Horizontal gene transfer
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. Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon. Michael Syvanen was among the earliest biologists to explore the potential significance of lateral gene transfer.  Syvanen published a series of papers on horizontal  gene transfer starting in 1984 ,  predicting that lateral gene transfer exists, has biological significance, and is a process that shaped evolutionary history from the very beginning of life on earth. Artificial horizontal gene transfer is a form of genetic engineering.
As Jain, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes." (see also Lake and Riveral, 2007). The phenomenon appears to have had some significance for  unicellular eukaryotes as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution."
There is some evidence that even higher plants and animals have been affected. Dr. Mae-Wan Ho, a noted scientist and critic of genetic engineering, 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)." But Richardson and Palmer (2007) are more cautious: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear."
Due to the increasing amount of evidence suggesting the importance of these phenomena for evolution (see below), molecular biologists such as Peter Gogarten have described horizontal gene transfer as a "A New Paradigm for Biology".
It should also be noted that the process is emphasised by Dr. Mae-Wan Ho as an important factor in "The Hidden Hazards of Genetic Engineering", as it may allow dangerous transgenic DNA (which is optimised for transfer) to spread from species to species.

# Prokaryotes
Horizontal gene transfer is common among bacteria, even very distantly-related ones.  This process is thought to be a significant cause of increased drug resistance; when one bacterial cell acquires resistance, it can quickly transfer the resistance genes to many species.  Enteric bacteria appear to exchange genetic material with each other within the gut in which they live.  There are three common mechanisms for horizontal gene transfer:
- 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.  Transformation is often used to insert novel genes into bacteria for experiments, or for industrial or medical applications.  See also molecular biology and biotechnology.
- 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.

# Eukaryotes
Analysis of DNA sequences suggests that horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome.  As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell.
Horizontal transfer of genes from bacteria to some fungi, especially the yeast Saccharomyces cerevisiae, has been well documented.
There is also recent evidence that the adzuki bean beetle has somehow acquired genetic material from its (non-beneficial) endosymbiont Wolbachia.  New examples have recently been reported, demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes. 
There is also evidence for horizontal transfer of mitochondrial genes to parasites of the Rafflesiaceae plant family from their hosts (also plants), and from chloroplasts of a not-yet-identified plant to the mitochondria of the bean Phaseolus.
"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."

# Evolutionary theory
Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene.  For example, given two distantly related bacteria that have exchanged a gene, a phylogenetic tree including those species will show them to be closely related because that gene is the same, even though most other genes have substantially diverged.  For this reason, it is often ideal to use other information to infer robust phylogenies, such as the presence or absence of genes, or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible.
For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16s rRNA gene, since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred.  Although this may be infrequent, validity of 16s rRNA-constructed phylogenetic trees must be reevaluated.
Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists should use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes."
Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of horizontal gene transfer. Combining the simple coalescence model of cladogenesis with rare HGT horizontal gene transfer events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."
Uprooting the Tree of Life by W. Ford Doolittle (Scientific American, February 2000, pp 72-77) contains a discussion of the Last Universal Common Ancestor, and the problems that arose with respect to that concept when one considers horizontal gene transfer. The article covers a wide area - the endosymbiont hypothesis for eukaryotes, the use of small subunit ribosomal RNA (SSU rRNA) as a measure of evolutionary distances (this was the field Carl Woese worked in when formulating the first modern "tree of life", and his research results with SSU rRNA led him to propose the Archaea as a third domain of life) and other relevant topics. Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus is cited in the article (p.76) as being an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase - the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an  Archaean, but whose HMGCoA genes are actually of bacterial origin.
Again on p.76, the article continues with:
The article continues with:
With regard to how horizontal gene transfer affects evolutionary theory (common descent, universal phylogenetic tree) Carl Woese says:

## Genes
There is evidence for historical horizontal transfer of the following genes:
- Lycopene cyclase for carotenoid biosynthesis, between Chlorobi and Cyanobacteria.