Editing Gene flow (section)

=== Horizontal gene transfer ===
{{Main|Horizontal gene transfer}}

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction, either through [[Transformation (genetics)|transformation]] (direct uptake of genetic material by a cell from its surroundings), [[bacterial conjugation|conjugation]] (transfer of [[plasmid|genetic material]] between two bacterial cells in direct contact), [[transduction (genetics)|transduction]] (injection of foreign DNA by a [[bacteriophage]] virus into the host cell) or [[Gene transfer agent|GTA-mediated transduction]] (transfer by a virus-like element produced by a bacterium) .<ref name=Johnston>{{cite journal | vauthors = Johnston C, Martin B, Fichant G, Polard P, Claverys JP | title = Bacterial transformation: distribution, shared mechanisms and divergent control | journal = Nature Reviews. Microbiology | volume = 12 | issue = 3 | pages = 181–96 | date = March 2014 | pmid = 24509783 | doi = 10.1038/nrmicro3199 | s2cid = 23559881 }}</ref><ref name="Langeetal">{{cite journal | vauthors = Lang AS, Zhaxybayeva O, Beatty JT | title = Gene transfer agents: phage-like elements of genetic exchange | journal = Nature Reviews. Microbiology | volume = 10 | issue = 7 | pages = 472–82 | date = June 2012 | pmid = 22683880 | pmc = 3626599 | doi = 10.1038/nrmicro2802 }}</ref>

Viruses can transfer genes between species.<ref>[https://non.fiction.org/lj/community/ref_courses/3484/enmicro.pdf{{dead link|date=January 2017 |bot=InternetArchiveBot |fix-attempted=yes }} dead link]{{Dead link|date=May 2024 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> Bacteria can incorporate genes from dead bacteria, exchange genes with living bacteria, and can exchange [[plasmid]]s across species boundaries.<ref>{{cite web |url=http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf |title=Archived copy |access-date=2005-12-31 |url-status=dead |archive-url=https://web.archive.org/web/20060218071130/http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf |archive-date=2006-02-18 }}</ref>
"Sequence comparisons suggest recent horizontal transfer of many [[gene]]s 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."<ref>{{cite web |url=http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html |title=Horizontal Gene Transfer |access-date=2005-12-31 |url-status=dead |archive-url=https://web.archive.org/web/20051016110855/http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html |archive-date=2005-10-16 }}</ref>

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research". Biologists [should] instead use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of an intertwined net to visualize the rich exchange and cooperative effects of horizontal gene transfer.<ref>{{Cite web |url=http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 |title=Horizontal Gene Transfer - A New Paradigm for Biology (from Evolutionary Theory Conference Summary), Esalen Center for Theory & Research |access-date=2005-12-31 |archive-date=2012-07-21 |archive-url=https://web.archive.org/web/20120721232310/http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 |url-status=dead }}</ref>

"Using single [[gene]]s as [[genetic markers|phylogenetic marker]]s, it is difficult to trace organismal [[phylogeny]] in the presence of HGT. Combining the simple [[coalescence (genetics)|coalescence]] model of [[cladogenesis]] with rare HGT 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."<ref>{{Cite web |url=http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf |title=Horizontal Gene Transfer - A New Paradigm for Biology (From Evolutionary Theory Conference Summary), Esalen Center for Theory & Research |access-date=2005-12-31 |archive-url=https://web.archive.org/web/20120721232310/http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 |archive-date=2012-07-21 |url-status=dead }}</ref>