What about those jumping genes?

It does, I guess, which makes me suspect contamination all the more. You find one or two genes, sure, that could be HGT. You find the whole thing? That's almost certainly contamination.

Crash writes:And, of course, this all has to have happened in one of the germline cells, which are protected by many layers of immune and caretaker cells, and then that gamete has to be the one that fertilizes or is fertilized to form a new organism.

phylogenomics writes:Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations.

wiki writes:Wolbachia is notable for significantly altering the reproductive capabilities of its hosts. These bacteria can infect many different types of organs, but are most notable for the infections of the testes and ovaries of their hosts.Wolbachia are known to cause four different phenotypes:* Male killing (death of infected males). This allows related infected females to be more likely to survive and reproduce.
* Feminization (infected males develop as females or infertile pseudo-females)
* Parthenogenesis (reproduction of infected females without males)
* Cytoplasmic incompatibility (the inability of Wolbachia-infected males to successfully reproduce with uninfected females or females infected with another Wolbachia strain). This has the advantage of making the Wolbachia strain more likely to become prevalent as opposed to other strains of Wolbachia. This can have the additional result of making Wolbachia more common as a whole.Wolbachia are present in mature eggs, but not mature sperm. Only infected females pass the infection on to their offspring. It is thought that the phenotypes caused by Wolbachia, especially cytoplasmic incompatibility, may be important in promoting speciation. [1][2] Wolbachia can also cause misleading results in molecular cladistical analyses (Johnstone & Hurst 1996).

Zimmer writes:Wolbachia spread so quickly, researchers realized, because they take control of their hosts' reproduction. And in the past decade, they've discovered that cytoplasmic incompatibility is only one of many tricks the bacteria use to do so. In some species of wasps, for example, Wolbachia completely alter the host's sex life, manipulating the host to give birth only to females which then no longer need to mate with males to reproduce. In other species, they allow males to be born but alter their hormones to feminize them and make them produce eggs.A fourth way Wolbachia can boost their reproductive success is to destroy their male hosts (and, paradoxically, themselves in the process). In a number of hosts, Wolbachia kill all of the male eggs that they infect. When the female hosts hatch, they don't have to compete with their brothers for food--in fact, their brothers are their food. By cannibalizing the male eggs, the Wolbachia-infected females increase their chances of survival.With so many of their brethren killed off, the few males that remain can enjoy remarkable reproductive success. A species that might normally be split 50-50 between males and females may become permanently skewed to females, as in the case of the Ugandan butterfly Jiggins studies.

Zimmer writes:But this sexist microbe may be the most common infectious bacterium on Earth. Although no vertebrates (humans included) are known to carry Wolbachia, infection is rampant in the invertebrate world, showing up in everything from fruit flies to shrimp, spiders, and even parasitic worms.

So maybe this supports the findings of insect genes in the human genome.

Do you think jumping genes could have played a significant role in the course of either biological or social evolution?

HM writes:Do you know of any mariner elements or transposons (if they are categorically different...

The mariner transposon of Drosophila mauritiana and the Tc1 transposable element (TE) of Caenorhabditis elegans are members of a superfamily of class II TEs that are found in a large number of organisms, ranging from fungi to vertebrates.

Mariner elements are generally about 1.3 kb long

Despite a low overall sequence identity (16%) across the superfamily (Robertson 1995), the transposases share several functional and predicted structural characters that suggest they are derived from a common ancestor (Plasterk et. al. 1999).

HM writes:...that are able to operate apart from viral activity?

wiki writes:(Transposons) are similar to viruses. Viruses and transposons share features in their genome structure and biochemical abilities.

Telomerase, the enzyme essential for maintaining chromosome length, is closely related to the reverse transcriptase of LINEs and may have evolved from it.RAG-1 and RAG-2. The proteins encoded by these genes are needed to assemble the repertoire of antibodies and T-cells receptors (TCRs) used by the adaptive immune system. The mechanism resembles that of the cut and paste method of Class II transposons , and the RAG genes may have evolved from them. If so, the event occurred some 450 million years ago when the jawed vertebrates evolved from jawless ancestors. Only jawed vertebrates have an adaptive immune system and the RAG-1 and RAG-2 genes that make it possible.

HM writes:Maybe transposons (on steroids?) are the mechanisms you're looking for. If they work for genes, then why not genomes?

No. Only fly genes. The only time I referenced whole-genome transfer was with respect to the OP artcile.

In a project for the Ministry of Agriculture, Fisheries and Food, Andy Brass and two colleagues at the University of Manchester compared the DNA of 80 000 different organisms, using over five million sequences. They found seven pairs of similar mariner sequences. For instance, 83 per cent of the sequence in the tsetse fly "Glossina palpalis", a blood-sucker that spreads human sleeping sickness, was the same as a sequence in humans.Such a close match is "strong suggestive evidence" that mariner has moved between tsetse flies and humans, Brass says. The transfer occurred recently in evolutionary terms, he thinks, although it is not clear whether mariner jumped from the fly to humans or vice versa.

Transposons of the mariner/Tc1 family are ubiquitous elements of eukaryotic genomes, occurring in virtually every taxon examined (1-3). Phylogenetic studies of mariner elements have provided compelling evidence for the occurrence of horizontal transfer across species during evolution, traversing distances as far as that separating insects and flatworms.

wiki writes:Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved.

wiki writes:While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material).

wiki writes: * Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). This process is relatively common in bacteria, but less common in eukaryotes.* Transduction, the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, commonly called a phage).* Bacterial conjugation, a process in which a living bacterial cell transfers genetic material through cell-to-cell contact.

TEs are a major component of all genomes and represent between 3 to 50% of the content of the genome, depending on the species (Capy et al., 1997). While TE interactions with the host genome remain poorly understood there are several examples of their impact on host functioning, structure and evolution. For example, Tn, bacterial composite elements (elements flanked by Insertion Sequences), provide several examples in which a gene involved in antibiotic resistance can be horizontally transferred, see for instance Berg & Howe (1989) and more recently, Hall (1997) and Recchia & Hall (1997). In Drosophila melanogaster, LINE-like elements such as TART and Het-A are used as a 'cap' at the extremities of the chromosomes to prevent their degradation (Pardue et al., 1997). Also in this species, the hobo element is involved in chromosomal inversions (Lim, 1988; Lyttle & Haymer, 1992; Lim & Simmons, 1994; Ladeveze et al., 1998). Gene regulation under the partial or complete control of retrotransposon LTRs (long-terminal repeats) or solo LTRs left by retrotransposons are another illustration of TE effects on host genome evolution (White et al., 1994; Britten, 1996; McDonald et al., 1997). This is also seen in the human alpha-amylase gene (Ting et al., 1992). Similarly, in the Saccharomyces cerevisiae genome, 331 Ty insertions (85% of which are solo LTRs) have been detected (Kim et al., 1998). These sequences are frequently inserted in tRNA genes or other transcribed genes (Hani & Feldmann, 1998). Therefore, they may have an impact on the expression profile of these genes. Thus, many of the interactions between TEs and their host genomes can be seen as a domestication of the former by the latter, or as a coevolution between the two entities.

Transposable elements of the mariner/Tc1 family are postulated to have spread by horizontal transfer and be relatively independent of host-specific factors. This was tested by introducing the Drosophila mauritiana element mariner into the human parasite Leishmania major, a trypanosomatid protozoan belonging to one of the most ancient eukaryotic lineages. Transposition in Leishmania was efficient, occurring in more than 20 percent of random transfectants, and proceeded by the same mechanism as in Drosophila. Insertional inactivation of a specific gene was obtained, and a modified mariner element was used to select for gene fusions, establishing mariner as a powerful genetic tool for Leishmania and other organisms. These experiments demonstrate the evolutionary range of mariner transposition in vivo and underscore the ability of this ubiquitous DNA to parasitize the eukaryotic genome.

wiki writes:Produced in salivary glands, saliva is 98% water, but it contains many important substances, including electrolytes, mucus, antibacterial compounds and various enzymes.

I seriously doubt that. How do you suppose it's possible to do a DNA analysis on a licked and sealed envelop?

Not true! A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.

nature reviews microbiology writes:For any gene to be horizontally transferred from one genome to another, at least four (sometimes five) distinct steps need to occur. First, a nucleic-acid molecule in the donor organism is prepared for transfer. This might entail the active packaging of nucleic acids into phage particles, plasmid replication from an origin that leads to conjugal transfer, or integron assembly. Second, the transfer step, which might or might not require physical contact between the donor and recipient organism, takes place. Third, the nucleic acid enters the recipient organisms through specific or non-specific means. Fourth, the nucleic-acid molecule is established in the recipient either as a self-replicating element or through recombination with, or transposition into, the recipient's chromosome. This existence can be transitory, as is the case with many plasmids of which maintenance by the recipient genome depends on selective pressure. Last, in step 5, stable inheritance in the recipient genome might ensue.

The National Institutes of Health would disagree. Check out this article on Saliva: Your Spitting Image

Saliva testing can be effective because it contains many of the same proteins that blood and urine do, the researchers said. New research shows these molecules can reveal the presence of diseases like cancer, and can be used to predict the number of cavities in a person's teeth.

Tony Raymond says there has been much misinformation about the invasiveness of sampling techniques."There is some concern that the taking of a buccal swab involved the aggressive and vigorous insertion of a large brush into the mouth of a suspect," he said. "Nothing could be further from the truth. The buccal swab itself is smaller and softer than a toothbrush."

Are you sure? If human genes are found in human saliva why can't tsetse-fly genes be found in tsetse-fly saliva?

However, molecular information on the individual tsetse salivary proteins and their biological activity remains scanty. Previous studies on Glossina morsitans saliva have reported the presence of a 11.3 kDa inhibitor of thrombin serine protease and esterase activities (Parker and Mant, 1979) and a >30 kDa protein fraction that inhibited the ADP-induced thrombocyte aggregation (Mant and Parker, 1981). In addition, a potent 32 AA blood meal-induced tsetse thrombin inhibitor (TTI), was characterised in salivary gland extracts. Purified TTI has been shown to abolish thrombin-induced platelet aggregation ([Cappello et al., 1996] and [Cappello et al., 1998]). Salivary extracts have also been demonstrated to exert an adenosine deaminase activity that might depend on translation of tsetse salivary growth factors 1 and 2 (TSGF-1 and TSGF-2).

HM writes:A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.

molbiogirl writes:Those aren't tsetse genes.

HM writes:Are you sure? If human genes are found in human saliva why can't tsetse-fly genes be found in tsetse-fly saliva?

Really, that sounds wrong to me.

This so-called "proof-of-principle" study marks the first report in the scientific literature that distinct patterns of "messenger RNA" not only are measurable in saliva but can indicate a developing tumor. Messenger RNA (mRNA) is the molecular intermediate between gene and protein, serving as a chemical record that an individual gene has been expressed.

Saliva, like other bodily fluids, has been used to monitor human health and disease. This study tests the hypothesis that informative human mRNA exists in cell-free saliva. If present, salivary mRNA may provide potential biomarkers to identify populations and patients at high risk for oral and systemic diseases. Unstimulated saliva was collected from ten normal subjects. RNA was isolated from the cell-free saliva supernatant and linearly amplified. High-density oligonucleotide microarrays were used to profile salivary mRNA. The results demonstrated that there are thousands of human mRNAs in cell-free saliva. Quantitative PCR (Q-PCR) analysis confirmed the present of mRNA identified by our microarray study. A reference database was generated based on the mRNA profiles in normal saliva. Our finding proposes a novel clinical approach to salivary diagnostics, Salivary Transcriptome Diagnostics (STD), for potential applications in disease diagnostics as well as normal health surveillance.