Reticulate evolution

Since the nineteenth century, scientists from different disciplines have studied how reticulate evolution occurs. Researchers have increasingly succeeded in identifying these mechanisms and processes. It has been found to be driven by symbiosis, symbiogenesis (endosymbiosis), lateral gene transfer, hybridization and infectious heredity.{{Cite book|title=Reticulate Evolution|volume = 3|last=Gontier|first=Nathalie|date=2015|publisher=Springer, Cham|pages=1–40|doi=10.1007/978-3-319-16345-1_1|chapter = Reticulate Evolution Everywhere|series = Interdisciplinary Evolution Research|hdl = 10451/45446|isbn = 978-3-319-16344-4|s2cid = 83465142}}

Symbiosis is a close and long-term biological interaction between two different biological organisms. Often, both of the organisms involved develop new features upon the interaction with the other organism. This may lead to the development of new, distinct organisms.{{Cite book|title=Symbiosis as a source of evolutionary innovation : speciation and morphogenesis|date=1991|publisher=MIT Press|author1=Margulis, Lynn |author1-link=Lynn Margulis |author2=Fester, René |isbn=9780262132695 |location=Cambridge, Mass. |oclc=22597587 }}{{page needed|date=October 2021}}{{Cite book|title=Symbiotic planet : a new look at evolution|last=Margulis|first=Lynn|date=1998|publisher=Basic Books|isbn=9780465072729|edition=1st|location=New York|oclc=46954542}}{{page needed|date=October 2021}} The alterations in genetic material upon symbiosis can occur via germline transmission or lateral transmission.{{Cite book|title=One plus one equals one : symbiosis and the evolution of complex life|last=M.|first=Archibald, John|isbn=9780199660599|edition=First|location=Oxford|oclc=881005592|year = 2014}}{{page needed|date=October 2021}}{{Cite book|title=The symbiotic habit|last=Douglas|first=A. E.|date=2010|publisher=Princeton University Press|isbn=9780691113418|location=Princeton, N.J.|oclc=437054000}}{{page needed|date=October 2021}} Therefore, the interaction between different organisms can drive evolution of one or both organisms.{{cite journal |last1=Dimijian |first1=Gregory G. |title=Evolving Together: The Biology of Symbiosis, Part 1 |journal=Baylor University Medical Center Proceedings |date=July 2000 |volume=13 |issue=3 |pages=217–226 |doi=10.1080/08998280.2000.11927677 |pmid=16389385 |pmc=1317043 }}

Symbiogenesis (endosymbiosis) is a special form of symbiosis whereby an organism lives inside another, different organism. Symbiogenesis is thought to be very important in the origin and evolution of eukaryotes. Eukaryotic organelles, such as mitochondria, have been theorized to have been originated from cell-invaded bacteria living inside another cell.{{cite journal |last1=López-García |first1=Purificación |last2=Eme |first2=Laura |last3=Moreira |first3=David |title=Symbiosis in eukaryotic evolution |journal=Journal of Theoretical Biology |date=December 2017 |volume=434 |pages=20–33 |doi=10.1016/j.jtbi.2017.02.031 |pmid=28254477 |pmc=5638015 |bibcode=2017JThBi.434...20L }}{{cite journal |id={{NAID|10020710101}} |last1=Mereschkowsky |first1=C. |title=Theorie der zwei Plasmaarten als Grundlage der Symbiogenesis, einer neuen Lehre von der Entstehung der Organismen |trans-title=Theory of the two types of plasma as the basis of symbiogenesis, a new theory of the origin of organisms |language=de |journal=Biologisches Centralblatt |year=1910 }}

Lateral gene transfer, or horizontal gene transfer, is the movement of genetic material between unicellular and/or multicellular organisms without a parent-offspring relationship. The horizontal transfer of genes results in new genes, which could give new functions to the recipient and thus could drive evolution.{{cite journal |last1=Boto |first1=Luis |title=Horizontal gene transfer in evolution: facts and challenges |journal=Proceedings of the Royal Society B: Biological Sciences |date=22 March 2010 |volume=277 |issue=1683 |pages=819–827 |doi=10.1098/rspb.2009.1679 |pmid=19864285 |pmc=2842723 }}

In the neo-Darwinian paradigm, one of the assumed definition of a species is that of Mayr's, which defines species based upon sexual compatibility.{{Cite book|title=Systematics and the origin of species, from the viewpoint of a zoologist|last=Mayr|first=Ernst|date=1942|publisher=Harvard University Press|isbn=9780674862500|edition=1st Harvard University Press pbk.|location=Cambridge, Mass.|oclc=41565294}}{{page needed|date=October 2021}} Mayr's definition therefore suggests that individuals that can produce fertile offspring must belong to the same species. However, in hybridization, two organisms produce offspring while being distinct species. During hybridization the characteristics of these two different species are combined yielding a new organism, called a hybrid, thus driving evolution.{{cite journal |last1=Barton |first1=N. H. |title=The role of hybridization in evolution |journal=Molecular Ecology |date=7 July 2008 |volume=10 |issue=3 |pages=551–568 |doi=10.1046/j.1365-294x.2001.01216.x |pmid=11298968 |s2cid=22129817 }}

Infectious agents, such as viruses, can infect the cells of host organisms. Viruses infect cells of other organisms in order to enable their own reproduction. Hereto, many viruses can insert copies of their genetic material into the host genome, potentially altering the phenotype of the host cell.{{cite journal |last1=Gifford |first1=Robert |last2=Tristem |first2=Michael |title=The Evolution, Distribution and Diversity of Endogenous Retroviruses |journal=Virus Genes |date=2003 |volume=26 |issue=3 |pages=291–315 |doi=10.1023/a:1024455415443 |pmid=12876457 |s2cid=34639116 }}{{cite journal |last1=Lower |first1=R. |last2=Lower |first2=J. |last3=Kurth |first3=R. |title=The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. |journal=Proceedings of the National Academy of Sciences |date=28 May 1996 |volume=93 |issue=11 |pages=5177–5184 |doi=10.1073/pnas.93.11.5177 |pmid=8643549 |pmc=39218 |bibcode=1996PNAS...93.5177L |doi-access=free }}{{Cite book|title=Virolution : die Macht der Viren in der Evolution|last=Frank.|first=Ryan|date=2010|publisher=Spektrum|isbn=978-3827425416|edition=1. Aufl|location=Heidelberg, Neckar|oclc=682040592}}{{page needed|date=October 2021}} When these viruses insert their genetic material in the genome of germ line cells, the modified host genome will be passed onto the offspring, yielding genetically differentiated organisms. Therefore, infectious heredity plays an important role in evolution, for example in the formation of the female placenta.{{Cite journal|last1=Knerr|first1=Ina|last2=Beinder|first2=Ernst|last3=Rascher|first3=Wolfgang|date=2002|title=Syncytin, a novel human endogenous retroviral gene in human placenta: Evidence for its dysregulation in preeclampsia and HELLP syndrome|journal=American Journal of Obstetrics and Gynecology|volume=186|issue=2|pages=210–213|doi=10.1067/mob.2002.119636|pmid=11854637}}{{cite journal |last1=Sugimoto |first1=Jun |last2=Schust |first2=Danny J. |title=Review: Human Endogenous Retroviruses and the Placenta |journal=Reproductive Sciences |date=November 2009 |volume=16 |issue=11 |pages=1023–1033 |doi=10.1177/1933719109336620 |pmid=19474286 |s2cid=21384697 }}

Reticulate evolution has played a key role in the evolution of some organisms such as bacteria and flowering plants.{{Cite book|title=Plant Speciation|last=Grant|first=V.|publisher=Columbia Univ. Press|year=1971|location=New York}}{{cite journal |last1=Jones |first1=D |last2=Sneath |first2=P H |title=Genetic transfer and bacterial taxonomy |journal=Bacteriological Reviews |date=March 1970 |volume=34 |issue=1 |pages=40–81 |doi=10.1128/br.34.1.40-81.1970 |pmid=4909647 |pmc=378348 }} However, most methods for studying cladistics have been based on a model of strictly branching cladogeny, without assessing the importance of reticulate evolution.{{Cite journal|last=Sneath|first=P. H. A.|date=1975|title=Cladistic Representation of Reticulate Evolution|journal=Systematic Zoology|volume=24|issue=3|pages=360–368|doi=10.2307/2412721|jstor=2412721}} Reticulation at chromosomal, genomic and species levels fails to be modelled by a bifurcating tree.

According to Ford Doolittle, an evolutionary and molecular biologist: “Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree”.{{cite journal |last1=Doolittle |first1=W. Ford |title=Phylogenetic Classification and the Universal Tree |journal=Science |date=25 June 1999 |volume=284 |issue=5423 |pages=2124–2128 |doi=10.1126/science.284.5423.2124 |pmid=10381871 }}

Reticulate evolution refers to evolutionary processes which cannot be successfully represented using a classical phylogenetic tree model,{{cite journal |last1=Legendre |first1=P |title=Reticulate Evolution:From Bacteria to Philosopher |journal=Journal of Classification |date=1 July 2000 |volume=17 |issue=2 |pages=153–157 |doi=10.1007/S003570000013 |s2cid=41323094 }} as it gives rise to rapid evolutionary change with horizontal crossings and mergings often preceding a pattern of vertical descent with modification.Gontier, Nathalie. (2015). Reticulate Evolution Everywhere. In Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious Heredity. Springer. pp. 1-40. {{ISBN|978-3-319-16344-4}} Reconstructing phylogenetic relationships under reticulate evolution requires adapted analytical methods. Reticulate evolution dynamics contradict the neo-Darwininan theory, compiled in the Modern Synthesis, by which the evolution of life occurs through natural selection and is displayed with a bifurcating or branching pattern. Frequent hybridisation between species in natural populations challenges the assumption that species have evolved from a common ancestor by simple branching, in which branches are genetically isolated.{{cite journal |last1=Xu |first1=S |last2=Atchley |first2=WR |last3=Fitch |first3=WM |title=Phylogenetic inference under the pure drift model. |journal=Molecular Biology and Evolution |date=November 1994 |volume=11 |issue=6 |pages=949–60 |doi=10.1093/oxfordjournals.molbev.a040175 |pmid=7815932 |doi-access=free }} The study of reticulate evolution is said to have been largely excluded from the modern synthesis. The urgent need for new models which take reticulate evolution into account has been stressed by many evolutionary biologists, such as Nathalie Gontier who has stated "reticulate evolution today is a vernacular concept for evolutionary change induced by mechanisms and processes of symbiosis, symbiogenesis, lateral gene transfer, hybridization, or divergence with gene flow, and infectious heredity". She calls for an extended evolutionary synthesis that integrates these mechanisms and processes of evolution.

Reticulate evolution has been extensively applied to plant hybridization in agriculture and gardening. The first commercial hybrids appeared in the early 1920s.{{cite book |doi=10.2134/agronmonogr18.3ed.c9 |chapter=Production of Hybrid Seed Corn |title=Corn and Corn Improvement |series=Agronomy Monographs |year=2015 |last1=Wych |first1=Robert D. |pages=565–607 |isbn=9780891182122 }} Since then, many protoplast fusion experiments have been carried out, some of which were aimed at improvement of crop species.{{cite book |doi=10.1007/978-3-642-73157-0_3 |chapter=Somatic Hybridization of Plants and its Use in Agriculture |title=Plant Cell Biotechnology |year=1988 |last1=Hamill |first1=John D. |last2=Cocking |first2=Edward C. |pages=21–41 |isbn=978-3-642-73159-4 }} Wild types possessing desirable agronomic traits are selected and fused in order to yield novel, improved species. The newly generated plant will be improved for traits such as better yield, greater uniformity, improved color, and disease resistance.{{cite journal |last1=Goulet |first1=Benjamin E. |last2=Roda |first2=Federico |last3=Hopkins |first3=Robin |title=Hybridization in Plants: Old Ideas, New Techniques |journal=Plant Physiology |date=January 2017 |volume=173 |issue=1 |pages=65–78 |doi=10.1104/pp.16.01340 |pmid=27895205 |pmc=5210733 }}

Reticulate evolution is regarded as a process that has shaped the histories of many organisms.{{cite journal |last1=Sessa |first1=Emily B. |last2=Zimmer |first2=Elizabeth A. |last3=Givnish |first3=Thomas J. |title=Reticulate evolution on a global scale: A nuclear phylogeny for New World Dryopteris (Dryopteridaceae) |journal=Molecular Phylogenetics and Evolution |date=September 2012 |volume=64 |issue=3 |pages=563–581 |doi=10.1016/j.ympev.2012.05.009 |pmid=22634937 |bibcode=2012MolPE..64..563S }} There is evidence of reticulation events in flowering plants, as the variation patterns between angiosperm families strongly suggests there has been widespread hybridisation.{{cite journal |last1=Grant |first1=Verne |title=The Role of Hybridization in the Evolution of the Leafty-Stemmed Gilias |journal=Evolution |date=March 1953 |volume=7 |issue=1 |pages=51–64 |doi=10.2307/2405571 |jstor=2405571 }} Grant states that phylogenetic networks, instead of phylogenetic trees, arise in all major groups of higher plants. Stable speciation events due to hybridisation between angiosperm species supports the occurrence of reticulate evolution and highlights the key role of reticulation in the evolution of plants.{{Cite book|title=Principles of angiosperm taxonomy|last1=Davis|first1=P. H|last2=Heywood|first2=V. H|date=1963|publisher=Oliver and Boyd|isbn=978-0882751290|location=Edinburgh |oclc = 5518166}}{{page needed|date=October 2021}}

Genetic transfer can occur across wide taxonomic levels in microorganisms and become stably integrated into the new microbial populations,{{cite journal |last1=Meynell |first1=E |last2=Meynell |first2=G G |last3=Datta |first3=N |title=Phylogenetic relationships of drug-resistance factors and other transmissible bacterial plasmids |journal=Bacteriological Reviews |date=March 1968 |volume=32 |issue=1 |pages=55–83 |doi=10.1128/br.32.1.55-83.1968 |pmid=4869941 |pmc=378292 }}{{cite journal |last1=Anderson |first1=E S |title=The Ecology of Transferable Drug Resistance in the Enterobacteria |journal=Annual Review of Microbiology |date=October 1968 |volume=22 |issue=1 |pages=131–180 |doi=10.1146/annurev.mi.22.100168.001023 |pmid=4879515 }} as has been observed through protein sequencing.{{cite journal |last1=Ambler |first1=R. P. |title=Bacterial Cytochromes C and Molecular Evolution |journal=Systematic Zoology |date=December 1973 |volume=22 |issue=4 |pages=554–565 |doi=10.2307/2412960 |jstor=2412960 }} Reticulation in bacteria usually only involves the transfer of only a few genes or parts of these. Reticulate evolution driven by lateral gene transfer has also been observed in marine life.{{cite journal |last1=Arnold |first1=Michael |last2=Fogarty |first2=Nicole |title=Reticulate Evolution and Marine Organisms: The Final Frontier? |journal=International Journal of Molecular Sciences |date=3 September 2009 |volume=10 |issue=9 |pages=3836–3860 |doi=10.3390/ijms10093836 |pmid=19865522 |pmc=2769149 |doi-access=free }} Lateral genetic transfer of photo-response genes between planktonic bacteria and Archaea has been evidenced in some groups, showing an associated increase in environmental adaptability in organisms inhabiting photic zones.{{cite journal |last1=Frigaard |first1=Niels-Ulrik |last2=Martinez |first2=Asuncion |last3=Mincer |first3=Tracy J. |last4=DeLong |first4=Edward F. |title=Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea |journal=Nature |date=February 2006 |volume=439 |issue=7078 |pages=847–850 |doi=10.1038/nature04435 |pmid=16482157 |bibcode=2006Natur.439..847F |s2cid=4427548 }}

Moreover, in the well-studied Darwin finches signs of reticulate evolution can be observed. Peter and Rosemary Grant, who carried out extensive research on the evolutionary processes of the Geospiza genus, found that hybridization occurs between some species of Darwin finches, yielding hybrid forms. This event could explain the origin of intermediate species.{{cite journal |title=Hybridization of Darwin's finches on Isla Daphne Major, Galápagos |journal=Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences |date=29 April 1993 |volume=340 |issue=1291 |pages=127–139 |doi=10.1098/rstb.1993.0052 |bibcode=1993RSPTB.340..127G |last1=Grant |first1=Peter R. }} Jonathan Weiner{{cite book |last1=Weiner |first1=Jonathan |title=The beak of the finch a story of evolution in our time |date=2012 |publisher=Brilliance Audio |isbn=978-1-4558-8422-3 }}{{page needed|date=October 2021}} commented on the observations of the Grants, suggesting the existence of reticulate evolution: "To the Grants, the whole tree of life now looks different from a year ago. The set of young twigs and shoots they study seems to be growing together in some seasons, apart in others. The same forces that created these lines are moving them toward fusion and then back toward fission."; and "The Grants are looking at a pattern that was once dismissed as insignificant in the tree of life. The pattern is known as reticulate evolution, from the Latin reticulum, diminutive for net. The finches' lines are not so much lines or branches at all. They are more like twiggy thickets, full of little networks and delicate webbings."

{{Reflist|refs=

{{cite journal | author=Xu S. | date=2000 | title=Phylogenetic analysis under reticulate evolution |journal=Molecular Biology and Evolution |volume=17 |issue=6 |pages=897–907 |pmid=10833196 | doi=10.1093/oxfordjournals.molbev.a026370|doi-access=free }} {{open access}}

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• [http://www.geo.arizona.edu/Antevs/ecol438/evolglos.html UA Geosciences, University of Arizona: Evolutionary Glossary]
• [http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes/08_HybridReticul_Larsen.pdf Hybridization and Reticulation: Trees, Networks, and Simulations]

• Arnold, M.L. (2008). Reticulate Evolution and Humans : Origins and Ecology. Oxford University Press. {{ISBN|978-0-19-953958-1}}
• Gontier, N. (2015). Reticulate Evolution Everywhere. In Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious Heredity. Springer. {{ISBN|978-3-319-16344-4}}
• Linder, R.C.; Moret, B.M.E.; Nakhleh, L; Warnow, T. (2003). [http://www.cs.utexas.edu/~phylo/resources/pdf/papers/psb04.pdf Network (Reticulate) Evolution: Biology, Models and Algorithms]. The University of Texas.
• {{cite journal |last1=Linder |first1=C. Randal |last2=Rieseberg |first2=Loren H. |title=Reconstructing patterns of reticulate evolution in plants |journal=American Journal of Botany |date=October 2004 |volume=91 |issue=10 |pages=1700–1708 |doi=10.3732/ajb.91.10.1700 |pmid=21652318 |pmc=2493047 }}

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Category:Evolutionary biology

Category:Extended evolutionary synthesis