, Sep (online 24 May) 2006. "...A significant impact on various aspects of human biology has been recently revealed...."
13 Sep 2006: A gene left behind from a viral infection is essential for sheep development — AAAS
23 Aug 2006: ...They hold a reserve of genetic information that could help them survive, or even become dominant, if environmental conditions change. — from the Marine Biological Laboratory
Olga Zhaxybayeva et al., "Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events" [abstract], doi:10.1101/gr.5322306, p 1099-1108 v 16, Genome Research, Sep (online 9 Aug) 2006. "...Genes from all functional categories are subject to transfer."
Jonathan Filèe et al., "A Selective Barrier to Horizontal Gene Transfer in the T4-Type Bacteriophages That Has Preserved a Core Genome with the Viral Replication and Structural Genes" [abstract], doi:10.1093/molbev/msl036, p 1688-1696 v 23, Molecular Biology and Evolution, Sep (online 16 Jun) 2006.
Alexander S. Mikheyev et al., "Cryptic sex and many-to-one coevolution in the fungus-growing ant symbiosis" [abstract], doi:10.1073/pnas.0601441103, p 10702-10706 v 103, Proc. Natl. Acad. Sci. USA, 11 Jul (online 30 Jun) 2006. "...We document long-distance horizontal transmission of symbionts..., suggesting both lack of pairwise coevolutionary specificity... and dispersal of symbionts independent of their ant hosts."
Zhenguo Lin et al., "Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer" [abstract], doi:10.1073/pnas.0604232103, p 10328-10333 v 103, Proc. Natl. Acad. Sci. USA, 5 Jul (online 23 Jun) 2006. "These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes."
Michael Freeling and Brian C. Thomas, "Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity" [abstract], p 805-814 v 16, Genome Research, 1 Jul 2006. "We argue that 'balanced gene drive' is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages."
3 Jul 2006: Segmental duplications are crucibles of evolution.
Zhenguo Lin et al., "Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and endosymbiotic gene transfer" [abstract], doi:10.1073/pnas.0604232103, Proc. Natl. Acad. Sci. USA, online 23 Jun 2006.
23 Jun 2006: Viruses' staggering diversity and promiscuity could make them the most creative force in evolution — Nature
Katherina J. Kechris et al., "Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study" [abstract], doi:10.1073/pnas.0603534103, p 9584-9589 v 103, Proc. Natl. Acad. Sci. USA, 20 Jun (online 12 Jun) 2006. "...A conclusive case for LGT has been made."
20 Jun 2006: Bats and horses are closely related, according to a genomic study using retroposon (L1) analysis.
Austin Burt and Robert Trivers, Genes in Conflict: The Biology of Selfish Genetic Elements [publisher's promo], ISBN 0-674-01713-7, Harvard University Press, 2006. Reviewed in —
Peter Hammerstein and Edward H. Hagen, "Broken Cogs or Strategic Agents?" — review of Genes in Conflict [summary], doi:10.1126/science.1125754, p 530 v 312, Science, 28 Apr 2006.
C. G. Kurland et al., "Genomics and the Irreducible Nature of Eukaryote Cells" [abstract], doi:10.1126/science.1121674, p 1011-1014 v 312, Science, 19 May 2006. "Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria."
15 Jun 2006: Novel genes derived from noncoding DNA have been identified....
Akihiko Koga et al., "Vertebrate DNA Transposon as a Natural Mutator: The Medaka Fish Tol2 Element Contributes to Genetic Variation without Recognizable Traces" [abstract], doi:10.1093/molbev/msl003, p 1414-1419 v 23, Molecular Biology and Evolution, Jul (online 3 May) 2006. "...The impact of DNA transposons on vertebrate genomes may be, and may have been, larger than commonly supposed."
Ross F. Waller et al., "Lateral Gene Transfer of a Multigene Region from Cyanobacteria to Dinoflagellates Resulting in a Novel Plastid-Targeted Fusion Protein" [abstract], doi:10.1093/molbev/msl008, p 1437-1443 v 23, Molecular Biology and Evolution, Jul (online 4 May) 2006. "The number of cases of lateral or horizontal gene transfer in eukaryotic genomes is growing steadily...."
Gil Bejerano et al., "A distal enhancer and an ultraconserved exon are derived from a novel retroposon" [abstract], doi:10.1038/nature04696, p 87-90 v 441, Nature, 14 May (online 16 Apr) 2006.
Hidenori Nishihara et al., "Functional noncoding sequences derived from SINEs in the mammalian genome" [abstract], doi:10.1101/gr.5255506, Genome Research, online 22 May 2006.
Vania Rosas-Magallanes et al., "Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis" [abstract], doi:10.1093/molbev/msj120, p 1129-1135 v 23, Molecular Biology and Evolution, Jun (online 6 Mar) 2006.
11 May 2006: It's clear now that you have many more genes in the viral world, so there are many interesting new enzymes to be found — Patrick Forterre
9 May 2006: The structure of a bacterial enzyme that inserts mobile gene cassettes has been resolved by French biochemists and geneticists.
4 May 2006: A gene captured from a mobile element fused with another gene to make a new primate gene.
3 May 2006: Genes undergo rapid mutation and selection immediately after transfer, according to biologists at McMaster University.
6 Apr 2006: The Genomic Impact of Eukaryotic Transposable Elements — a science conference.
Gaby G. M. Doxiadis et al., "Reactivation by exon shuffling of a conserved HLA-DR3-like pseudogene segment in a New World primate species" [abstract], doi:10.1073/pnas.0600643103, Proc. Natl. Acad. Sci. USA, online 31 Mar 2006.
24 Mar 2006: Viruses And The Evolution Of Life, by Luis P. Villarreal
Maureen L. Coleman et al., "Genomic Islands and the Ecology and Evolution of Prochlorococcus" [abstract], doi:10.1126/science.1122050, p 1768-1770 v 311, Science, 24 Mar 2006. "We postulate that lateral gene transfer in genomic islands is an important mechanism for local specialization in the oceans." Also see a press release:
...Interplay between genes and viruses in tiny ocean plankton, National Science Foundation, 23 Mar 2006.
20 Mar 2006: Advantageous genes, probably introduced by retroviruses... — Barry Blumberg
15 Mar 2006: The paradigm for evolution among prokaryotes has completely shifted.
Vladimir V. Kapitonov and Jerzy Jurka, "Self-synthesizing DNA transposons in eukaryotes" [abstract], doi:10.1073/pnas.0600833103, p 4540-4545 v 103, Proc. Natl. Acad. Sci. USA, 21 Mar (online 14 Mar) 2006.
Yuji Inagaki et al., "Recombination between elongation factor 1α genes from distantly related archaeal lineages" [abstract], doi:10.1073/pnas.0600744103, p 4528-4533 v 103, Proc. Natl. Acad. Sci. USA, 21 Mar (online 14 Mar) 2006. "These findings suggest that [homologous recombination] occurs across a much larger evolutionary distance than generally accepted and affects highly conserved essential 'informational' genes."
2 Mar 2006: Endogenous proviruses are widespread in nature...
28 Feb 2006: Can Viruses Make Us Human? by Luis P. Villarreal.
24 Feb 2006: Retroposed genes have contributed to human evolution.
Niels-Ulrik Frigaard, "Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea" [abstract | Editor's Summary], doi:10.1038/nature04435, p 847-850 v 439, Nature, 16 Feb 2006.
Roy Britten, "Transposable elements have contributed to thousands of human proteins" [abstract], doi:10.1073pnas.0510007103, p 1798-1803 v 103, Proc. Natl. Acad. Sci. USA, 7 Feb (online 27 Jan) 2006.
...Evolution of signalling pathways, EurekAlert!, 7 Feb 2006. "The results also show that multi-component pathways evolve, in part, by the insertion of novel proteins between existing pathway components."
Zhixi Su et al., "Evolution of alternative splicing after gene duplication" [abstract], doi:10.1101/gr.4197006, p 182-189 v 16, Genome Research, Feb 2006 (online 19 Dec 2005). "These results support the subfunctionization model of alternative splicing.... In the early stage after gene duplication, young duplicates may take over a certain amount of protein function diversity that previously was carried out by the alternative splicing mechanism."
Cas Simons et al., "Transposon-free regions in mammalian genomes" [abstract], doi:10.1101/gr.4624306, p 164-172 v 16, Genome Research, Feb 2006 (online 19 Dec 2005). "...A conclusion difficult to reconcile with current conceptions of gene regulation."
2 Feb 2006: A toxin found only in spiders and bacteria was probably installed by gene transfer.
28 Jan 2006: Important aspects of the history of life are replicable and predictable.
Chris Tyler-Smith et al., "The rise and fall of the ape Y chromosome?" [abstract], doi:10.1038/ng0206-141, p 141-143 v 38, Nature Genetics, Feb 2006. "The sequence of a second chimpanzee Y chromosome ...reveals the recent gain of one [gene] on the human lineage...."
18 Jan 2006: We hypothesize that these 'jumping genomic segments' are part of an ongoing evolutionary process... — Evan Eichler.
John Whitfield, "Base Invaders" [link], doi:10.1038/439130a, p 130-131 v 439, Nature, 12 Jan 2006. "Could viruses have invented DNA as a way to sneak into cells?"
5 Jan 2006: "Evolution in Action" was the number one "Breakthrough of the Year" according to Science.
Open email to Tom Ray about the need for gene transfer, 31 Dec 2005.
Masayuki Machida et al., "Genome sequencing and analysis of Aspergillus oryzae" [abstract], doi:10.1038/nature04300, p 1157-1161 v 438, Nature, 22 Dec 2005. "...The increase in genome size seems to be due to an ...acquisition of sequence...." Also see commentary:
André Goffeau, "Genomics: Multiple moulds" [text], doi:10.1038/4381092b, p 1092-1093 v 438, Nature, 22 Dec 2005. "...Species closely related ...have similar gene acquisitions."
Olin K. Silander, Daniel M. Weinreich et al., "Widespread genetic exchange among terrestrial bacteriophages" [abstract], doi:10.1073/pnas.0503074102, p 19009-19014 v 102, Proc. Natl. Acad. Sci. USA, 27 Dec (online 19 Dec) 2005. "This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa."
Robert G. Beiko et al., "Highways of gene sharing in prokaryotes," [abstract], doi:10.1073/pnas.0504068102, p 14332-14337 v 102, Proc. Natl. Acad. Sci. USA, 4 Oct 2005. "...Foreign DNA must be integrated into the genome via illegitimate rather than homologous recombination. However, if organisms in the environment are subjected to a constant 'rain' of DNA, then these rare processes will occur in evolutionary time, and will be fixed in a lineage especially if they confer a selective advantage on the recipient organism."
Chris T. Yohn et al., "Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans" [text], doi:10.1371/journal.pbio.0030110, p 577-587 v 3 n 4, PLoS Biology, e110, Apr (online 1 Mar) 2005.
Alexander A. Hopitzan et al., "Molecular Evolution of Ankyrin: Gain of Function in Vertebrates by Acquisition of an Obscurin/Titin-Binding–Related Domain" [abstract], doi:10.1093/molbev/msj004, p 46-55 v 23, Molecular Biology and Evolution, Jan 2006 (online 31 Aug 2005). "Our data indicate that an ancestral ankyrin acquired an 18-aa module which was preserved in the Ecdysozoa/deuterostome divide, but it was subsequently lost from arthropods. Successive duplications of the module led to a gain of function in vertebrates as it acquired obscurin/titin-binding activity."
Anat Caspi and Lior Pachter, "Identification of transposable elements using multiple alignments of related genomes" [abstract], doi:10.1101/gr.4361206, Genome Research, online 14 Dec 2005.
8 Dec 2005: Simple sea anemones and coral have many genes thought to be exclusive to higher animals and some plants.
2 Dec 2005: Transformation and conjugation are examined in detail.
Yoshihiko Sakaguchi et al., "The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny" [Open Access abstract], doi:10.1073/pnas.0505503102, p 17472-17477 v 102, Proc. Natl. Acad. Sci. USA, 29 Nov (online 15 Nov) 2005. "...BoNTX phages comprise a divergent phage family, probably generated by exchanging genomic segments among BoNTX phages and their relatives."
HIV inserts into human genome using a DNA-associated protein, EurekAlert!, 27 Nov 2005. "This implies that LEDGF is part of the machinery that helps dictate the placement of retroviral integration sites within chromosomes."
25 Nov 2005: A small marine worm has complex genes like humans'.
Photosynthetic bacteria may be able to live without solar light — a reply from Larry Klaes, 22 Nov 2005.
Nancy A. Moran et al., "The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes" [abstract], doi:10.1073/pnas.0507029102, p 16919-16926 v 102, Proc. Natl. Acad. Sci. USA, 22 Nov (online 29 Sep) 2005. "We propose that, in these mutualistic symbionts, phage-borne toxin genes provide defense to the aphid host...."
21 Nov 2005: Gene transfer, not duplication, has modified bacterial metabolism....
15 Nov 2005: Plant virus can change insect vectors.
15 Nov 2005: Photosynthesis genes in marine viruses.
Miroslav Oborník and Beverley R. Green, "Mosaic Origin of the Heme Biosynthesis Pathway in Photosynthetic Eukaryotes" [abstract], doi:10.1093/molbev/msi230, p 2343-2353 v 22, Molecular Biology and Evolution, Dec (online 10 Aug) 2005. "...This suggests that genes were either transferred from the primary endosymbiont ...or replaced with genes from other sources...."
Wei-Jen Chang, Paul D. Bryson, Han Liang, Mann Kyoon Shin, and Laura F. Landweber, "The evolutionary origin of a complex scrambled gene" [abstract], doi:10.1073/pnas.0505734102, p 15144-15148 v 102, Proc. Natl. Acad. Sci. USA, 18 Oct (online 10 Oct) 2005.
17 Oct 2005: The principal process by which new gene functions arise is by making use of preexisting genes — Roy J. Britten
30 Sep 2005: The chimp genome has been sequenced. At least seventeen human genes contain exons missing in chimps.
Nancy A. Moran et al., "The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes" [abstract], doi:10.1073/pnas.0507029102, Proc. Natl. Acad. Sci. USA, online 29 Sep 2005.
Flu Virus Jumps from Horses to Dogs by Martin Ensernik, ScienceNow, 26 Sep 2005.
26 Sep 2005: Common bacteria share an infinite gene pool?!
23 Sep 2005: Today's protein families have been fine-tuned from ancient templates.
22 Sep 2005: Prokaryote genomes reveal extensive gene transfer.
18 Sep 2005: Mobile Genetic Elements afford their prokaryotic hosts access to vast genetic resources — Laura S. Frost et al.
16 Sep 2005: ...All the genes for building those complex animals existed long before [the Cambrian] explosion — Lewis Wolpert
Rebecca K. Cowan et al., "MUSTANG Is a Novel Family of Domesticated Transposase Genes Found in Diverse Angiosperms" [abstract], doi:10.1093/molbev/msi202, p 2084-2089 v 22, Molecular Biology and Evolution, Oct (online 29 Jun) 2005.
Focus on Horizontal Gene Transfer — a selection of recently published Reviews, Perspectives and Research Highlights on the topic of HGT from the Nature Reviews journals.... also recent original Research Papers, News & Views and Reviews published by Nature, Nature Genetics, Nature Biotechnology and Heredity, 1 Sep 2005.
Julia E. Kravchenko et al., "Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin" [abstract], doi:10.1038/nature03848, p 735-739 v 436, Nature, 4 Aug 2005.
Edward C. Holmes et al., "Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses" [text], doi:10.1371/journal.pbio.0030300, v 3 n 9, Public Library of Science, Sep 2005.
Victor Kunin et al., "The net of life: Reconstructing the microbial phylogenetic network" [abstract], doi:10.1101/gr.3666505, p 954-959 v 15, Genome Research, online 17 Jun 2005. "We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs."
Matthew Berriman et al., "The Genome of the African Trypanosome Trypanosoma brucei" [abstract], doi:10.1126/science.1112642, p 416-422 v 309, Science, 15 Jul 2005. "Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites...."
24 Aug 2005: More than 80 new exons per genome per million years emerge among rodents.
Patrik Inderbitzin et al., "Lateral transfer of mating system in Stemphylium" [abstract], doi:10.1073/pnas.0501918102, p 11390-11395 v 102, Proc. Natl. Acad. Sci. USA, 9 Aug (online 29 Jul) 2005.
6 Aug 2005: Parallel evolution has been observed in fruitflies.
Serge N. Vinogradov et al., "Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life" [abstract], doi:10.1073/pnas.0502103102, Proc. Natl. Acad. Sci. USA, online 1 Aug 2005. "Phylogenetic trees ...indicate the possibility of past horizontal globin gene transfers from bacteria to eukaryotes."
30 Jul 2005: Gene transfer in fungi.
Elena Serviene et al., "Genome-wide screen identifies host genes affecting viral RNA recombination" [abstract], doi:10.1073/pnas.0504844102, Proc. Natl. Acad. Sci. USA, online 18 Jul 2005.
Sarah J. Wheelan, Yasunori Aizawa, et al., "Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution" [abstract], doi:10.1101/gr.3688905, Genome Research, online 15 Jul 2005.
Artem S. Novozhilov et al., "Mathematical Modeling of Evolution of Horizontally Transferred Genes" [abstract], p 1721-1732 v 22, Molecular Biology and Evolution, Aug 2005. "Horizontally acquired sequences can be fixed in a population only when they confer a substantial selective advantage onto the recipient and therefore are subject to strong positive selection.... Our modeling results are compatible with the notion of a pivotal role of horizontal gene transfer in the evolution of prokaryotes."
Manuel Zúñiga et al., "Horizontal Gene Transfer in the Molecular Evolution of Mannose PTS Transporters" [abstract], p 1673-1685 v 22, Molecular Biology and Evolution, Aug 2005.
Stolen gene allows insect virus to enter cells, by Shawna Williams, Cornell News Service, 1 Jul 2005.
1 Jul 2005: A new microbial tree of life has been drawn by geneticists at EMBL.
27 Jun 2005: "Gene duplication is the primary source of new genes."
Virus Uses Tiny RNA to Evade the Immune System, Howard Hughes Medical Institute, 2 Jun 2005.
W. Martin, "Lateral gene transfer and other possibilities" [pdf], p 565-566 v 94, Heredity, Jun (online 30 Mar) 2005.
Same Fold in Viral Shells Point to Common Ancestry, re: Michael Rossmann, Newswise.com, 18 May 2005.
Jumping Genes and the Red Planet, re: Carrine Blank, Astrobiology Magazine, 13 May 2005.
Edward Coe and Lee B. Kass, "Proof of physical exchange of genes on the chromosomes" (Perspective about Harriet Creighton and Barbara McClintock) [abstract], p 6641-6646 v 102, Proc. Natl. Acad. Sci. USA, 10 May 2005.
A. Carolin Frank et al., "Functional Divergence and Horizontal Transfer of Type IV Secretion Systems" [abstract], p 1325-1336 v 22 n 5, Molecular Biology and Evolution, May 2005.
Howard Ochman, Emmanuelle Lerat and Vincent Daubin, "Examining bacterial species under the specter of gene transfer and exchange" [abstract], doi:10.1073/pnas.0502035102, p 6595-6599 v 102 suppl 1, Proc. Nat. Acad. Sci., USA, 3 May (online 25 Apr) 2005.
Colin MacIlwain, "Stray seeds had antibiotic-resistance genes," doi:10.1038/434548a [text], p 548 v 434, Nature, 31 Mar 2005. "...There is a small chance that they could flow from crops to microorganisms."
Loïc Ponger and Wen-Hsiung Li, "Evolutionary Diversification of DNA Methyltransferases in Eukaryotic Genomes," doi:10.1093/molbev/msi098 [abstract], p 1119-1128 v 22 n 4, Molecular Biology and Evolution, Apr 2005. "...Suggesting that horizontal transfers of MTases occurred between eukaryotes and prokaryotes."
Sabine E. Hammer, Sabine Strehl and Sylvia Hagemann, "Homologs of Drosophila P Transposons Were Mobile in Zebrafish but Have Been Domesticated in a Common Ancestor of Chicken and Human," doi:10.1093/molbev/msi068 [abstract], p 833-844 v 22 n 4, Molecular Biology and Evolution, Apr 2005.
24 Mar 2005: Plants can overwrite unhealthy genes.
16 Mar 2005: Life’s Solution, by Simon Conway Morris.
28 Feb 2005: Can pre-existing genetic programs be pieced together?
24 Feb 2005: Prokaryote to eukaryote gene transfer is evident in the sequenced genome of an intesinal parasite.
Duplication Makes a New Primate Gene — a new CA webpage, 21 Feb 2005.
Wim Broothaerts et al., "Gene transfer to plants by diverse species of bacteria," doi:10.1038/nature03309 [abstract], p 629-633 v 433, Nature, 10 Feb 2005.
3 Feb 2005: Complex early genes.
13 Jan 2005: Genes from retroviruses.
1 Jan 2005: Gene exchange among archaebacteria from salt pools in Spain.
27 Dec 2004: Plastid Portability.
Liqin Zhou et al., "Transposition of hAT elements links transposable elements and V(D)J recombination" [abstract], 10.1038/nature03157, p 995-102 v 432, Nature, 23/30 Dec 2004. The movement of transposable elements is linked to the process which underlies the combinatorial formation of antigen receptor genes.
Ulfar Bergthorsson et al., "Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella" [abstract], 10.1073/pnas.0408336102, Proc. Natl. Acad. Sci. USA, online 14 Dec 2004.
Peter Wenzl et al., "A Functional Screen Identifies Lateral Transfer of B-Glucuronidase (gus) from Bacteria to Fungi" [abstract], p 308-316 v 22 n 2, Molecular Biology and Evolution 2005, online 13 Oct 2004.
Tsuyoshi Tanaka, Yoshio Tateno and Takashi Gojobori, "Evolution of Vitamin B6 (Pyridoxine) Metabolism by Gain and Loss of Genes" [abstract], p 243-250 v 22 n 2, Molecular Biology and Evolution 2005, online 13 Oct 2004.
Stephen P. Goff, "Genetic Control of Retrovirus Susceptibility in Mammalian Cells" [abstract], p 61-85, Annual Review of Genetics, Dec 2004.
Min Chen et al., "Unique Origin and Lateral Transfer of Prokaryotic Chlorophyll-b and Chlorophyll-d Light-Harvesting Systems" [abstract], p 22-28 v 22 n 1, Molecular Biology and Evolution 2005, online 8 Sep 2004.
26 Nov 2004: The evolution of a new fruitfly gene...
Huge New Virus Defies Classification by Michael Schirber, Live Science, 11 Nov 2004. "There are more than 1,200 genes.... [including] translation genes. The researchers are not yet sure, though, if the virus actually uses them."
23 Nov 2004: Human genes composed mainly of mobile elements.
21 Nov 2004: Evidence that 1,183 human genes were "born" 3-4 million years ago, by duplication and divergence....
19 Nov 2004: Plant-to-plant gene transfer is illuminated by geneticists at Indiana University.
30 Oct 2004: "Horizontal transfer ...is a continuing and persistent means of creating biological novelty," says Andrew Knoll.
29 Oct 2004: Pack-MULE transposable elements mediate gene evolution in plants.
28 Oct 2004: A diatom genome has been sequenced. (Transfer is noted.)
Ken Jopp wonders what gene transfer has to do with CA, and Klyce replies, 21 Oct 2004.
21 Oct 2004: Eukaryote-to-eukaryote lateral gene transfer....
Bacteria are genetically modified by lightning by Andy Coghlan, New Scientist, 19 Oct 2004. "By opening up pores in soil bacteria it allows them to pick up any stray DNA present."
Giant virus qualifies as 'living organism' by Mark Peplow, News@nature.com, 14 Oct 2004.
9 Oct 2004: Retroelements that confer a selective advantage.
14 Sep 2004: Halobacteria can repair badly damaged DNA.
Wei-Gang Qiu et al., "Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing" [abstract], 10.1073/pnas.0402745101, Proc. Natl. Acad. Sci. USA, online 16 Sep 2004.
P. S. G. Chain et al., "Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis" [abstract], 10.1073/pnas.0404012101, Proc. Natl. Acad. Sci. USA, online 9 Sep 2004.
9 Sep 2004: The ring of life!
Arturo Medrano-Soto et al., "Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes" [abstract], p 1884-1894 v 21 n 10, Molecular Biology and Evolution, Oct 2004.
Fabiana Herédia et al., "Complex Evolution of gypsy in Drosophilid Species" [abstract], p 1831-1842 v 21 n 10, Molecular Biology and Evolution, Oct 2004. "...Discrepancy between the phylogeny of gypsy elements and the relationship of their host species ...allow us to infer a complex evolutionary pattern that could include ...several cases of horizontal transmission."
1 Sep 2004: Gene transfer among eukaryotes.
Norbert Bannert and Reinhard Kurth, "Retroelements and the human genome: New perspectives on an old relation" [abstract], 10.1073/pnas.0404838101, Proc. Natl. Acad. Sci. USA online 13 Aug 2004.
Philippa Melamed, Kok Leong Chong and Maria Vang Johansen, "Evidence for lateral gene transfer from salmonids to two Schistosome species" [abstract], p 786-787 v 36, Nature Genetics, Aug 2004.
Charles C. Davis and Kenneth J. Wurdack, "Host-to-Parasite Gene Transfer in Flowering Plants: Phylogenetic Evidence from Malpighiales" [abstract], p 676-678 v 305, Science, 30 Jul 2004.
27 Jul 2004: More about photosynthesis by gene transfer.
Chun Y. Huang, Michael A. Ayliffe and Jeremy N. Timmis, "Simple and complex nuclear loci created by newly transferred chloroplast DNA in tobacco" [abstract], p 9710-9715 v 101, Proc. Natl. Acad. Sci. USA, 29 June 2004. "...Studies on organelle DNA transfer ...in real time."
Weilong Hao and G. B. Golding, "Patterns of Bacterial Gene Movement" [abstract], p 1294-1307 v 21 n 7, Mol. Biol. Evol., July 2004. "...Many of the insertions are specific to each organism and are lost before related species can evolve."
Ulrich Genschel, "Coenzyme A Biosynthesis: Reconstruction of the Pathway in Archaea and an Evolutionary Scenario Based on Comparative Genomics," p 1242-1251 v 21 n 7, Mol. Biol. Evol., July 2004. "The phylogenies of these enzymes indicate that they were acquired from bacterial thermophiles through horizontal gene transfer."
3 Jun 2004: More animal genes came from bacteria.
Carl R. Woese, "A New Biology for a New Century" [abstract], p 173-186 v 68, Microbiology and Molecular Biology Reviews, DOI:10.1128/MMBR.68.2.173-186.2004, June 2004. Once the cellular translation machinery was in place, "HGT... is postulated merely to diminish (dramatically) in scope and frequency.... until HGT and cellular organization reach the levels at which they exist today."
27 May 2004: Microbes have stolen some of our genes!
5 May 2004: Viruses old as life?
Tracey Allen K. Freitas et al., "Ancestral hemoglobins in Archaea" [abstract], Proc. Natl. Acad. Sci. USA, 27 Apr 2004.
16 Apr 2004: The rat genome has been sequenced.
Robert Belshaw et al., "Long-term reinfection of the human genome by endogenous retroviruses" [abstract], Proc. Natl. Acad. Sci. USA online, 25 Mar 2004.
Haig H. Kazazian, Jr., "Mobile Elements: Drivers of Genome Evolution" [abstract], p 1626-1632 v 303, Science, 12 Mar 2004.
Jennifer F. Hughes and John M. Coffin, "Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: Implications for human and viral evolution" [abstract], Proc. Natl. Acad. Sci. USA online, 2 Feb 2004.
30 Jan 2004: Organelles transfer genes, wholesale, to eukaryotes.
2003, December 31: Stress can increase the rate of horizontal gene transfer.
Alan Herbert, "The four Rs of RNA-directed evolution" [abstract], p 19-25 v 36 n 1, Nature Genetics, Jan 2004. "The estimated percentage of the [human] genome derived from retrotransposition has increased [to] 45%...."
Aoife McLysaght, Pierre F. Baldi and Brandon S. Gaut, "Extensive gene gain associated with adaptive evolution of poxviruses" [abstract], p 15655-15660 v 100, Proc. Natl. Acad. Sci. USA, 23 Dec 2003.
2003, December 22: A species of coral contains many sequences matching ones from genes thought to be peculiar to vertebrates.
Frederic D. Bushman, "Integration Site Selection by Retroviruses and LTR-Retrotransposons" [abstract], p 135-138 v 115, Cell, 17 October 2003.
2003, October 19: The NASA Astrobiology Institute Virus Focus Group Workshop.
2003, October 11: As the burgeoning genome databases are analysed....
C. Neal Stewart et al., "Transgene Introgression from Genetically Modified Crops to Their Wild Relatives" [abstract], p 806-817 v 4, Nature Reviews Genetics, October 2003.
Louie N. van de Lagemaat, "Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions" [abstract], p 530-536 v 19 n 10, Trends in Genetics, October 2003.
Do microbes belong to one big gene pool or to numerous smaller ones? — Dave Ward, Montana State University, Bozeman, 24 Sep 2003.
Hyosig Won and Susanne S. Renner, "Horizontal gene transfer from flowering plants to Gnetum" [abstract], PNAS Online, 8 September 2003.
Camilla L. Nesbø and W. Ford Doolittle, "Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles" [abstract], PNAS Online, 28 Aug 2003.
Stephen J. Gould et al., "The Trojan exosome hypothesis" [abstract], PNAS Online, 28 Aug 2003. "We propose that retroviruses exploit a cell-encoded pathway of intercellular vesicle traffic, exosome exchange...."
C. G. Kurland, "Horizontal gene transfer: A critical view" [abstract], p 9658-9662 v 100, Proc. Natl. Acad. Sci. USA, 19 Aug 2003. A conservative opinion.
2003, August 14: Photosynthesis genes in a virus...
2003, August 8: Gene transfer, wholesale?
Masamichi Kohiyama et al., " Bacterial Sex: Playing Voyeurs 50 Years Later" [abstract], p 802-803 v 301, Science, 8 Aug 2003.
Sandra Stegemann et al., "High-frequency gene transfer from the chloroplast genome to the nucleus" [abstract], p 8828-8833 v 100, Proc. Natl. Acad. Sci. USA, 22 Jul 2003. "...The escape of genetic material from the chloroplast to the nuclear genome occurs much more frequently than generally believed and thus may contribute significantly to intraspecific and intraorganismic genetic variation."
2003, July 20: More genes seem to precede the need for themselves.
2003, July 10: The role of gene transfer in evolution is greater than previously thought.
2003, June 30: Introns can cause new stretches of DNA to be precisely inserted into genomes.
2003, June 19: Horizontal gene transfer as a significant evolutionary driver may require an addendum to the Darwinian synthesis.
...Snippets of DNA persist in soil for millennia, by Sid Perkins, Science News Online, 19 Apr 2003.
2003, April 16: Point mutations are less important than rearrangements of longer DNA strands in evolution....
Extreme Lifeforms, an introduction to viruses from Astrobiology Magazine, 2 Apr 2003.
2003, March 12: More on transposable elements (TEs).
K.A. Frazer et al., "Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates" [text], p 341-346 v 13 n 3, Genome Res., Mar 2003.
Chun Y. Huang, et al., "Direct measurement of the transfer rate of chloroplast DNA into the nucleus" [abstract], p 72-76 v 422, Nature, 6 Mar 2003. "It has been estimated that 1,700 protein-coding nuclear genes of Arabidopsis thaliana were acquired from cyanobacteria."
Michael W. Gaunt, et al., "Mechanisms of genetic exchange in American Trypanosomes," p 936-939 v 421, Nature, 27 Feb 2003.
2003, February 20: Regulatory sequences donated by transposable elements (TEs) contribute to human evolution.
2003, February 18: Humanoid gene arose abruptly?
James R. Brown, "Ancient horizontal gene transfer," doi:10.1038/nrg1000 [abstract], p 121-132 v 4, Nature Reviews Genetics, Feb 2003.
2003, January 28: Trypanosomes got genes from plants.
2003, January 23: Wingless stick insects have re-evolved wings.
2003, January 17: Horizontal gene transfer...
Konstantin I. Pyatkov, et al., "Penelope retroelements from Drosophila virilis are active after transformation of Drosophila melanogaster" [abstract], p 16150-16155 v 99 n 25, Proc. Natl. Acad. Sci. USA, 25 November 2002. "No insect retroelement has previously been reported to be actively transcribed and to increase in copy number after interspecific transformation."
2002, November 28: Chimps to humans by viral infection? [followup]
2002, November 24: Photosynthesis evolved by gene transfer.
Rafael Zardoya, et al., "Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment" [abstract], p 14893-14896 v 99 n 23, Proc. Natl. Acad. Sci. USA, 12 November 2002. "...Plant glycerol transporters may [have] resulted from a single event of horizontal gene transfer from bacteria, which we have estimated to have occurred 1,200 million years ago...."
Horizontal gene transfer, there's no mistaking it, by Bea Perks, BioMedNet, 13 Sep 2002.
Dental bacteria swap resistance, BBCNews, 15 Sep 2002.
Pär K. Ingvarsson and Douglas R. Taylor, "Genealogical evidence for epidemics of selfish genes" [abstract], p 11265-11269 v 99 n 17, Proc. Natl. Acad. Sci. USA, 20 August 2002. "Some genetic elements spread infectiously in populations by increasing their rate of genetic transmission at the expense of other genes in the genome."
2002, August 19: New evolution theory is survival by gene sharing.
'Jumping genes' create ripples in the genome - and perhaps species' evolution, EurekAlert!, 15 August 2002.
2002, 1 August: Evolutionary advance from chimps to humans linked to viruses.
2002, July 7: Acquiring Genomes by Margulis and Sagan.
Parasite or partner? Study suggests new role for junk DNA, EurekAlert!, 12 May 2002, re:
Tammy A. Morrish et al., "DNA repair mediated by endonuclease-independent LINE-1 retrotransposition" [abstract], p 159-165 v 31 n 2, Nature Genetics, June 2002.
2002, May 11: Lateral DNA Transfer by Frederic Bushman.
Virginia L. Waters, "Conjugation between bacterial and mammalian cells" [abstract], Nature Genetics, December 2001.
2002, Apr 27: Human endogenous retroviruses (HERVs)= as much as 8% of the human genome.
Researchers use 'Sleeping Beauty' enzyme to genetically modify a mouse, by David Largaespada et al., University of Minnesota News Service, 1 Apr 2002.
Jumping genes make 'designer' animals easy, by Sylvia Pagàn Westphal, New Scientist, 27 Mar 2002.
2002, March 18: Plant gene in a worm.
Johann de Vries and Wilfried Wackernagel, "Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination" [abstract], p 2094-2099 v 99, Proc. Nat. Acad. Sci., USA, 19 Feb 2002.
Marc Prudhomme et al., "Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae" [abstract], p 2100-2105 v 99, Proc. Nat. Acad. Sci., USA, 19 Feb 2002.
Complete genome sequence of... Ralstonia solanacearum sheds light on the mechanisms governing pathogenicity, Paris, 30 Jan 2002. "This genome undergoes rapid evolution, in particular through the acquisition of genes by horizontal gene transfer...."
2001, December 21: A gene needed for multcellularity is present in a single-celled organism.
Carlos Lois et al., "Germline Transmission and Tissue-Specific Expression of Transgenes Delivered by Lentiviral Vectors" [abstract], Sciencexpress, 10 Jan 2002.
Jennifer F. Hughes and John M. Coffin, "Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution" [abstract], p 487-489 v 29 n 4, Nature Genetics online 12 November 2001.
Makoto Nagano et al., "Transgenic mice produced by retroviral transduction of male germ-line stem cells" [abstract], p 13090-13095 v 98 n 23, Proc. Natl. Acad. Sci. USA, 6 November 2001.
Scientists report first transgenic animal developed via retroviral DNA insertion into male germ-line stem cells, by Steve Bradt, EurekAlert, 22 Oct 2001.
Mikio Yoshiyama et al., "Possible Horizontal Transfer of a Transposable Element from Host to Parasitoid" [abstract], p 1952-1958 v 18, Molecular Biology and Evolution, October 2001.
2001, October 5: Science features genome research...
Constance Holden, "A Virus in the Family?" [html], p 1987 v 293, Science, 14 September 2001. Philip Bell says, "The transition from a primitive cell to a complex one involves so many changes, it's hard to imagine them all occurring together without the involvement of a virus."
2001, Sep 7: A reply from Damon Lisch discusses transposons.
Genes Passed From Crops to Weeds Persist for Generations, by Holly Wagner, Ohio State University, 9 August 2001.
Lightning jumpstarts evolution: Shocked bacteria swap genes, by Tom Clarke, Nature Science Update, 1 August 2001. The title would lead most people to think that Darwinism has received another confirmation. But as the subtitle explains, horizontal gene transfer — and Cosmic Ancestry — are actually supported by the research.
Staph bacteria are prolific gene swappers, researchers show, EurekAlert, 9 July 2001.
Lateral Thinking: Gene transfer between species likeliest in microorganisms, The Scientist, 9 July 2001.
Different Staph Species Can Exchange Resistance Gene, UniSci.com, 25 May 2001.
Nicholas Wade, "Link Between Human Genes and Bacteria Is Hotly Debated" [text], The New York Times, 18 May 2001. We think the issue in this NYT story and the next two Science Online stories is all about jealousy between the two competing teams that sequenced the human genome. Certainly the case for horizontal gene transfer as a major factor in evolution is not in jeopardy.
Steven L. Salzberg et al., "Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?" [abstract], Science Online, 17 May 2001.
Jan O. Andersson and Camilla L. Nesbo, "Are There Bugs in Our Genome?" [abstract], Science Online, 17 May 2001.
Many Bacteria Take Evolutionary Shortcut, Drop Genes, UniSci.com, 11 May 2001. "Many bacteria may evolve primarily by acquiring genes from each other, or by dropping whole genes that are no longer needed."
Is schizophrenia caused by an enemy within?, New Scientist, 14 April 2001. "We all carry around retroviral DNA from viruses that inserted themselves into the human genome millions of years ago."
2001, March 14: Transposons as a creative force.
2001, February 17: Gene transfer in archaea —
2001, February 12: The human genome has only about 30,000 genes.
Bacterium Can Alter Evolution Of Another Species, UniSci, 8 February 2001.
Gene Sequence of Deadly E. coli Reveals Surprisingly Dynamic Genome, National Institutes of Health, 24 January 2001.
Horizontal Gene Transfer - A New Paradigm for Biology, Peter Gogarten, Esalen Invitational Conference on Evolutionary Theory, 5-10 Nov 2000.
Hiroyuki Ogata et al., "Selfish DNA in Protein-Coding Genes of Rickettsia," [abstract] p 347-350 v 290, Science, 13 October 2000.
Genetic Parasites and a Whole Lot More: Transposable elements generate DNA mutations, alter gene expression, and otherwise fuel genetic diversity, by Barry A. Palevitz, New Scientist, 16 October 2000.
2000, October 15: Entire genetic regions appear to have been transferred between species.
2000, September 27: Prions can turn on genetic programs.
Using Transposons, Not Viruses, In Gene Therapy, UniSci, 22 August 2000.
Jumping Gene Caught In Midair In 3-D View, UniSci, 7 July 2000.
2000, June 14: The genesis of life on earth... remains an unyielding problem.
2000, May 24: An enzyme from a bacterial virus carries out the efficient, site-specific integration of incoming plasmids into human DNA.
2000, May 18: Horizontal gene transfer produces extremely dynamic bacterial genomes.
2000, April 14: The microbial biosphere as a "World Wide Web" (Joshua Lederberg).
2000, April 9: A DNA virus... could have been the ancestor of the eukaryotic replication system.
2000, February 29: Another gene installed by a virus appears to serve an important human function.
2000, February 25: Some horizontally transferred genes target the host's germ cells.
2000, January 21: Scientific American recognizes the evolutionary importance of lateral gene transfer.
1999, December 7: Germ-line transmission of transgenes.
1999, November 12: Genes installed by a virus benefit future generations of mammals.
1999, November 9: Human Genome Bears a Virus Related to HIV.
1999, November 4: Horizontal Gene Transfer, Michael Syvanen and Clarence I. Kado, eds.
1999, October 14: Retroviruses appear ancient.
1999, September 2: Viruses have been found deep under the Greenland icepack.
Mobile DNA Sequences Could Be The Cause Of Chromosomal Mutations During The Evolution Of Species, ScienceDaily, 21 July 1999.
Viruses 'steal bacteria DNA'— "...But within the virus' genetic make-up were scores of genes from a variety of bacterial species. Most of them, however, had functions that were not useful to viruses, such as involvement in building bacteria cell walls." BBCNews, 15 July 1999.
Mark J. Gibbs and Georg F. Weiller, "Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus" [abstract], p 8022-8027 v 96, Proc Natl Acad Sci USA, 6 July 1999.
1999, May 27: Cholera-causing bacteria acquire their toxicity from viruses; and lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
1999, May 12: Lamarck's Signature: How Retrogenes Are Changing Darwin's Natural Selection Paradigm.
1999, April 1: A virus can shuttle gene sequences between bacteria and their animal hosts.
Ravi Jain et al., "Horizontal transfer among genomes: The Complexity Hypothesis" [text], p 3801-6 v 96, PNAS, 30 March 1999.
James A. Lake, Ravi Jain and Maria C. Rivera, "Mix and Match in the Tree of Life" [summary], p 2027-2028 v 283, Science. 26 March 1999.
1999, March 5: Three geneticists, examining evolution at the molecular level....
1999, March 3: Up to 1% of the human genome is represented by human endogenous retroviruses (HERVs) and their fragments that are likely footprints of ancient primate germ-cell infections that occurred 10-60 million years ago.
Roger W. Hendrix, Margaret C. M. Smith, R. Neil Burns, Michael E. Ford and Graham F. Hatfull. "Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage" [abstract], p 2192-2197 v 96 n 5, Proc. Nat. Acad. Sci., USA, 2 March, 1999.
1998, December 11: The genome of a tiny worm contains many genes with no similarity to previously known genes.
A "Fossil" Virus Involved In AIDS Drug Resistance?, EurekAlert!, 4 December 1998.
1998, November 30: Biologists find evidence that a certain intron underwent cross-species horizontal transfer over 1,000 times during angiosperm evolution.
Jumping genes are nature's casanovas, by Toby Murcott of BBC Science. November 24, 1998.
Roald Ravatn, Sonja Studer, Alexander J. B. Zehnder and Jan Roelof van der Meer. "Int-B13, an Unusual Site-Specific Recombinase of the Bacteriophage P4 Integrase Family, Is Responsible for Chromosomal Insertion of the 105-Kilobase clc Element of Pseudomonas sp. Strain B13" [abstract], p 5505-5514, v 180, n 21, Journal of Bacteriology, November 1998.
1998, November 3: Two geneticists find evidence for "a predominating integration mechanism," that inserts acquired foreign genes into genomes in clustered fragments.
1998, October 23: The genome of Chlamidia trachomatis contains some 35 eukaryotic genes...
1998, August 25: We owe the repertoire of our immune system to one transposon insertion, which occurred 450 million years ago in the ancestor of the jawed fishes.
1998, August 12: The paradigm shifts toward lateral gene transfer as the primary driver of evolution.
1998, July 28: Carl R. Woese says lateral gene transfer is more important than vertical inheritance at first.
W. Ford Doolittle. "Patterns of phylogeny: symbiosis, chimaerism and gene transfer in the origin of eukaryotes," given at "Life: from Local Origins to Global Persistence," a NASA Astrobiology workshop at the University of New Hampshire, June 8-10, 1998.
Jeffrey G. Lawrence. "Roles of Horizontal Genetic Transfer in Prokaryotic Evolution," given at "Life: from Local Origins to Global Persistence," a NASA Astrobiology workshop at the University of New Hampshire, June 8-10, 1998.
Haig H. Kazazian, Jr. and John V. Moran. "The impact of L1 retrotransposons on the human genome" p 19-24 v 19, Nature Genetics, May 1998.
1998, April 24: Versatile Gene Uptake System Found in Cholera Bacterium may capture many different types of genes.
1998, March 26: The importance of horizontal gene transfer in evolution is becoming apparent to mainstream biologists — bacteriophage collagen!
1997, December 19: Horizontal gene transfer is looking more important than ever as a driver of evolution.
1997, November 23: The integration of genes from a non retroviral RNA virus into the DNA of eukaryotic cells has been demonstrated.
Gavin D. Recchia and Ruth M. Hall. "Origins of the mobile gene cassettes found in integrons" [abstract], p 389-394 v 5 n 10, Trends in Microbiology, 10 October 1997.
Margaret G. Kidwell and Damon Lisch, "Transposable elements as sources of variation in animals and plants" [text], p 7704-7711 v 94, Proc. Nat. Acad. Sci., USA., July 1997.
Wen-Hsiung Li. "Evolution by Transposition and Horizontal Transfer," p 335-377 (chapter 12), Molecular Evolution, Sinauer Associates, Inc., Publishers, 1997.
Wolfgang J. Miller, John F. McDonald and Wilhelm Pinsker. "Molecular domestication of mobile elements" [abstract], p 261-270 v 100, Genetica, 1997.
ReferencesIt 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.